Starting phenix.real_space_refine on Mon Aug 25 04:46:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8toa_41441/08_2025/8toa_41441.cif Found real_map, /net/cci-nas-00/data/ceres_data/8toa_41441/08_2025/8toa_41441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8toa_41441/08_2025/8toa_41441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8toa_41441/08_2025/8toa_41441.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8toa_41441/08_2025/8toa_41441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8toa_41441/08_2025/8toa_41441.map" } resolution = 3.69 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 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= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11061 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 10339 2.51 5 N 2867 2.21 5 O 3271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16570 Number of models: 1 Model: "" Number of chains: 15 Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Chain: "D" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "E" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Chain: "A" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "B" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 101} Chain: "C" Number of atoms: 3699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3699 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 3699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3699 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 3699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3699 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.65, per 1000 atoms: 0.22 Number of scatterers: 16570 At special positions: 0 Unit cell: (140.27, 138.61, 159.36, 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 93 16.00 O 3271 8.00 N 2867 7.00 C 10339 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 458 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 268 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 66 " distance=2.02 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 272 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 465 " - pdb=" SG CYS C 469 " distance=2.02 Simple disulfide: pdb=" SG CYS I 4 " - pdb=" SG CYS I 458 " distance=2.03 Simple disulfide: pdb=" SG CYS I 42 " - pdb=" SG CYS I 268 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 66 " distance=2.02 Simple disulfide: pdb=" SG CYS I 87 " - pdb=" SG CYS I 129 " distance=2.03 Simple disulfide: pdb=" SG CYS I 272 " - pdb=" SG CYS I 296 " distance=2.03 Simple disulfide: pdb=" SG CYS I 465 " - pdb=" SG CYS I 469 " distance=2.03 Simple disulfide: pdb=" SG CYS K 4 " - pdb=" SG CYS K 458 " distance=2.03 Simple disulfide: pdb=" SG CYS K 42 " - pdb=" SG CYS K 268 " distance=2.04 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 66 " distance=2.03 Simple disulfide: pdb=" SG CYS K 87 " - pdb=" SG CYS K 129 " distance=2.03 Simple disulfide: pdb=" SG CYS K 272 " - pdb=" SG CYS K 296 " distance=2.03 Simple disulfide: pdb=" SG CYS K 465 " - pdb=" SG CYS K 469 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied NAG-ASN " NAG B 201 " - " ASN B 26 " " NAG C 601 " - " ASN C 28 " " NAG C 602 " - " ASN C 403 " " NAG C 603 " - " ASN C 231 " " NAG E 201 " - " ASN E 26 " " NAG I 601 " - " ASN I 403 " " NAG I 602 " - " ASN I 28 " " NAG I 603 " - " ASN I 231 " " NAG K 601 " - " ASN K 403 " " NAG K 602 " - " ASN K 28 " " NAG L 201 " - " ASN L 26 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 712.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3816 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 44 sheets defined 18.7% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.593A pdb=" N ASP L 87 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 84 through 88' Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.594A pdb=" N ASP E 87 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 84 through 88' Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.985A pdb=" N THR C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 removed outlier: 4.109A pdb=" N ASP C 67 " --> pdb=" O PRO C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'C' and resid 358 through 377 Processing helix chain 'C' and resid 395 through 448 removed outlier: 5.254A pdb=" N GLU C 435 " --> pdb=" O LEU C 431 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 483 through 489 removed outlier: 4.114A pdb=" N GLN C 489 " --> pdb=" O GLU C 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 62 removed outlier: 4.014A pdb=" N THR I 61 " --> pdb=" O LEU I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 67 removed outlier: 4.111A pdb=" N ASP I 67 " --> pdb=" O PRO I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 104 removed outlier: 3.763A pdb=" N LEU I 98 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU I 104 " --> pdb=" O GLN I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 186 Processing helix chain 'I' and resid 358 through 377 removed outlier: 3.977A pdb=" N SER I 364 " --> pdb=" O LYS I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 