Starting phenix.real_space_refine on Sat Feb 17 15:54:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9f_20696/02_2024/6u9f_20696.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9f_20696/02_2024/6u9f_20696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9f_20696/02_2024/6u9f_20696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9f_20696/02_2024/6u9f_20696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9f_20696/02_2024/6u9f_20696.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9f_20696/02_2024/6u9f_20696.pdb" } resolution = 4.35 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= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 12081 2.51 5 N 3273 2.21 5 O 3789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19179 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5399 Classifications: {'peptide': 717} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'CIS': 6, 'PTRANS': 19, 'TRANS': 691} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 625 Unresolved non-hydrogen dihedrals: 404 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 11, 'ASN:plan1': 14, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 239 Chain: "C" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5399 Classifications: {'peptide': 717} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'CIS': 6, 'PTRANS': 19, 'TRANS': 691} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 625 Unresolved non-hydrogen dihedrals: 404 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 11, 'ASN:plan1': 14, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 239 Chain: "E" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5399 Classifications: {'peptide': 717} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'CIS': 6, 'PTRANS': 19, 'TRANS': 691} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 625 Unresolved non-hydrogen dihedrals: 404 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 11, 'ASN:plan1': 14, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 239 Chain: "B" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 994 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'TRANS': 131} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 994 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'TRANS': 131} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 994 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'TRANS': 131} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 10.50, per 1000 atoms: 0.55 Number of scatterers: 19179 At special positions: 0 Unit cell: (103.79, 103.79, 243.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 3789 8.00 N 3273 7.00 C 12081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.12 Conformation dependent library (CDL) restraints added in 3.8 seconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4974 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 36 sheets defined 18.1% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.608A pdb=" N THR A 8 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP A 9 " --> pdb=" O LYS A 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4 through 9' Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.999A pdb=" N ALA A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 52 removed outlier: 4.201A pdb=" N SER A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 50 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 86 removed outlier: 3.601A pdb=" N LEU A 69 " --> pdb=" O TYR A 65 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 107 Processing helix chain 'A' and resid 125 through 146 removed outlier: 3.679A pdb=" N ILE A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 133 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 158 through 166 Processing helix chain 'A' and resid 246 through 254 removed outlier: 4.007A pdb=" N ASN A 251 " --> pdb=" O HIS A 247 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N PHE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 254 " --> pdb=" O PHE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 removed outlier: 4.108A pdb=" N LYS A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 354 Processing helix chain 'A' and resid 387 through 399 removed outlier: 3.642A pdb=" N LEU A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 399 " --> pdb=" O GLN A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 removed outlier: 3.571A pdb=" N GLN A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.810A pdb=" N GLN A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 578 " --> pdb=" O CYS A 574 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 776 removed outlier: 3.771A pdb=" N GLU A 775 " --> pdb=" O GLY A 772 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASN A 776 " --> pdb=" O SER A 773 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 772 through 776' Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.608A pdb=" N THR C 8 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP C 9 " --> pdb=" O LYS C 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4 through 9' Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.999A pdb=" N ALA C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS C 34 " --> pdb=" O PRO C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 removed outlier: 4.200A pdb=" N SER C 49 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN C 50 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 86 removed outlier: 3.601A pdb=" N LEU C 69 " --> pdb=" O TYR C 65 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER C 71 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 125 through 146 removed outlier: 3.679A pdb=" N ILE C 132 " --> pdb=" O PRO C 128 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG C 133 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 158 through 166 Processing helix chain 'C' and resid 246 through 254 removed outlier: 4.006A pdb=" N ASN C 251 " --> pdb=" O HIS C 247 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N PHE C 252 " --> pdb=" O LYS C 248 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 254 " --> pdb=" O PHE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 336 removed outlier: 4.107A pdb=" N LYS C 336 " --> pdb=" O ALA C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 387 through 399 removed outlier: 3.642A pdb=" N LEU C 396 " --> pdb=" O PHE C 392 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN C 399 " --> pdb=" O GLN C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 428 removed outlier: 3.570A pdb=" N GLN C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 581 removed outlier: 3.809A pdb=" N GLN C 577 " --> pdb=" O TYR C 573 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 578 " --> pdb=" O CYS C 574 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR C 579 " --> pdb=" O SER C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 776 removed outlier: 3.771A pdb=" N GLU C 775 " --> pdb=" O GLY C 772 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN C 776 " --> pdb=" O SER C 773 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 772 through 776' Processing helix chain 'E' and resid 4 through 9 removed outlier: 3.609A pdb=" N THR E 8 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP E 9 " --> pdb=" O LYS E 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4 through 9' Processing helix chain 'E' and resid 28 through 36 removed outlier: 3.999A pdb=" N ALA E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS E 34 " --> pdb=" O PRO E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 52 removed outlier: 4.201A pdb=" N SER E 49 " --> pdb=" O ASN E 45 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN E 50 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 86 removed outlier: 3.601A pdb=" N LEU E 69 " --> pdb=" O TYR E 65 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER E 71 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR E 78 " --> pdb=" O ASP E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 125 through 146 removed outlier: 3.679A pdb=" N ILE E 132 " --> pdb=" O PRO E 128 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG E 133 " --> pdb=" O HIS E 129 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS E 134 " --> pdb=" O ASP E 130 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU E 139 " --> pdb=" O ILE E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 158 Processing helix chain 'E' and resid 158 through 