Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 12:30:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9f_20696/07_2023/6u9f_20696.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9f_20696/07_2023/6u9f_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_20696/07_2023/6u9f_20696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9f_20696/07_2023/6u9f_20696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9f_20696/07_2023/6u9f_20696.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9f_20696/07_2023/6u9f_20696.pdb" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 9.36, per 1000 atoms: 0.49 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: 6.97 Conformation dependent library (CDL) restraints added in 2.9 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: 1.17 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: 6.38 Time building geometry restraints manager: 7.54 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: 2.350 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: 10.330 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 46.740 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.780 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.404 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 outliers start: 3 outliers final: 0 residues processed: 511 average time/residue: 0.3357 time to fit residues: 253.2289 Evaluate side-chains 219 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.339 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1415 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.9990 chunk 76 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 228 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 355 ASN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN E 355 ASN E 371 ASN E 545 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 19413 Z= 0.246 Angle : 0.721 10.213 26214 Z= 0.384 Chirality : 0.050 0.174 3093 Planarity : 0.004 0.041 3393 Dihedral : 7.678 37.302 2622 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.86 % Twisted Proline : 5.26 % Twisted General : 0.16 % 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: -3.97 (0.14), residues: 2472 helix: -2.43 (0.18), residues: 432 sheet: -1.70 (0.18), residues: 663 loop : -3.31 (0.14), residues: 1377 *********************** 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 319 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2780 time to fit residues: 142.3066 Evaluate side-chains 183 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.438 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2004 ------------------------------------------------------------------------------- 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: 0.0670 chunk 71 optimal weight: 20.0000 chunk 190 optimal weight: 0.0670 chunk 155 optimal weight: 0.0270 chunk 63 optimal weight: 0.9980 chunk 229 optimal weight: 4.9990 chunk 247 optimal weight: 0.6980 chunk 204 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 overall best weight: 0.3514 ------------------------------------------------------------------------------- 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 180 GLN C 611 ASN D 116 ASN F 51 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 19413 Z= 0.140 Angle : 0.615 9.974 26214 Z= 0.322 Chirality : 0.048 0.174 3093 Planarity : 0.003 0.035 3393 Dihedral : 6.544 34.288 2622 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer Outliers : 0.10 % 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: -3.34 (0.15), residues: 2472 helix: -1.26 (0.21), residues: 450 sheet: -1.20 (0.19), residues: 681 loop : -3.24 (0.15), residues: 1341 *********************** 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 307 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 305 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 307 average time/residue: 0.2737 time to fit residues: 135.4735 Evaluate side-chains 187 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 2.227 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1813 time to fit residues: 3.7159 ------------------------------------------------------------------------------- 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: 5.9990 chunk 172 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 243 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 355 ASN C 371 ASN ** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 718 ASN B 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 19413 Z= 0.362 Angle : 0.739 9.123 26214 Z= 0.393 Chirality : 0.050 0.197 3093 Planarity : 0.004 0.038 3393 Dihedral : 6.975 38.622 2622 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer Outliers : 0.05 % 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: -3.12 (0.16), residues: 2472 helix: -0.61 (0.24), residues: 432 sheet: -1.26 (0.19), residues: 663 loop : -3.12 (0.15), residues: 1377 *********************** 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 227 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 2.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.2712 time to fit residues: 100.9859 Evaluate side-chains 154 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.444 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3327 ------------------------------------------------------------------------------- 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: 0.9980 chunk 138 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 0.0040 chunk 207 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- 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 718 ASN ** 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** ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN D 116 ASN F 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 19413 Z= 0.206 Angle : 0.624 9.441 26214 Z= 0.333 Chirality : 0.048 0.167 3093 Planarity : 0.003 0.037 3393 Dihedral : 6.419 35.061 2622 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.86 % Twisted Proline : 5.26 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.16), residues: 2472 helix: 0.03 (0.26), residues: 432 sheet: -0.92 (0.20), residues: 696 loop : -3.10 (0.15), residues: 1344 *********************** 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 236 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2624 time to fit residues: 102.3106 Evaluate side-chains 160 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.603 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4248 ------------------------------------------------------------------------------- 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: 0.8980 chunk 219 optimal weight: 0.0970 chunk 48 optimal weight: 0.8980 chunk 143 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 243 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 128 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 611 ASN ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN C 611 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** ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 19413 Z= 0.144 Angle : 0.570 9.502 26214 Z= 0.301 Chirality : 0.047 0.159 3093 Planarity : 0.003 0.035 3393 Dihedral : 5.790 31.800 2622 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer Outliers : 0.00 % 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: -2.41 (0.17), residues: 2472 helix: 0.64 (0.27), residues: 423 sheet: -0.69 (0.21), residues: 681 loop : -2.97 (0.15), residues: 1368 *********************** 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 259 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.2713 time to fit residues: 115.2577 Evaluate side-chains 167 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.292 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1202 ------------------------------------------------------------------------------- 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: 1.9990 chunk 27 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 137 optimal weight: 0.4980 chunk 205 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 242 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** 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** D 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4685 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= 0.173 Angle : 0.585 9.966 26214 Z= 0.308 Chirality : 0.047 0.175 3093 Planarity : 0.003 0.035 3393 Dihedral : 5.731 32.188 2622 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer Outliers : 0.00 % 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: -2.31 (0.17), residues: 2472 helix: 0.86 (0.27), residues: 423 sheet: -0.69 (0.21), residues: 693 loop : -2.94 (0.16), residues: 1356 *********************** 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 243 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2584 time to fit residues: 104.5831 Evaluate side-chains 163 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.566 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3073 ------------------------------------------------------------------------------- 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: 7.9990 chunk 96 optimal weight: 0.6980 chunk 145 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 154 optimal weight: 0.0980 chunk 165 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 190 optimal weight: 0.1980 chunk 220 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 ASN ** C 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 ASN ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN F 114 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4831 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= 0.158 Angle : 0.586 9.940 26214 Z= 0.305 Chirality : 0.048 0.186 3093 Planarity : 0.003 0.036 3393 Dihedral : 5.595 31.046 2622 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer Outliers : 0.05 % 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: -2.23 (0.17), residues: 2472 helix: 0.74 (0.27), residues: 444 sheet: -0.56 (0.21), residues: 678 loop : -2.91 (0.16), residues: 1350 *********************** 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 252 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 252 average time/residue: 0.2757 time to fit residues: 113.7280 Evaluate side-chains 165 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 2.495 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1859 time to fit residues: 3.7131 ------------------------------------------------------------------------------- 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: 0.0070 chunk 212 optimal weight: 2.9990 chunk 226 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 204 optimal weight: 0.8980 chunk 214 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 611 ASN ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 GLN ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5007 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= 0.157 Angle : 0.574 9.928 26214 Z= 0.301 Chirality : 0.048 0.182 3093 Planarity : 0.003 0.034 3393 Dihedral : 5.497 30.977 2622 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.86 % Twisted Proline : 5.26 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.17), residues: 2472 helix: 0.91 (0.27), residues: 444 sheet: -0.49 (0.21), residues: 675 loop : -2.90 (0.16), residues: 1353 *********************** 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 243 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2666 time to fit residues: 106.7723 Evaluate side-chains 167 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.429 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2979 ------------------------------------------------------------------------------- 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: 2.9990 chunk 146 optimal weight: 0.0030 chunk 113 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 251 optimal weight: 0.6980 chunk 231 optimal weight: 3.9990 chunk 199 optimal weight: 0.0030 chunk 20 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN C 718 ASN ** C 740 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 19413 Z= 0.135 Angle : 0.567 10.197 26214 Z= 0.296 Chirality : 0.048 0.180 3093 Planarity : 0.003 0.034 3393 Dihedral : 5.317 30.239 2622 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.86 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.17), residues: 2472 helix: 1.06 (0.27), residues: 444 sheet: -0.36 (0.22), residues: 645 loop : -2.90 (0.15), residues: 1383 ********************** 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 256 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.2686 time to fit residues: 113.9998 Evaluate side-chains 177 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.389 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4350 ------------------------------------------------------------------------------- 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: 0.2980 chunk 184 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 200 optimal weight: 0.0470 chunk 83 optimal weight: 10.0000 chunk 205 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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** ** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** 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 39 ASN D 51 GLN D 116 ASN F 114 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.096839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087417 restraints weight = 57783.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.088930 restraints weight = 36333.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089945 restraints weight = 25292.833| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 19413 Z= 0.138 Angle : 0.561 10.085 26214 Z= 0.294 Chirality : 0.048 0.176 3093 Planarity : 0.003 0.033 3393 Dihedral : 5.240 29.832 2622 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer Outliers : 0.00 % 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: -2.09 (0.17), residues: 2472 helix: 1.17 (0.27), residues: 450 sheet: -0.44 (0.22), residues: 642 loop : -2.93 (0.15), residues: 1380 =============================================================================== Job complete usr+sys time: 3496.11 seconds wall clock time: 65 minutes 18.13 seconds (3918.13 seconds total)