448 Processing helix chain 'I' and resid 466 through 475 Processing helix chain 'I' and resid 479 through 489 removed outlier: 4.479A pdb=" N TYR I 483 " --> pdb=" O ASP I 479 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLU I 485 " --> pdb=" O SER I 481 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLU I 486 " --> pdb=" O LYS I 482 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLN I 489 " --> pdb=" O GLU I 485 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 62 removed outlier: 4.039A pdb=" N THR K 61 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 67 removed outlier: 3.899A pdb=" N ASP K 67 " --> pdb=" O PRO K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 105 removed outlier: 3.807A pdb=" N LEU K 98 " --> pdb=" O ASN K 94 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU K 104 " --> pdb=" O GLN K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 186 Processing helix chain 'K' and resid 358 through 378 removed outlier: 4.489A pdb=" N SER K 364 " --> pdb=" O LYS K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 447 Processing helix chain 'K' and resid 468 through 473 removed outlier: 3.831A pdb=" N ILE K 473 " --> pdb=" O CYS K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 484 through 490 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.594A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA H 96 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 92 through 93 removed outlier: 3.720A pdb=" N TYR H 93 " --> pdb=" O THR H 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.713A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.953A pdb=" N LEU L 11 " --> pdb=" O ASP L 110 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL L 109 " --> pdb=" O GLY L 89 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE L 53 " --> pdb=" O TRP L 40 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU L 51 " --> pdb=" O ARG L 42 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR L 54 " --> pdb=" O ASN L 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'D' and resid 57 through 59 removed outlier: 3.593A pdb=" N GLU D 46 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA D 96 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 92 through 93 removed outlier: 3.719A pdb=" N TYR D 93 " --> pdb=" O THR D 113 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.713A pdb=" N SER E 7 " --> pdb=" O SER E 22 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.953A pdb=" N LEU E 11 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL E 109 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY E 89 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 53 " --> pdb=" O TRP E 40 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG E 42 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU E 51 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR E 54 " --> pdb=" O ASN E 58 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.534A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 96 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 94 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 93 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 67 through 69 Processing sheet with id=AB7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.633A pdb=" N LEU B 11 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 109 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 89 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'C' and resid 352 through 356 removed outlier: 3.674A pdb=" N GLY C 352 " --> pdb=" O ASN C 349 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C 346 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS C 4 " --> pdb=" O ARG C 346 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLN C 348 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS C 2 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 14 through 16 removed outlier: 3.898A pdb=" N THR C 14 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AC4, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AC5, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.832A pdb=" N PHE C 223 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP C 171 " --> pdb=" O HIS C 224 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 108 through 109 Processing sheet with id=AC7, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AC8, first strand: chain 'C' and resid 158 through 160 Processing sheet with id=AC9, first strand: chain 'C' and resid 272 through 274 removed outlier: 3.691A pdb=" N CYS C 272 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY C 277 " --> pdb=" O TYR C 274 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 2 through 3 removed outlier: 3.741A pdb=" N ILE I 3 " --> pdb=" O PHE I 459 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 14 through 16 removed outlier: 3.973A pdb=" N THR I 14 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL I 26 " --> pdb=" O THR I 14 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 33 through 34 Processing sheet with id=AD4, first