166 Processing helix chain 'E' and resid 246 through 254 removed outlier: 4.006A pdb=" N ASN E 251 " --> pdb=" O HIS E 247 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N PHE E 252 " --> pdb=" O LYS E 248 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU E 254 " --> pdb=" O PHE E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 336 removed outlier: 4.107A pdb=" N LYS E 336 " --> pdb=" O ALA E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 354 Processing helix chain 'E' and resid 387 through 399 removed outlier: 3.642A pdb=" N LEU E 396 " --> pdb=" O PHE E 392 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN E 399 " --> pdb=" O GLN E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 428 removed outlier: 3.572A pdb=" N GLN E 427 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 581 removed outlier: 3.809A pdb=" N GLN E 577 " --> pdb=" O TYR E 573 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU E 578 " --> pdb=" O CYS E 574 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR E 579 " --> pdb=" O SER E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 772 through 776 removed outlier: 3.771A pdb=" N GLU E 775 " --> pdb=" O GLY E 772 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN E 776 " --> pdb=" O SER E 773 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 772 through 776' Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 215 removed outlier: 3.852A pdb=" N GLU A 181 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 267 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 324 through 327 removed outlier: 3.876A pdb=" N GLY A 235 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 234 " --> pdb=" O CYS A 227 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 224 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 564 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE A 561 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS A 618 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 563 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS A 616 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 565 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 614 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 569 " --> pdb=" O ASP A 610 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 615 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 525 " --> pdb=" O TYR A 615 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A 522 " --> pdb=" O ILE A 455 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 346 removed outlier: 3.534A pdb=" N ASN A 345 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 363 through 365 removed outlier: 7.480A pdb=" N SER A 363 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N VAL A 418 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASP A 365 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 417 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 419 " --> pdb=" O TYR A 402 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 461 through 464 removed outlier: 6.239A pdb=" N LYS A 464 " --> pdb=" O PHE A 492 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N SER A 494 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 466 through 467 removed outlier: 3.501A pdb=" N GLU A 480 " --> pdb=" O ASN A 467 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 637 through 640 removed outlier: 6.725A pdb=" N LEU A 736 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS A 744 " --> pdb=" O GLN A 740 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 692 through 695 removed outlier: 3.570A pdb=" N LEU A 713 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 779 through 781 removed outlier: 3.601A pdb=" N SER A 802 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG A 814 " --> pdb=" O SER A 802 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 804 " --> pdb=" O PHE A 812 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP B 18 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 15 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR B 37 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE B 36 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N SER F 47 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS B 38 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN D 55 " --> pdb=" O SER F 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER D 75 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER D 76 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 86 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE D 88 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 214 through 215 removed outlier: 3.852A pdb=" N GLU C 181 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN C 267 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 324 through 327 removed outlier: 3.876A pdb=" N GLY C 235 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN C 234 " --> pdb=" O CYS C 227 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 224 " --> pdb=" O PHE C 568 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG C 564 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE C 561 " --> pdb=" O LYS C 618 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS C 618 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN C 563 " --> pdb=" O LYS C 616 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS C 616 " --> pdb=" O GLN C 563 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 565 " --> pdb=" O THR C 614 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR C 614 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 569 " --> pdb=" O ASP C 610 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR C 615 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 525 " --> pdb=" O TYR C 615 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU C 522 " --> pdb=" O ILE C 455 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AB5, first strand: chain 'C' and resid 342 through 346 removed outlier: 3.534A pdb=" N ASN C 345 " --> pdb=" O PRO C 377 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 363 through 365 removed outlier: 7.480A pdb=" N SER C 363 " --> pdb=" O TYR C 416 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N VAL C 418 " --> pdb=" O SER C 363 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ASP C 365 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS C 417 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 419 " --> pdb=" O TYR C 402 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 461 through 464 removed outlier: 6.239A pdb=" N LYS C 464 " --> pdb=" O PHE C 492 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N SER C 494 " --> pdb=" O LYS C 464 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 466 through 467 removed outlier: 3.502A pdb=" N GLU C 480 " --> pdb=" O ASN C 467 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 637 through 640 removed outlier: 6.724A pdb=" N LEU C 736 " --> pdb=" O ILE C 748 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS C 744 " --> pdb=" O GLN C 740 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 692 through 695 removed outlier: 3.570A pdb=" N LEU C 713 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 779 through 781 removed outlier: 3.601A pdb=" N SER C 802 " --> pdb=" O ARG C 814 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG C 814 " --> pdb=" O SER C 802 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 804 " --> pdb=" O PHE C 812 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 214 through 215 removed outlier: 3.852A pdb=" N GLU E 181 " --> pdb=" O ASN E 267 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN E 267 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 324 through 327 removed outlier: 3.876A pdb=" N GLY E 235 " --> pdb=" O PHE E 326 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN E 234 " --> pdb=" O CYS E 227 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 224 " --> pdb=" O PHE E 568 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG E 564 " --> pdb=" O GLU E 228 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE E 561 " --> pdb=" O LYS E 618 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS E 618 " --> pdb=" O ILE E 561 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN E 563 " --> pdb=" O LYS E 616 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS E 616 " --> pdb=" O GLN E 563 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS E 565 " --> pdb=" O THR E 614 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR E 614 " --> pdb=" O LYS E 565 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS E 569 " --> pdb=" O ASP E 610 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR E 615 " --> pdb=" O LEU E 525 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU E 525 " --> pdb=" O TYR E 615 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU E 522 " --> pdb=" O ILE E 455 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 240 through 241 Processing sheet with id=AC6, first strand: chain 'E' and resid 342 through 346 removed outlier: 3.534A pdb=" N ASN E 345 " --> pdb=" O PRO E 377 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 363 through 365 removed outlier: 7.479A pdb=" N SER E 363 " --> pdb=" O TYR E 416 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N VAL E 418 " --> pdb=" O SER E 363 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASP E 365 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS E 417 " --> pdb=" O LYS E 404 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL E 419 " --> pdb=" O TYR E 402 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 461 through 464 removed outlier: 6.240A pdb=" N LYS E 464 " --> pdb=" O PHE E 492 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N SER E 494 " --> pdb=" O LYS E 464 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 466 through 467 removed outlier: 3.501A pdb=" N GLU E 480 " --> pdb=" O ASN E 467 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 637 through 640 removed outlier: 6.725A pdb=" N LEU E 736 " --> pdb=" O ILE E 748 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS E 744 " --> pdb=" O GLN E 740 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 692 through 695 removed outlier: 3.569A pdb=" N LEU E 713 " --> pdb=" O TYR E 692 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 779 through 781 removed outlier: 3.601A pdb=" N SER E 802 " --> pdb=" O ARG E 814 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG E 814 " --> pdb=" O SER E 802 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 804 " --> pdb=" O PHE E 812 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.524A pdb=" N ASP D 18 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 15 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR D 37 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 44 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ASN F 55 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER B 46 " --> pdb=" O ASN F 55 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER F 75 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER F 76 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 86 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE F 88 " --> pdb=" O SER F 91 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 91 through 95 removed outlier: 3.661A pdb=" N ILE B 88 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 86 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 76 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 55 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR F 37 " --> pdb=" O LYS F 29 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU F 15 " --> pdb=" O LEU F 30 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP F 18 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 100 through 102 removed outlier: 5.889A pdb=" N ILE B 100 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASN D 116 " --> pdb=" O ILE F 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AD8, first strand: chain 'B' and resid 115 through 117 removed outlier: 5.772A pdb=" N ASN B 116 " --> pdb=" O ILE D 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 123 through 124 removed outlier: 7.968A pdb=" N ILE B 123 " --> pdb=" O ILE F 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 522 hydrogen bonds defined for protein. 1389 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: 7.68 Time building geometry restraints manager: 7.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6284 1.34 - 1.46: 3013 1.46 - 1.57: 10071 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 19413 Sorted by residual: bond pdb=" CB ASN A 387 " pdb=" CG ASN A 387 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.80e+00 bond pdb=" CB ASN C 387 " pdb=" CG ASN C 387 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.71e+00 bond pdb=" CB ASN E 387 " pdb=" CG ASN E 387 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.60e+00 bond pdb=" CA ASN E 545 " pdb=" CB ASN E 545 " ideal model delta sigma weight residual 1.531 1.459 0.072 3.28e-02 9.30e+02 4.82e+00 bond pdb=" CA ASN C 545 " pdb=" CB ASN C 545 " ideal model delta sigma weight residual 1.531 1.460 0.071 3.28e-02 9.30e+02 4.63e+00 ... (remaining 19408 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.05: 214 105.05 - 112.30: 9923 112.30 - 119.55: 6520 119.55 - 126.80: 9425 126.80 - 134.05: 132 Bond angle restraints: 26214 Sorted by residual: angle pdb=" N PRO E 30 " pdb=" CA PRO E 30 " pdb=" CB PRO E 30 " ideal model delta sigma weight residual 102.33 110.31 -7.98 1.18e+00 7.18e-01 4.58e+01 angle pdb=" N PRO A 30 " pdb=" CA PRO A 30 " pdb=" CB PRO A 30 " ideal model delta sigma weight residual 102.33 110.29 -7.96 1.18e+00 7.18e-01 4.55e+01 angle pdb=" N PRO C 30 " pdb=" CA PRO C 30 " pdb=" CB PRO C 30 " ideal model delta sigma weight residual 102.33 110.25 -7.92 1.18e+00 7.18e-01 4.51e+01 angle pdb=" N PRO C 128 " pdb=" CA PRO C 128 " pdb=" CB PRO C 128 " ideal model delta sigma weight residual 103.44 110.01 -6.57 1.12e+00 7.97e-01 3.44e+01 angle pdb=" N PRO A 128 " pdb=" CA PRO A 128 " pdb=" CB PRO A 128 " ideal model delta sigma weight residual 103.44 109.99 -6.55 1.12e+00 7.97e-01 3.42e+01 ... (remaining 26209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 11386 16.06 - 32.12: 530 32.12 - 48.18: 39 48.18 - 64.24: 0 64.24 - 80.30: 3 Dihedral angle restraints: 11958 sinusoidal: 4404 harmonic: 7554 Sorted by residual: dihedral pdb=" CA PHE A 672 " pdb=" C PHE A 672 " pdb=" N GLN A 673 " pdb=" CA GLN A 673 " ideal model delta harmonic sigma weight residual 180.00 134.69 45.31 0 5.00e+00 4.00e-02 8.21e+01 dihedral pdb=" CA PHE C 672 " pdb=" C PHE C 672 " pdb=" N GLN C 673 " pdb=" CA GLN C 673 " ideal model delta harmonic sigma weight residual 180.00 134.71 45.29 0 5.00e+00 4.00e-02 8.21e+01 dihedral pdb=" CA PHE E 672 " pdb=" C PHE E 672 " pdb=" N GLN E 673 " pdb=" CA GLN E 673 " ideal model delta harmonic sigma weight residual 180.00 134.73 45.27 0 5.00e+00 4.00e-02 8.20e+01 ... (remaining 11955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2008 0.052 - 0.104: 740 0.104 - 0.155: 275 0.155 - 0.207: 54 0.207 - 0.259: 16 Chirality restraints: 3093 Sorted by residual: chirality pdb=" CB ILE A 455 " pdb=" CA ILE A 455 " pdb=" CG1 ILE A 455 " pdb=" CG2 ILE A 455 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB ILE C 455 " pdb=" CA ILE C 455 " pdb=" CG1 ILE C 455 " pdb=" CG2 ILE C 455 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA PRO E 30 " pdb=" N PRO E 30 " pdb=" C PRO E 30 " pdb=" CB PRO E 30 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3090 not shown) Planarity restraints: 3393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 217 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C LYS E 217 " -0.046 2.00e-02 2.50e+03 pdb=" O LYS E 217 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN E 218 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 217 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" C LYS A 217 " -0.046 2.00e-02 2.50e+03 pdb=" O LYS A 217 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN A 218 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 217 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C LYS C 217 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS C 217 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN C 218 " -0.015 2.00e-02 2.50e+03 ... (remaining 3390 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1851 2.73 - 3.28: 17258 3.28 - 3.82: 29188 3.82 - 4.36: 34093 4.36 - 4.90: 57081 Nonbonded interactions: 139471 Sorted by model distance: nonbonded pdb=" O SER B 98 " pdb=" OG1 THR F 106 " model vdw 2.193 2.440 nonbonded pdb=" OG1 THR D 106 " pdb=" O SER F 98 " model vdw 2.199 2.440 nonbonded pdb=" OD1 ASN B 39 " pdb=" OG SER F 47 " model vdw 2.214 2.440 nonbonded pdb=" NH2 ARG A 730 " pdb=" OD1 ASN E 724 " model vdw 