strand: chain 'I' and resid 50 through 52 Processing sheet with id=AD5, first strand: chain 'I' and resid 140 through 142 removed outlier: 8.387A pdb=" N VAL I 170 " --> pdb=" O PRO I 245 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP I 171 " --> pdb=" O HIS I 224 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 140 through 142 removed outlier: 8.387A pdb=" N VAL I 170 " --> pdb=" O PRO I 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 203 through 204 removed outlier: 3.777A pdb=" N VAL I 193 " --> pdb=" O PHE I 204 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 272 through 274 removed outlier: 3.693A pdb=" N CYS I 272 " --> pdb=" O ILE I 279 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY I 277 " --> pdb=" O TYR I 274 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 14 through 16 removed outlier: 3.890A pdb=" N THR K 14 " --> pdb=" O VAL K 26 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL K 26 " --> pdb=" O THR K 14 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 30 through 31 Processing sheet with id=AE2, first strand: chain 'K' and resid 33 through 34 Processing sheet with id=AE3, first strand: chain 'K' and resid 49 through 50 removed outlier: 6.341A pdb=" N ILE K 77 " --> pdb=" O ILE K 258 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 90 through 92 removed outlier: 7.445A pdb=" N LYS K 91 " --> pdb=" O PHE K 223 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N TRP K 225 " --> pdb=" O LYS K 91 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP K 171 " --> pdb=" O HIS K 224 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER K 249 " --> pdb=" O LEU K 168 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL K 170 " --> pdb=" O ARG K 247 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ARG K 247 " --> pdb=" O VAL K 170 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 121 through 124 removed outlier: 4.626A pdb=" N ASN K 123 " --> pdb=" O TRP K 142 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TRP K 142 " --> pdb=" O ASN K 123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 158 through 160 Processing sheet with id=AE7, first strand: chain 'K' and resid 277 through 278 removed outlier: 3.703A pdb=" N GLY K 277 " --> pdb=" O TYR K 274 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 451 through 452 removed outlier: 3.545A pdb=" N GLU K 452 " --> pdb=" O GLU K 460 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1269 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: 2.55 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5110 1.34 - 1.46: 3854 1.46 - 1.58: 7822 1.58 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 16918 Sorted by residual: bond pdb=" N VAL K 10 " pdb=" CA VAL K 10 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.11e-02 8.12e+03 1.32e+01 bond pdb=" CA PRO A 40 " pdb=" C PRO A 40 " ideal model delta sigma weight residual 1.514 1.534 -0.020 5.50e-03 3.31e+04 1.32e+01 bond pdb=" N VAL A 37 " pdb=" CA VAL A 37 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.11e-02 8.12e+03 1.28e+01 bond pdb=" N VAL A 115 " pdb=" CA VAL A 115 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.11e-02 8.12e+03 1.24e+01 bond pdb=" N ILE B 53 " pdb=" CA ILE B 53 " ideal model delta sigma weight residual 1.458 1.497 -0.040 1.18e-02 7.18e+03 1.13e+01 ... (remaining 16913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 22231 2.85 - 5.70: 616 5.70 - 8.55: 45 8.55 - 11.41: 13 11.41 - 14.26: 2 Bond angle restraints: 22907 Sorted by residual: angle pdb=" CA GLY B 106 " pdb=" C GLY B 106 " pdb=" O GLY B 106 " ideal model delta sigma weight residual 122.22 118.31 3.91 6.50e-01 2.37e+00 3.61e+01 angle pdb=" CA GLY B 71 " pdb=" C GLY B 71 " pdb=" O GLY B 71 " ideal model delta sigma weight residual 122.52 117.92 4.60 7.90e-01 1.60e+00 3.39e+01 angle pdb=" C ASN C 475 " pdb=" N ASN C 476 " pdb=" CA ASN C 476 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.75e+01 angle pdb=" N GLU I 435 " pdb=" CA GLU I 435 " pdb=" CB GLU I 435 " ideal model delta sigma weight residual 110.28 118.01 -7.73 1.55e+00 4.16e-01 2.49e+01 angle pdb=" N THR I 477 " pdb=" CA THR I 477 " pdb=" C THR I 477 " ideal model delta sigma weight residual 114.56 108.36 6.20 1.27e+00 6.20e-01 2.38e+01 ... (remaining 22902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.41: 9683 26.41 - 52.82: 484 52.82 - 79.23: 55 79.23 - 105.64: 7 105.64 - 132.04: 1 Dihedral angle restraints: 10230 sinusoidal: 4233 harmonic: 5997 Sorted by residual: dihedral pdb=" CA THR B 99 " pdb=" C THR B 99 " pdb=" N PRO B 100 " pdb=" CA PRO B 100 " ideal model delta harmonic sigma weight residual 180.00 47.96 132.04 0 5.00e+00 4.00e-02 6.97e+02 dihedral pdb=" CB CYS K 465 " pdb=" SG CYS K 465 " pdb=" SG CYS K 469 " pdb=" CB CYS K 469 " ideal model delta sinusoidal sigma weight residual -86.00 -174.22 88.22 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS C 42 " pdb=" SG CYS C 42 " pdb=" SG CYS C 268 " pdb=" CB CYS C 268 " ideal model delta sinusoidal sigma weight residual -86.00 1.78 -87.78 1 1.00e+01 