2.252 2.520 nonbonded pdb=" O TYR C 505 " pdb=" OG SER C 686 " model vdw 2.264 2.440 ... (remaining 139466 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.600 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 54.250 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 : 0.009 0.072 19413 Z= 0.557 Angle : 1.102 9.606 26214 Z= 0.603 Chirality : 0.064 0.259 3093 Planarity : 0.005 0.061 3393 Dihedral : 9.472 80.296 6984 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.43 % Favored : 86.57 % Rotamer: Outliers : 0.15 % Allowed : 0.91 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.86 % Twisted Proline : 5.26 % Twisted General : 0.98 % 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: -4.71 (0.13), residues: 2472 helix: -4.25 (0.10), residues: 420 sheet: -2.06 (0.19), residues: 666 loop : -3.42 (0.13), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP E 334 HIS 0.014 0.003 HIS F 6 PHE 0.027 0.004 PHE A 633 TYR 0.020 0.003 TYR E 627 ARG 0.009 0.001 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 511 time to evaluate : 2.524 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: A 177 LEU cc_start: 0.8921 (mt) cc_final: 0.8279 (tt) REVERT: A 182 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8621 (pt) REVERT: A 185 ASN cc_start: 0.8740 (m-40) cc_final: 0.8089 (t0) REVERT: A 268 ASP cc_start: 0.8135 (m-30) cc_final: 0.7703 (p0) REVERT: A 299 ASP cc_start: 0.8317 (m-30) cc_final: 0.8103 (t0) REVERT: A 326 PHE cc_start: 0.8889 (m-80) cc_final: 0.8560 (m-80) REVERT: A 390 ASP cc_start: 0.9437 (m-30) cc_final: 0.9162 (m-30) REVERT: A 438 LYS cc_start: 0.8507 (mttt) cc_final: 0.8002 (mmtt) REVERT: A 506 ILE cc_start: 0.9400 (mt) cc_final: 0.9099 (tp) REVERT: A 523 ILE cc_start: 0.9296 (mt) cc_final: 0.9014 (tt) REVERT: A 529 ASN cc_start: 0.9041 (m-40) cc_final: 0.8665 (m-40) REVERT: A 557 LYS cc_start: 0.7705 (mttt) cc_final: 0.7256 (mppt) REVERT: A 568 PHE cc_start: 0.8268 (m-10) cc_final: 0.7967 (m-10) REVERT: A 570 ARG cc_start: 0.8418 (ttp-170) cc_final: 0.7624 (ptm160) REVERT: A 653 LYS cc_start: 0.8641 (tttt) cc_final: 0.8005 (tppt) REVERT: A 685 ASN cc_start: 0.8025 (m-40) cc_final: 0.7804 (t0) REVERT: A 771 LEU cc_start: 0.8950 (mt) cc_final: 0.8685 (mm) REVERT: A 778 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7659 (tt0) REVERT: C 177 LEU cc_start: 0.8843 (mt) cc_final: 0.8175 (tt) REVERT: C 185 ASN cc_start: 0.8763 (m-40) cc_final: 0.8094 (t0) REVERT: C 228 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8005 (mt-10) REVERT: C 263 ASP cc_start: 0.8241 (m-30) cc_final: 0.7853 (m-30) REVERT: C 268 ASP cc_start: 0.8325 (m-30) cc_final: 0.7398 (p0) REVERT: C 326 PHE cc_start: 0.9001 (m-80) cc_final: 0.8607 (m-80) REVERT: C 438 LYS cc_start: 0.8681 (mttt) cc_final: 0.8085 (mttp) REVERT: C 529 ASN cc_start: 0.9154 (m-40) cc_final: 0.8824 (m-40) REVERT: C 550 LEU cc_start: 0.8948 (mt) cc_final: 0.8624 (pt) REVERT: C 557 LYS cc_start: 0.7984 (mttt) cc_final: 0.7485 (mptt) REVERT: C 574 CYS cc_start: 0.6303 (m) cc_final: 0.5870 (m) REVERT: C 638 ILE cc_start: 0.9112 (mt) cc_final: 0.8491 (pt) REVERT: C 653 LYS cc_start: 0.8438 (tttt) cc_final: 0.7861 (tppt) REVERT: C 696 ILE cc_start: 0.7851 (mt) cc_final: 0.6759 (mm) REVERT: C 771 LEU cc_start: 0.8831 (mt) cc_final: 0.8310 (mt) REVERT: C 774 LYS cc_start: 0.8858 (tttt) cc_final: 0.8639 (ttmt) REVERT: C 792 LEU cc_start: 0.8929 (mt) cc_final: 0.8546 (tt) REVERT: E 177 LEU cc_start: 0.8665 (mt) cc_final: 0.8039 (tt) REVERT: E 182 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8415 (pt) REVERT: E 185 ASN cc_start: 0.8674 (m-40) cc_final: 0.7980 (t0) REVERT: E 263 ASP cc_start: 0.8178 (m-30) cc_final: 0.7977 (m-30) REVERT: E 268 ASP cc_start: 0.8202 (m-30) cc_final: 0.7563 (p0) REVERT: E 326 PHE cc_start: 0.8886 (m-80) cc_final: 0.8316 (m-80) REVERT: E 438 LYS cc_start: 0.8472 (mttt) cc_final: 0.7962 (mttp) REVERT: E 506 ILE cc_start: 0.9410 (mt) cc_final: 0.9206 (tp) REVERT: E 529 ASN cc_start: 0.8999 (m-40) cc_final: 0.8724 (m-40) REVERT: E 550 LEU cc_start: 0.8997 (mt) cc_final: 0.8706 (pt) REVERT: E 557 LYS cc_start: 0.7789 (mttt) cc_final: 0.7363 (mppt) REVERT: E 566 LEU cc_start: 0.9125 (mt) cc_final: 0.8739 (mp) REVERT: E 568 PHE cc_start: 0.8100 (m-10) cc_final: 0.7581 (m-10) REVERT: E 570 ARG cc_start: 0.8096 (ttp-170) cc_final: 0.7529 (ptp-170) REVERT: E 638 ILE cc_start: 0.9039 (mt) cc_final: 0.8793 (tp) REVERT: E 653 LYS cc_start: 0.8570 (tttt) cc_final: 0.7976 (tppt) REVERT: E 685 ASN cc_start: 0.8039 (m-40) cc_final: 0.7803 (t0) REVERT: E 725 GLN cc_start: 0.8883 (mt0) cc_final: 0.8244 (mt0) REVERT: E 771 LEU cc_start: 0.8843 (mt) cc_final: 0.8579 (mm) REVERT: B 18 ASP cc_start: 0.8196 (p0) cc_final: 0.7899 (p0) REVERT: B 31 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7383 (mp0) REVERT: B 42 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7909 (mm-30) REVERT: B 65 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8116 (tp30) REVERT: B 78 MET cc_start: 0.8542 (ttt) cc_final: 0.8332 (ttt) REVERT: B 90 ASN cc_start: 0.8035 (m-40) cc_final: 0.7653 (t0) REVERT: D 26 CYS cc_start: 0.7770 (m) cc_final: 0.7207 (p) REVERT: D 31 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7862 (mt-10) REVERT: D 42 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7984 (mm-30) REVERT: F 31 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7951 (mp0) REVERT: F 78 MET cc_start: 0.8465 (ttt) cc_final: 0.8242 (ttt) outliers start: 3 outliers final: 0 residues processed: 511 average time/residue: 0.3316 time to fit residues: 249.2030 Evaluate side-chains 256 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 228 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 371 ASN A 385 ASN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN C 180 GLN C 355 ASN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN C 611 ASN E 180 GLN E 355 ASN E 371 ASN E 545 ASN E 611 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19413 Z= 0.246 Angle : 0.711 10.139 26214 Z= 0.379 Chirality : 0.049 0.169 3093 Planarity : 0.004 0.041 3393 Dihedral : 7.652 37.315 2622 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 0.10 % Allowed : 2.18 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.86 % Twisted Proline : 5.26 % Twisted General : 0.20 % 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: -3.98 (0.14), residues: 2472 helix: -2.41 (0.18), residues: 432 sheet: -1.73 (0.18), residues: 657 loop : -3.30 (0.14), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 236 HIS 0.005 0.001 HIS F 6 PHE 0.018 0.002 PHE A 803 TYR 0.020 0.001 TYR A 579 ARG 0.004 0.001 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 340 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8730 (mt) cc_final: 0.8308 (tt) REVERT: A 185 ASN cc_start: 0.8477 (m-40) cc_final: 0.7869 (t0) REVERT: A 263 ASP cc_start: 0.7938 (m-30) cc_final: 0.7697 (m-30) REVERT: A 268 ASP cc_start: 0.7931 (m-30) cc_final: 0.7526 (p0) REVERT: A 299 ASP cc_start: 0.8354 (m-30) cc_final: 0.8148 (t0) REVERT: A 326 PHE cc_start: 0.8776 (m-80) cc_final: 0.8236 (m-80) REVERT: A 390 ASP cc_start: 0.9380 (m-30) cc_final: 0.9073 (m-30) REVERT: A 436 ASP cc_start: 0.6776 (m-30) cc_final: 0.6278 (m-30) REVERT: A 438 LYS cc_start: 0.8512 (mttt) cc_final: 0.8161 (mmtt) REVERT: A 557 LYS cc_start: 0.7588 (mttt) cc_final: 0.7242 (mppt) REVERT: A 568 PHE cc_start: 0.8182 (m-10) cc_final: 0.7820 (m-10) REVERT: A 569 LYS cc_start: 0.8447 (mmmm) cc_final: 0.7957 (mmmm) REVERT: A 570 ARG cc_start: 0.8191 (ttp-170) cc_final: 0.6864 (ttm-80) REVERT: A 653 LYS cc_start: 0.8647 (tttt) cc_final: 0.8166 (ttpt) REVERT: A 775 GLU cc_start: 0.8561 (mp0) cc_final: 0.8052 (mp0) REVERT: A 778 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7563 (tt0) REVERT: C 177 LEU cc_start: 0.8591 (mt) cc_final: 0.8096 (tt) REVERT: C 185 ASN cc_start: 0.8676 (m-40) cc_final: 0.7846 (t0) REVERT: C 230 ILE cc_start: 0.9161 (pt) cc_final: 0.8898 (pt) REVERT: C 263 ASP cc_start: 0.8079 (m-30) cc_final: 0.7815 (m-30) REVERT: C 299 ASP cc_start: 0.8476 (m-30) cc_final: 0.8114 (t0) REVERT: C 326 PHE cc_start: 0.8868 (m-80) cc_final: 0.8263 (m-80) REVERT: C 438 LYS cc_start: 0.8706 (mttt) cc_final: 0.8194 (mttm) REVERT: C 504 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7892 (pm20) REVERT: C 550 LEU cc_start: 0.8971 (mt) cc_final: 0.8753 (pt) REVERT: C 557 LYS cc_start: 0.7885 (mttt) cc_final: 0.7373 (mppt) REVERT: C 574 CYS cc_start: 0.6245 (m) cc_final: 0.5894 (m) REVERT: C 638 ILE cc_start: 0.9119 (mt) cc_final: 0.8576 (pt) REVERT: C 653 LYS cc_start: 0.8373 (tttt) cc_final: 0.7809 (tppt) REVERT: E 185 ASN cc_start: 0.8519 (m-40) cc_final: 0.7742 (t0) REVERT: E 214 LEU cc_start: 0.8696 (tp) cc_final: 0.8423 (tt) REVERT: E 225 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7352 (mt-10) REVERT: E 230 ILE cc_start: 0.9334 (pt) cc_final: 0.9040 (pt) REVERT: E 263 ASP cc_start: 0.8216 (m-30) cc_final: 0.7840 (m-30) REVERT: E 268 ASP cc_start: 0.8080 (m-30) cc_final: 0.7387 (p0) REVERT: E 299 ASP cc_start: 0.8527 (m-30) cc_final: 0.8268 (t70) REVERT: E 326 PHE cc_start: 0.8597 (m-80) cc_final: 0.7869 (m-80) REVERT: E 438 LYS cc_start: 0.8529 (mttt) cc_final: 0.7933 (mttp) REVERT: E 522 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8047 (mp0) REVERT: E 550 LEU cc_start: 0.8944 (mt) cc_final: 0.8706 (pt) REVERT: E 557 LYS cc_start: 0.7611 (mttt) cc_final: 0.7268 (mppt) REVERT: E 568 PHE cc_start: 0.8239 (m-10) cc_final: 0.7867 (m-10) REVERT: E 638 ILE cc_start: 0.9103 (mt) cc_final: 0.8776 (tp) REVERT: E 650 ASN cc_start: 0.8732 (p0) cc_final: 0.8487 (p0) REVERT: E 653 LYS cc_start: 0.8551 (tttt) cc_final: 0.7905 (tppt) REVERT: E 725 GLN cc_start: 0.8889 (mt0) cc_final: 0.8262 (mt0) REVERT: B 31 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7120 (mp0) REVERT: B 69 LEU cc_start: 0.7963 (mp) cc_final: 0.7741 (tt) REVERT: B 90 ASN cc_start: 0.7855 (m-40) cc_final: 0.7487 (t0) REVERT: B 124 ASP cc_start: 0.7376 (m-30) cc_final: 0.7051 (t0) REVERT: D 31 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7053 (mp0) REVERT: D 99 ASN cc_start: 0.8402 (t0) cc_final: 0.8187 (t0) REVERT: D 116 ASN cc_start: 0.7448 (m-40) cc_final: 0.7233 (m-40) REVERT: F 5 ASP cc_start: 0.8640 (m-30) cc_final: 0.8319 (m-30) REVERT: F 90 ASN cc_start: 0.7864 (m110) cc_final: 0.7578 (t0) outliers start: 2 outliers final: 1 residues processed: 342 average time/residue: 0.2777 time to fit residues: 149.6325 Evaluate side-chains 215 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 0.0270 chunk 71 optimal weight: 20.0000 chunk 190 optimal weight: 1.9990 chunk 155 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 229 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 chunk 183 optimal weight: 6.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 GLN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 611 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19413 Z= 0.140 Angle : 0.602 9.836 26214 Z= 0.318 Chirality : 0.048 0.175 3093 Planarity : 0.003 0.034 3393 Dihedral : 6.482 34.028 2622 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.86 % Twisted Proline : 5.26 % Twisted General : 0.12 % 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: -3.32 (0.15), residues: 2472 helix: -1.17 (0.22), residues: 450 sheet: -1.21 (0.19), residues: 681 loop : -3.25 (0.15), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 334 HIS 0.006 0.001 HIS C 301 PHE 0.014 0.001 PHE A 449 TYR 0.017 0.001 TYR E 579 ARG 0.003 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 2.513 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: A 263 ASP cc_start: 0.7892 (m-30) cc_final: 0.7014 (m-30) REVERT: A 326 PHE cc_start: 0.8472 (m-80) cc_final: 0.8034 (m-80) REVERT: A 390 ASP cc_start: 0.9367 (m-30) cc_final: 0.9038 (m-30) REVERT: A 438 LYS cc_start: 0.8510 (mttt) cc_final: 0.8009 (mmtt) REVERT: A 516 ILE cc_start: 0.8791 (mt) cc_final: 0.8343 (mt) REVERT: A 529 ASN cc_start: 0.8920 (m-40) cc_final: 0.8671 (m-40) REVERT: A 557 LYS cc_start: 0.7571 (mttt) cc_final: 0.7166 (mppt) REVERT: A 569 LYS cc_start: 0.8339 (mmmm) cc_final: 0.7954 (mmmt) REVERT: A 570 ARG cc_start: 0.7936 (ttp-170) cc_final: 0.7273 (ptm160) REVERT: A 653 LYS cc_start: 0.8649 (tttt) cc_final: 0.8102 (ttpt) REVERT: A 775 GLU cc_start: 0.8625 (mp0) cc_final: 0.8089 (mp0) REVERT: A 778 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7660 (tt0) REVERT: C 177 LEU cc_start: 0.8888 (mt) cc_final: 0.8343 (tt) REVERT: C 230 ILE cc_start: 0.9070 (pt) cc_final: 0.8558 (pt) REVERT: C 268 ASP cc_start: 0.8037 (m-30) cc_final: 0.7610 (p0) REVERT: C 326 PHE cc_start: 0.8551 (m-80) cc_final: 0.7980 (m-80) REVERT: C 438 LYS cc_start: 0.8622 (mttt) cc_final: 0.7978 (mttp) REVERT: C 504 GLU cc_start: 0.8568 (mm-30) cc_final: 0.7880 (pm20) REVERT: C 557 LYS cc_start: 0.7719 (mttt) cc_final: 0.7403 (mptt) REVERT: C 579 TYR cc_start: 0.7107 (t80) cc_final: 0.6823 (t80) REVERT: C 626 GLU cc_start: 0.8356 (mp0) cc_final: 0.7973 (mp0) REVERT: C 638 ILE cc_start: 0.9082 (mt) cc_final: 0.8423 (pt) REVERT: C 653 LYS cc_start: 0.8404 (tttt) cc_final: 0.7862 (tppt) REVERT: C 725 GLN cc_start: 0.8792 (mt0) cc_final: 0.8431 (mp10) REVERT: E 177 LEU cc_start: 0.8770 (mt) cc_final: 0.8419 (tt) REVERT: E 185 ASN cc_start: 0.8575 (m-40) cc_final: 0.7686 (t0) REVERT: E 230 ILE cc_start: 0.9195 (pt) cc_final: 0.8594 (pt) REVERT: E 263 ASP cc_start: 0.8110 (m-30) cc_final: 0.7902 (m-30) REVERT: E 268 ASP cc_start: 0.8197 (m-30) cc_final: 0.7497 (p0) REVERT: E 326 PHE cc_start: 0.8353 (m-80) cc_final: 0.7650 (m-80) REVERT: E 395 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8609 (mm-40) REVERT: E 438 LYS cc_start: 0.8483 (mttt) cc_final: 0.7844 (mttp) REVERT: E 516 ILE cc_start: 0.8800 (mt) cc_final: 0.8335 (mt) REVERT: E 522 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7938 (mp0) REVERT: E 557 LYS cc_start: 0.7625 (mttt) cc_final: 0.7300 (mppt) REVERT: E 626 GLU cc_start: 0.8307 (mp0) cc_final: 0.7993 (mp0) REVERT: E 653 LYS cc_start: 0.8528 (tttt) cc_final: 0.7784 (tppt) REVERT: E 711 ILE cc_start: 0.8975 (pt) cc_final: 0.8773 (pt) REVERT: E 725 GLN cc_start: 0.8704 (mt0) cc_final: 0.8255 (mt0) REVERT: B 55 ASN cc_start: 0.8346 (t0) cc_final: 0.8102 (p0) REVERT: B 65 GLU cc_start: 0.7308 (tp30) cc_final: 0.5934 (tp30) REVERT: B 90 ASN cc_start: 0.7905 (m-40) cc_final: 0.7595 (t0) REVERT: D 31 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7050 (mp0) REVERT: D 99 ASN cc_start: 0.8363 (t0) cc_final: 0.8115 (t0) REVERT: D 116 ASN cc_start: 0.7251 (m-40) cc_final: 0.7031 (m-40) REVERT: F 90 ASN cc_start: 0.7965 (m110) cc_final: 0.7744 (t0) REVERT: F 124 ASP cc_start: 0.7855 (m-30) cc_final: 0.7135 (t0) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2726 time to fit residues: 138.6611 Evaluate side-chains 211 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 1.9990 chunk 172 optimal weight: 0.0870 chunk 118 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 153 optimal weight: 0.4980 chunk 230 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN C 611 ASN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN E 611 ASN E 718 ASN B 121 GLN F 39 ASN F 51 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19413 Z= 0.182 Angle : 0.603 9.268 26214 Z= 0.319 Chirality : 0.048 0.219 3093 Planarity : 0.003 0.035 3393 Dihedral : 6.182 35.013 2622 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 0.10 % Allowed : 2.03 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.86 % Twisted Proline : 5.26 % Twisted General : 0.08 % 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: -2.87 (0.16), residues: 2472 helix: -0.25 (0.25), residues: 432 sheet: -1.07 (0.20), residues: 663 loop : -3.04 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 334 HIS 0.004 0.001 HIS F 6 PHE 0.012 0.001 PHE A 449 TYR 0.016 0.001 TYR A 579 ARG 0.003 0.001 ARG E 386 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 278 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8731 (mt) cc_final: 0.7898 (tt) REVERT: A 326 PHE cc_start: 0.8651 (m-80) cc_final: 0.8098 (m-80) REVERT: A 390 ASP cc_start: 0.9394 (m-30) cc_final: 0.9102 (m-30) REVERT: A 438 LYS cc_start: 0.8541 (mttt) cc_final: 0.7957 (mmtt) REVERT: A 557 LYS cc_start: 0.7578 (mttt) cc_final: 0.7267 (mppt) REVERT: A 568 PHE cc_start: 0.8255 (m-80) cc_final: 0.7818 (m-10) REVERT: A 653 LYS cc_start: 0.8634 (tttt) cc_final: 0.8149 (ttpt) REVERT: A 775 GLU cc_start: 0.8708 (mp0) cc_final: 0.8048 (mp0) REVERT: A 778 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7621 (tt0) REVERT: C 177 LEU cc_start: 0.8711 (mt) cc_final: 0.8279 (tt) REVERT: C 230 ILE cc_start: 0.9075 (pt) cc_final: 0.8625 (pt) REVERT: C 326 PHE cc_start: 0.8634 (m-80) cc_final: 0.8024 (m-80) REVERT: C 336 LYS cc_start: 0.8788 (mttt) cc_final: 0.8561 (mmtm) REVERT: C 438 LYS cc_start: 0.8711 (mttt) cc_final: 0.7945 (mttp) REVERT: C 504 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7782 (pm20) REVERT: C 557 LYS cc_start: 0.7774 (mttt) cc_final: 0.7387 (mppt) REVERT: C 626 GLU cc_start: 0.8438 (mp0) cc_final: 0.8085 (mp0) REVERT: C 638 ILE cc_start: 0.9102 (mt) cc_final: 0.8508 (pt) REVERT: C 653 LYS cc_start: 0.8433 (tttt) cc_final: 0.7881 (tppt) REVERT: E 230 ILE cc_start: 0.9212 (pt) cc_final: 0.8699 (pt) REVERT: E 268 ASP cc_start: 0.8033 (m-30) cc_final: 0.7484 (p0) REVERT: E 326 PHE cc_start: 0.8548 (m-80) cc_final: 0.7887 (m-80) REVERT: E 438 LYS cc_start: 0.8543 (mttt) cc_final: 0.7836 (mttp) REVERT: E 522 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7992 (mp0) REVERT: E 557 LYS cc_start: 0.7900 (mttt) cc_final: 0.7478 (mppt) REVERT: E 626 GLU cc_start: 0.8382 (mp0) cc_final: 0.8080 (mp0) REVERT: E 653 LYS cc_start: 0.8554 (tttt) cc_final: 0.7872 (tppt) REVERT: E 725 GLN cc_start: 0.8609 (mt0) cc_final: 0.8226 (mt0) REVERT: E 733 ASP cc_start: 0.6771 (m-30) cc_final: 0.6431 (m-30) REVERT: B 55 ASN cc_start: 0.8404 (t0) cc_final: 0.7805 (p0) REVERT: D 99 ASN cc_start: 0.8424 (t0) cc_final: 0.8152 (t0) REVERT: D 116 ASN cc_start: 0.7286 (m-40) cc_final: 0.7038 (m-40) REVERT: F 77 ILE cc_start: 0.8692 (mt) cc_final: 0.8437 (tt) REVERT: F 124 ASP cc_start: 0.7702 (m-30) cc_final: 0.6955 (t70) outliers start: 2 outliers final: 0 residues processed: 280 average time/residue: 0.2727 time to fit residues: 122.7118 Evaluate side-chains 195 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 611 ASN ** E 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19413 Z= 0.196 Angle : 0.595 9.119 26214 Z= 0.317 Chirality : 0.048 0.163 3093 Planarity : 0.003 0.036 3393 Dihedral : 6.094 34.331 2622 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.86 % Twisted Proline : 5.26 % Twisted General : 0.12 % 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: -2.61 (0.16), residues: 2472 helix: 0.24 (0.26), residues: 432 sheet: -0.91 (0.20), residues: 675 loop : -2.98 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 334 HIS 0.004 0.001 HIS B 6 PHE 0.012 0.001 PHE A 803 TYR 0.017 0.001 TYR C 505 ARG 0.003 0.001 ARG E 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8768 (mt) cc_final: 0.7952 (tt) REVERT: A 230 ILE cc_start: 0.9060 (mt) cc_final: 0.8799 (pt) REVERT: A 326 PHE cc_start: 0.8667 (m-80) cc_final: 0.8186 (m-80) REVERT: A 390 ASP cc_start: 0.9437 (m-30) cc_final: 0.9152 (m-30) REVERT: A 438 LYS cc_start: 0.8567 (mttt) cc_final: 0.7964 (mmtt) REVERT: A 557 LYS cc_start: 0.7560 (mttt) cc_final: 0.7207 (mppt) REVERT: A 568 PHE cc_start: 0.8325 (m-80) cc_final: 0.7629 (m-10) REVERT: A 569 LYS cc_start: 0.8343 (mmmm) cc_final: 0.7905 (mmmm) REVERT: A 775 GLU cc_start: 0.8728 (mp0) cc_final: 0.8029 (mp0) REVERT: C 177 LEU cc_start: 0.8658 (mt) cc_final: 0.8194 (tt) REVERT: C 230 ILE cc_start: 0.9063 (pt) cc_final: 0.8626 (pt) REVERT: C 326 PHE cc_start: 0.8637 (m-80) cc_final: 0.8076 (m-80) REVERT: C 438 LYS cc_start: 0.8675 (mttt) cc_final: 0.7932 (mttp) REVERT: C 504 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7838 (pm20) REVERT: C 557 LYS cc_start: 0.7711 (mttt) cc_final: 0.7406 (mppt) REVERT: C 568 PHE cc_start: 0.8329 (m-80) cc_final: 0.8066 (m-10) REVERT: C 626 GLU cc_start: 0.8472 (mp0) cc_final: 0.8147 (mp0) REVERT: C 653 LYS cc_start: 0.8452 (tttt) cc_final: 0.7846 (tppt) REVERT: E 177 LEU cc_start: 0.8639 (mt) cc_final: 0.8321 (tt) REVERT: E 230 ILE cc_start: 0.9262 (pt) cc_final: 0.8760 (pt) REVERT: E 268 ASP cc_start: 0.8341 (m-30) cc_final: 0.7570 (p0) REVERT: E 326 PHE cc_start: 0.8548 (m-80) cc_final: 0.7918 (m-80) REVERT: E 438 LYS cc_start: 0.8572 (mttt) cc_final: 0.7854 (mttp) REVERT: E 522 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8041 (mp0) REVERT: E 557 LYS cc_start: 0.7936 (mttt) cc_final: 0.7522 (mppt) REVERT: E 568 PHE cc_start: 0.8196 (m-80) cc_final: 0.7904 (m-10) REVERT: E 626 GLU cc_start: 0.8396 (mp0) cc_final: 0.8088 (mp0) REVERT: E 653 LYS cc_start: 0.8604 (tttt) cc_final: 0.7909 (tppt) REVERT: B 13 GLN cc_start: 0.8705 (mp10) cc_final: 0.7555 (mm-40) REVERT: B 55 ASN cc_start: 0.8477 (t0) cc_final: 0.7773 (p0) REVERT: D 99 ASN cc_start: 0.8386 (t0) cc_final: 0.8070 (t0) REVERT: F 124 ASP cc_start: 0.7676 (m-30) cc_final: 0.7101 (t0) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.2671 time to fit residues: 111.5520 Evaluate side-chains 184 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.4980 chunk 219 optimal weight: 0.0030 chunk 48 optimal weight: 0.8980 chunk 143 optimal weight: 20.0000 chunk 60 optimal weight: 0.5980 chunk 243 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 chunk 80 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 GLN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN E 180 GLN E 611 ASN ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN D 116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19413 Z= 0.129 Angle : 0.550 9.542 26214 Z= 0.290 Chirality : 0.047 0.158 3093 Planarity : 0.003 0.031 3393 Dihedral : 5.586 31.036 2622 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.05 % Allowed : 1.22 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.86 % Twisted Proline : 3.51 % Twisted General : 0.12 % 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: -2.33 (0.17), residues: 2472 helix: 0.46 (0.26), residues: 453 sheet: -0.67 (0.20), residues: 726 loop : -2.96 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.003 0.001 HIS B 6 PHE 0.010 0.001 PHE C 568 TYR 0.019 0.001 TYR C 505 ARG 0.002 0.000 ARG E 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 2.451 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: A 177 LEU cc_start: 0.8702 (mt) cc_final: 0.7883 (tt) REVERT: A 192 ASN cc_start: 0.8975 (m-40) cc_final: 0.8461 (t0) REVERT: A 302 GLU cc_start: 0.6733 (pp20) cc_final: 0.6181 (pp20) REVERT: A 326 PHE cc_start: 0.8436 (m-80) cc_final: 0.8046 (m-80) REVERT: A 390 ASP cc_start: 0.9408 (m-30) cc_final: 0.9107 (m-30) REVERT: A 438 LYS cc_start: 0.8557 (mttt) cc_final: 0.7941 (mmtt) REVERT: A 557 LYS cc_start: 0.7591 (mttt) cc_final: 0.7302 (mppt) REVERT: A 568 PHE cc_start: 0.8322 (m-80) cc_final: 0.7696 (m-10) REVERT: A 569 LYS cc_start: 0.8279 (mmmm) cc_final: 0.7877 (mmmm) REVERT: A 775 GLU cc_start: 0.8610 (mp0) cc_final: 0.7949 (mp0) REVERT: C 192 ASN cc_start: 0.9057 (m-40) cc_final: 0.8343 (t0) REVERT: C 230 ILE cc_start: 0.9001 (pt) cc_final: 0.8633 (pt) REVERT: C 326 PHE cc_start: 0.8425 (m-80) cc_final: 0.7878 (m-80) REVERT: C 428 ARG cc_start: 0.8064 (tpm170) cc_final: 0.7787 (tpm170) REVERT: C 438 LYS cc_start: 0.8760 (mttt) cc_final: 0.8284 (ttmt) REVERT: C 471 ASP cc_start: 0.7115 (m-30) cc_final: 0.6865 (m-30) REVERT: C 504 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7806 (pm20) REVERT: C 538 ILE cc_start: 0.9345 (mt) cc_final: 0.8914 (tp) REVERT: C 557 LYS cc_start: 0.7564 (mttt) cc_final: 0.7243 (mppt) REVERT: C 568 PHE cc_start: 0.8327 (m-80) cc_final: 0.7980 (m-10) REVERT: C 626 GLU cc_start: 0.8433 (mp0) cc_final: 0.8192 (mp0) REVERT: C 653 LYS cc_start: 0.8471 (tttt) cc_final: 0.8041 (ttpt) REVERT: E 230 ILE cc_start: 0.9228 (pt) cc_final: 0.8726 (pt) REVERT: E 268 ASP cc_start: 0.8207 (m-30) cc_final: 0.7474 (p0) REVERT: E 326 PHE cc_start: 0.8411 (m-80) cc_final: 0.7788 (m-80) REVERT: E 438 LYS cc_start: 0.8609 (mttt) cc_final: 0.8140 (ttmt) REVERT: E 471 ASP cc_start: 0.7345 (m-30) cc_final: 0.7021 (m-30) REVERT: E 522 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8086 (mp0) REVERT: E 557 LYS cc_start: 0.7946 (mttt) cc_final: 0.7546 (mppt) REVERT: E 568 PHE cc_start: 0.8221 (m-80) cc_final: 0.7856 (m-10) REVERT: E 626 GLU cc_start: 0.8399 (mp0) cc_final: 0.8061 (mp0) REVERT: E 653 LYS cc_start: 0.8638 (tttt) cc_final: 0.7903 (tppt) REVERT: B 13 GLN cc_start: 0.8733 (mp10) cc_final: 0.7726 (mm-40) REVERT: B 55 ASN cc_start: 0.8401 (t0) cc_final: 0.7745 (p0) REVERT: D 13 GLN cc_start: 0.8732 (mp10) cc_final: 0.7650 (mm-40) REVERT: D 99 ASN cc_start: 0.8333 (t0) cc_final: 0.8038 (t0) REVERT: D 116 ASN cc_start: 0.7153 (m-40) cc_final: 0.6940 (m-40) REVERT: F 13 GLN cc_start: 0.8717 (mp10) cc_final: 0.7798 (mm-40) REVERT: F 70 LEU cc_start: 0.8659 (mp) cc_final: 0.8359 (mp) REVERT: F 77 ILE cc_start: 0.8605 (mt) cc_final: 0.8275 (tt) REVERT: F 124 ASP cc_start: 0.7761 (m-30) cc_final: 0.7184 (t0) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.2798 time to fit residues: 126.6241 Evaluate side-chains 201 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 242 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 ASN ** E 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 764 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19413 Z= 0.183 Angle : 0.572 9.624 26214 Z= 0.302 Chirality : 0.047 0.172 3093 Planarity : 0.003 0.033 3393 Dihedral : 5.675 31.619 2622 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 0.05 % Allowed : 0.81 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.86 % Twisted Proline : 5.26 % Twisted General : 0.12 % 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: -2.21 (0.17), residues: 2472 helix: 0.66 (0.27), residues: 444 sheet: -0.53 (0.21), residues: 696 loop : -2.90 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 334 HIS 0.004 0.001 HIS F 6 PHE 0.013 0.001 PHE E 492 TYR 0.019 0.001 TYR E 692 ARG 0.003 0.001 ARG E 386 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 255 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8748 (mt) cc_final: 0.7863 (tt) REVERT: A 192 ASN cc_start: 0.9007 (m-40) cc_final: 0.8478 (t0) REVERT: A 302 GLU cc_start: 0.6496 (pp20) cc_final: 0.6055 (pp20) REVERT: A 326 PHE cc_start: 0.8547 (m-80) cc_final: 0.8090 (m-80) REVERT: A 390 ASP cc_start: 0.9447 (m-30) cc_final: 0.9136 (m-30) REVERT: A 438 LYS cc_start: 0.8606 (mttt) cc_final: 0.7966 (mmtt) REVERT: A 557 LYS cc_start: 0.7582 (mttt) cc_final: 0.7293 (mppt) REVERT: A 568 PHE cc_start: 0.8404 (m-80) cc_final: 0.7705 (m-10) REVERT: A 569 LYS cc_start: 0.8330 (mmmm) cc_final: 0.7943 (mmmm) REVERT: A 725 GLN cc_start: 0.8304 (mt0) cc_final: 0.7941 (mt0) REVERT: A 775 GLU cc_start: 0.8633 (mp0) cc_final: 0.7950 (mp0) REVERT: C 192 ASN cc_start: 0.9094 (m-40) cc_final: 0.8335 (t0) REVERT: C 230 ILE cc_start: 0.9047 (pt) cc_final: 0.8631 (pt) REVERT: C 326 PHE cc_start: 0.8679 (m-80) cc_final: 0.8104 (m-80) REVERT: C 438 LYS cc_start: 0.8801 (mttt) cc_final: 0.8333 (ttmt) REVERT: C 471 ASP cc_start: 0.7035 (m-30) cc_final: 0.6655 (m-30) REVERT: C 504 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7813 (pm20) REVERT: C 538 ILE cc_start: 0.9352 (mt) cc_final: 0.8948 (tp) REVERT: C 557 LYS cc_start: 0.7640 (mttt) cc_final: 0.7333 (mppt) REVERT: C 568 PHE cc_start: 0.8194 (m-80) cc_final: 0.7871 (m-10) REVERT: C 626 GLU cc_start: 0.8461 (mp0) cc_final: 0.8245 (mp0) REVERT: C 653 LYS cc_start: 0.8469 (tttt) cc_final: 0.8071 (ttpt) REVERT: E 177 LEU cc_start: 0.8753 (mt) cc_final: 0.8420 (tt) REVERT: E 230 ILE cc_start: 0.9227 (pt) cc_final: 0.8770 (pt) REVERT: E 268 ASP cc_start: 0.8246 (m-30) cc_final: 0.7306 (p0) REVERT: E 326 PHE cc_start: 0.8582 (m-80) cc_final: 0.7901 (m-80) REVERT: E 438 LYS cc_start: 0.8609 (mttt) cc_final: 0.8169 (ttmt) REVERT: E 471 ASP cc_start: 0.7615 (m-30) cc_final: 0.7210 (m-30) REVERT: E 522 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8111 (mp0) REVERT: E 557 LYS cc_start: 0.7884 (mttt) cc_final: 0.7541 (mppt) REVERT: E 568 PHE cc_start: 0.8232 (m-80) cc_final: 0.7782 (m-10) REVERT: E 569 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7833 (mmtp) REVERT: E 626 GLU cc_start: 0.8445 (mp0) cc_final: 0.8124 (mp0) REVERT: E 653 LYS cc_start: 0.8658 (tttt) cc_final: 0.7901 (tppt) REVERT: B 13 GLN cc_start: 0.8724 (mp10) cc_final: 0.7753 (mm-40) REVERT: D 13 GLN cc_start: 0.8751 (mp10) cc_final: 0.7725 (mm-40) REVERT: D 99 ASN cc_start: 0.8451 (t0) cc_final: 0.8169 (t0) REVERT: F 13 GLN cc_start: 0.8696 (mp10) cc_final: 0.7724 (mm-40) REVERT: F 124 ASP cc_start: 0.7592 (m-30) cc_final: 0.7106 (t0) outliers start: 1 outliers final: 1 residues processed: 256 average time/residue: 0.2746 time to fit residues: 113.9372 Evaluate side-chains 185 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 154 optimal weight: 0.2980 chunk 165 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 190 optimal weight: 0.0270 chunk 220 optimal weight: 1.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 740 GLN ** E 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN D 116 ASN F 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19413 Z= 0.160 Angle : 0.558 9.690 26214 Z= 0.294 Chirality : 0.047 0.205 3093 Planarity : 0.003 0.035 3393 Dihedral : 5.524 30.829 2622 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.86 % Twisted Proline : 5.26 % Twisted General : 0.12 % 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: -2.13 (0.17), residues: 2472 helix: 0.84 (0.27), residues: 444 sheet: -0.53 (0.20), residues: 723 loop : -2.89 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 334 HIS 0.003 0.001 HIS F 6 PHE 0.011 0.001 PHE A 568 TYR 0.017 0.001 TYR C 692 ARG 0.003 0.001 ARG E 386 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8684 (mt) cc_final: 0.7803 (tt) REVERT: A 192 ASN cc_start: 0.9049 (m-40) cc_final: 0.8461 (t0) REVERT: A 217 LYS cc_start: 0.5292 (mttt) cc_final: 0.5031 (pttt) REVERT: A 228 GLU cc_start: 0.8515 (tt0) cc_final: 0.8203 (tt0) REVERT: A 302 GLU cc_start: 0.6468 (pp20) cc_final: 0.5956 (pp20) REVERT: A 326 PHE cc_start: 0.8514 (m-80) cc_final: 0.8098 (m-80) REVERT: A 390 ASP cc_start: 0.9440 (m-30) cc_final: 0.9138 (m-30) REVERT: A 438 LYS cc_start: 0.8612 (mttt) cc_final: 0.7955 (mmtt) REVERT: A 471 ASP cc_start: 0.7288 (m-30) cc_final: 0.7082 (m-30) REVERT: A 557 LYS cc_start: 0.7488 (mttt) cc_final: 0.7202 (mppt) REVERT: A 568 PHE cc_start: 0.8338 (m-80) cc_final: 0.7895 (m-10) REVERT: A 725 GLN cc_start: 0.8288 (mt0) cc_final: 0.7943 (mt0) REVERT: A 775 GLU cc_start: 0.8609 (mp0) cc_final: 0.7971 (mp0) REVERT: C 192 ASN cc_start: 0.9110 (m-40) cc_final: 0.8350 (t0) REVERT: C 230 ILE cc_start: 0.9032 (pt) cc_final: 0.8633 (pt) REVERT: C 326 PHE cc_start: 0.8630 (m-80) cc_final: 0.8090 (m-80) REVERT: C 438 LYS cc_start: 0.8789 (mttt) cc_final: 0.8288 (ttmt) REVERT: C 471 ASP cc_start: 0.7400 (m-30) cc_final: 0.6978 (m-30) REVERT: C 504 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7843 (pm20) REVERT: C 557 LYS cc_start: 0.7630 (mttt) cc_final: 0.7322 (mppt) REVERT: C 568 PHE cc_start: 0.8300 (m-80) cc_final: 0.7953 (m-10) REVERT: C 653 LYS cc_start: 0.8515 (tttt) cc_final: 0.8099 (ttpt) REVERT: E 177 LEU cc_start: 0.8743 (mt) cc_final: 0.8390 (tt) REVERT: E 230 ILE cc_start: 0.9240 (pt) cc_final: 0.8792 (pt) REVERT: E 268 ASP cc_start: 0.8286 (m-30) cc_final: 0.7389 (p0) REVERT: E 326 PHE cc_start: 0.8533 (m-80) cc_final: 0.7886 (m-80) REVERT: E 438 LYS cc_start: 0.8646 (mttt) cc_final: 0.8189 (ttmt) REVERT: E 471 ASP cc_start: 0.7800 (m-30) cc_final: 0.7324 (m-30) REVERT: E 522 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8137 (mp0) REVERT: E 557 LYS cc_start: 0.7903 (mttt) cc_final: 0.7544 (mppt) REVERT: E 568 PHE cc_start: 0.8203 (m-80) cc_final: 0.7663 (m-10) REVERT: E 569 LYS cc_start: 0.7976 (mmtt) cc_final: 0.7773 (mmtp) REVERT: E 626 GLU cc_start: 0.8448 (mp0) cc_final: 0.8120 (mp0) REVERT: E 653 LYS cc_start: 0.8679 (tttt) cc_final: 0.8226 (ttmt) REVERT: E 687 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8303 (ptpp) REVERT: B 13 GLN cc_start: 0.8689 (mp10) cc_final: 0.7717 (mm-40) REVERT: D 13 GLN cc_start: 0.8781 (mp10) cc_final: 0.7813 (mm-40) REVERT: D 99 ASN cc_start: 0.8315 (t0) cc_final: 0.8094 (t0) REVERT: F 13 GLN cc_start: 0.8747 (mp10) cc_final: 0.7842 (mm-40) REVERT: F 18 ASP cc_start: 0.7750 (p0) cc_final: 0.7474 (p0) REVERT: F 20 LYS cc_start: 0.8722 (mttt) cc_final: 0.8342 (ttpt) REVERT: F 124 ASP cc_start: 0.7635 (m-30) cc_final: 0.7061 (t0) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2572 time to fit residues: 104.9408 Evaluate side-chains 185 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 226 optimal weight: 0.5980 chunk 136 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 214 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 740 GLN ** E 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN F 114 ASN F 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19413 Z= 0.181 Angle : 0.567 9.618 26214 Z= 0.300 Chirality : 0.048 0.195 3093 Planarity : 0.003 0.034 3393 Dihedral : 5.564 31.466 2622 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.86 % Twisted Proline : 5.26 % Twisted General : 0.12 % 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: -2.11 (0.17), residues: 2472 helix: 0.92 (0.27), residues: 444 sheet: -0.52 (0.21), residues: 678 loop : -2.83 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 334 HIS 0.004 0.001 HIS F 6 PHE 0.014 0.001 PHE E 492 TYR 0.017 0.001 TYR A 692 ARG 0.007 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8694 (mt) cc_final: 0.7756 (tt) REVERT: A 192 ASN cc_start: 0.9105 (m-40) cc_final: 0.8527 (t0) REVERT: A 217 LYS cc_start: 0.5235 (mttt) cc_final: 0.5011 (pttt) REVERT: A 302 GLU cc_start: 0.6505 (pp20) cc_final: 0.5917 (pp20) REVERT: A 326 PHE cc_start: 0.8562 (m-80) cc_final: 0.8100 (m-80) REVERT: A 390 ASP cc_start: 0.9465 (m-30) cc_final: 0.9159 (m-30) REVERT: A 438 LYS cc_start: 0.8598 (mttt) cc_final: 0.7945 (mmtt) REVERT: A 465 GLU cc_start: 0.8188 (pt0) cc_final: 0.7849 (pm20) REVERT: A 471 ASP cc_start: 0.7697 (m-30) cc_final: 0.7342 (m-30) REVERT: A 482 ARG cc_start: 0.8780 (mtt180) cc_final: 0.7516 (mtt180) REVERT: A 557 LYS cc_start: 0.7567 (mttt) cc_final: 0.7289 (mppt) REVERT: A 725 GLN cc_start: 0.8366 (mt0) cc_final: 0.7975 (mt0) REVERT: A 775 GLU cc_start: 0.8618 (mp0) cc_final: 0.7949 (mp0) REVERT: C 192 ASN cc_start: 0.9143 (m-40) cc_final: 0.8363 (t0) REVERT: C 230 ILE cc_start: 0.9005 (pt) cc_final: 0.8468 (pt) REVERT: C 326 PHE cc_start: 0.8707 (m-80) cc_final: 0.8140 (m-80) REVERT: C 438 LYS cc_start: 0.8800 (mttt) cc_final: 0.8364 (ttmt) REVERT: C 504 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8169 (mp0) REVERT: C 538 ILE cc_start: 0.9340 (mt) cc_final: 0.8931 (tp) REVERT: C 557 LYS cc_start: 0.7563 (mttt) cc_final: 0.7272 (mppt) REVERT: C 568 PHE cc_start: 0.8275 (m-80) cc_final: 0.7869 (m-10) REVERT: C 569 LYS cc_start: 0.8285 (mmmm) cc_final: 0.8034 (mmmm) REVERT: C 653 LYS cc_start: 0.8527 (tttt) cc_final: 0.8085 (ttpt) REVERT: E 177 LEU cc_start: 0.8834 (mt) cc_final: 0.8388 (tt) REVERT: E 230 ILE cc_start: 0.9239 (pt) cc_final: 0.8802 (pt) REVERT: E 268 ASP cc_start: 0.8284 (m-30) cc_final: 0.7335 (p0) REVERT: E 326 PHE cc_start: 0.8555 (m-80) cc_final: 0.7967 (m-80) REVERT: E 438 LYS cc_start: 0.8663 (mttt) cc_final: 0.8189 (ttmt) REVERT: E 471 ASP cc_start: 0.7776 (m-30) cc_final: 0.7359 (m-30) REVERT: E 522 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8105 (mp0) REVERT: E 557 LYS cc_start: 0.7915 (mttt) cc_final: 0.7559 (mppt) REVERT: E 568 PHE cc_start: 0.8206 (m-80) cc_final: 0.7614 (m-10) REVERT: E 569 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7767 (mmtp) REVERT: E 626 GLU cc_start: 0.8451 (mp0) cc_final: 0.8155 (mp0) REVERT: E 653 LYS cc_start: 0.8680 (tttt) cc_final: 0.8229 (ttmt) REVERT: E 687 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8387 (ptpp) REVERT: B 13 GLN cc_start: 0.8713 (mp10) cc_final: 0.7775 (mm-40) REVERT: D 13 GLN cc_start: 0.8773 (mp10) cc_final: 0.7810 (mm-40) REVERT: D 99 ASN cc_start: 0.8469 (t0) cc_final: 0.8175 (t0) REVERT: F 13 GLN cc_start: 0.8729 (mp10) cc_final: 0.7813 (mm-40) REVERT: F 18 ASP cc_start: 0.7827 (p0) cc_final: 0.7566 (p0) REVERT: F 20 LYS cc_start: 0.8772 (mttt) cc_final: 0.8340 (ttpt) REVERT: F 124 ASP cc_start: 0.7557 (m-30) cc_final: 0.7098 (t0) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.2702 time to fit residues: 105.1892 Evaluate side-chains 186 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 3.9990 chunk 146 optimal weight: 0.0270 chunk 113 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 251 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 154 optimal weight: 0.0670 chunk 122 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN D 116 ASN F 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19413 Z= 0.158 Angle : 0.563 9.895 26214 Z= 0.296 Chirality : 0.048 0.190 3093 Planarity : 0.003 0.034 3393 Dihedral : 5.474 30.993 2622 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.86 % Twisted Proline : 5.26 % Twisted General : 0.08 % 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: -2.07 (0.17), residues: 2472 helix: 1.05 (0.27), residues: 435 sheet: -0.49 (0.21), residues: 678 loop : -2.83 (0.15), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 334 HIS 0.003 0.001 HIS F 6 PHE 0.010 0.001 PHE A 293 TYR 0.020 0.001 TYR A 692 ARG 0.003 0.001 ARG E 386 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8643 (mt) cc_final: 0.7648 (tt) REVERT: A 192 ASN cc_start: 0.9070 (m-40) cc_final: 0.8508 (t0) REVERT: A 228 GLU cc_start: 0.8626 (tt0) cc_final: 0.8417 (tt0) REVERT: A 248 LYS cc_start: 0.4964 (mmtt) cc_final: 0.4166 (mttp) REVERT: A 302 GLU cc_start: 0.6563 (pp20) cc_final: 0.5975 (pp20) REVERT: A 326 PHE cc_start: 0.8509 (m-80) cc_final: 0.8029 (m-80) REVERT: A 390 ASP cc_start: 0.9462 (m-30) cc_final: 0.9154 (m-30) REVERT: A 438 LYS cc_start: 0.8621 (mttt) cc_final: 0.7963 (mmtt) REVERT: A 471 ASP cc_start: 0.7840 (m-30) cc_final: 0.7371 (m-30) REVERT: A 557 LYS cc_start: 0.7536 (mttt) cc_final: 0.7267 (mppt) REVERT: A 568 PHE cc_start: 0.8310 (m-80) cc_final: 0.7969 (m-10) REVERT: A 650 ASN cc_start: 0.8358 (p0) cc_final: 0.8006 (t0) REVERT: A 725 GLN cc_start: 0.8334 (mt0) cc_final: 0.7961 (mt0) REVERT: A 775 GLU cc_start: 0.8631 (mp0) cc_final: 0.7995 (mp0) REVERT: C 192 ASN cc_start: 0.9115 (m-40) cc_final: 0.8396 (t0) REVERT: C 230 ILE cc_start: 0.8994 (pt) cc_final: 0.8515 (pt) REVERT: C 294 ASN cc_start: 0.8602 (t0) cc_final: 0.8233 (t0) REVERT: C 326 PHE cc_start: 0.8650 (m-80) cc_final: 0.8114 (m-80) REVERT: C 438 LYS cc_start: 0.8812 (mttt) cc_final: 0.8369 (ttmt) REVERT: C 504 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8183 (mp0) REVERT: C 557 LYS cc_start: 0.7515 (mttt) cc_final: 0.7255 (mppt) REVERT: C 568 PHE cc_start: 0.8246 (m-80) cc_final: 0.7883 (m-10) REVERT: C 569 LYS cc_start: 0.8263 (mmmm) cc_final: 0.8018 (mmmm) REVERT: C 626 GLU cc_start: 0.8530 (mp0) cc_final: 0.8328 (mp0) REVERT: C 653 LYS cc_start: 0.8522 (tttt) cc_final: 0.8085 (ttpt) REVERT: E 177 LEU cc_start: 0.8741 (mt) cc_final: 0.8361 (tt) REVERT: E 230 ILE cc_start: 0.9232 (pt) cc_final: 0.8799 (pt) REVERT: E 268 ASP cc_start: 0.8245 (m-30) cc_final: 0.7328 (p0) REVERT: E 326 PHE cc_start: 0.8517 (m-80) cc_final: 0.7937 (m-80) REVERT: E 438 LYS cc_start: 0.8650 (mttt) cc_final: 0.8189 (ttmt) REVERT: E 465 GLU cc_start: 0.8164 (pt0) cc_final: 0.7856 (pm20) REVERT: E 471 ASP cc_start: 0.7773 (m-30) cc_final: 0.7338 (m-30) REVERT: E 482 ARG cc_start: 0.8639 (mtt180) cc_final: 0.7800 (mtt180) REVERT: E 522 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8161 (mp0) REVERT: E 557 LYS cc_start: 0.7868 (mttt) cc_final: 0.7516 (mppt) REVERT: E 568 PHE cc_start: 0.8247 (m-80) cc_final: 0.7696 (m-10) REVERT: E 569 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7669 (mmtp) REVERT: E 626 GLU cc_start: 0.8455 (mp0) cc_final: 0.8143 (mp0) REVERT: E 653 LYS cc_start: 0.8675 (tttt) cc_final: 0.8227 (ttmt) REVERT: E 687 LYS cc_start: 0.8674 (mmtt) cc_final: 0.8406 (ptpp) REVERT: B 13 GLN cc_start: 0.8708 (mp10) cc_final: 0.7769 (mm-40) REVERT: D 13 GLN cc_start: 0.8775 (mp10) cc_final: 0.7672 (mm-40) REVERT: D 99 ASN cc_start: 0.8351 (t0) cc_final: 0.8077 (t0) REVERT: F 13 GLN cc_start: 0.8769 (mp10) cc_final: 0.7887 (mm-40) REVERT: F 18 ASP cc_start: 0.7768 (p0) cc_final: 0.7560 (p0) REVERT: F 20 LYS cc_start: 0.8782 (mttt) cc_final: 0.8331 (ttpt) REVERT: F 124 ASP cc_start: 0.7586 (m-30) cc_final: 0.7062 (t0) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2645 time to fit residues: 103.7312 Evaluate side-chains 189 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 3.9990 chunk 61 optimal weight: 0.0270 chunk 184 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 205 optimal weight: 0.0770 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 0.0570 chunk 175 optimal weight: 3.9990 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN ** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.088032 restraints weight = 57068.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089526 restraints weight = 35844.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.090597 restraints weight = 24920.634| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19413 Z= 0.120 Angle : 0.542 10.167 26214 Z= 0.285 Chirality : 0.048 0.196 3093 Planarity : 0.003 0.032 3393 Dihedral : 5.188 29.661 2622 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.86 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.17), residues: 2472 helix: 1.31 (0.27), residues: 459 sheet: -0.37 (0.22), residues: 633 loop : -2.83 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 334 HIS 0.002 0.000 HIS B 6 PHE 0.009 0.001 PHE A 293 TYR 0.017 0.001 TYR A 692 ARG 0.004 0.000 ARG A 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3790.41 seconds wall clock time: 70 minutes 48.81 seconds (4248.81 seconds total)