1.00e-02 9.23e+01 ... (remaining 10227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2074 0.083 - 0.167: 380 0.167 - 0.250: 38 0.250 - 0.334: 2 0.334 - 0.417: 3 Chirality restraints: 2497 Sorted by residual: chirality pdb=" CB ILE C 279 " pdb=" CA ILE C 279 " pdb=" CG1 ILE C 279 " pdb=" CG2 ILE C 279 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CB ILE I 279 " pdb=" CA ILE I 279 " pdb=" CG1 ILE I 279 " pdb=" CG2 ILE I 279 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CB VAL I 234 " pdb=" CA VAL I 234 " pdb=" CG1 VAL I 234 " pdb=" CG2 VAL I 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 2494 not shown) Planarity restraints: 3007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 273 " 0.016 2.00e-02 2.50e+03 2.64e-02 1.40e+01 pdb=" CG TYR I 273 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR I 273 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR I 273 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR I 273 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR I 273 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR I 273 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 273 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 63 " -0.048 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO C 64 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 38 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO I 39 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO I 39 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 39 " -0.038 5.00e-02 4.00e+02 ... (remaining 3004 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 11 1.82 - 2.59: 197 2.59 - 3.36: 20630 3.36 - 4.13: 40965 4.13 - 4.90: 71697 Nonbonded interactions: 133500 Sorted by model distance: nonbonded pdb=" OD2 ASP D 107 " pdb=" CD1 TRP D 109 " model vdw 1.051 3.260 nonbonded pdb=" OD2 ASP H 107 " pdb=" CD1 TRP H 109 " model vdw 1.051 3.260 nonbonded pdb=" OD2 ASP H 107 " pdb=" CG TRP H 109 " model vdw 1.308 3.260 nonbonded pdb=" OD2 ASP D 107 " pdb=" CG TRP D 109 " model vdw 1.308 3.260 nonbonded pdb=" OD2 ASP D 107 " pdb=" NE1 TRP D 109 " model vdw 1.541 3.120 ... (remaining 133495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'L' } ncs_group { reference = (chain 'C' and resid 1 through 602) selection = (chain 'I' and resid 1 through 602) selection = chain 'K' } 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: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 14.640 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.378 16955 Z= 0.527 Angle : 1.079 14.256 22988 Z= 0.654 Chirality : 0.063 0.417 2497 Planarity : 0.007 0.078 2996 Dihedral : 14.713 132.044 6342 Min Nonbonded Distance : 1.051 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.36 % Favored : 92.35 % Rotamer: Outliers : 1.62 % Allowed : 2.95 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.84 (0.16), residues: 2079 helix: -0.74 (0.25), residues: 318 sheet: -2.32 (0.24), residues: 423 loop : -2.11 (0.14), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 38 TYR 0.063 0.003 TYR I 273 PHE 0.034 0.003 PHE E 103 TRP 0.045 0.003 TRP K 404 HIS 0.020 0.002 HIS I 8 Details of bonding type rmsd covalent geometry : bond 0.00669 (16918) covalent geometry : angle 1.07522 (22907) SS BOND : bond 0.00546 ( 24) SS BOND : angle 1.69208 ( 48) hydrogen bonds : bond 0.19358 ( 474) hydrogen bonds : angle 8.93884 ( 1269) Misc. bond : bond 0.26959 ( 2) link_NAG-ASN : bond 0.00282 ( 11) link_NAG-ASN : angle 2.03621 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 445 time to evaluate : 0.650 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: B 9 LEU cc_start: 0.8330 (tp) cc_final: 0.8041 (tt) REVERT: B 57 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7299 (p90) REVERT: B 95 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6580 (pt0) REVERT: K 43 SER cc_start: 0.7355 (p) cc_final: 0.7062 (p) REVERT: K 488 MET cc_start: 0.6358 (ttp) cc_final: 0.5963 (ttp) outliers start: 29 outliers final: 0 residues processed: 457 average time/residue: 0.1153 time to fit residues: 79.3925 Evaluate side-chains 319 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 317 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 95 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN H 30 ASN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 1 GLN D 30 ASN A 1 GLN A 30 ASN A 39 GLN B 6 GLN B 98 GLN C 7 HIS C 259 GLN I 259 GLN I 463 HIS K 425 ASN ** K 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.126498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.099283 restraints weight = 49817.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.102693 restraints weight = 25962.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.104827 restraints weight = 17172.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.106163 restraints weight = 13225.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.106896 restraints weight = 11217.365| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16955 Z= 0.163 Angle : 0.732 13.252 22988 Z= 0.378 Chirality : 0.044 0.191 2497 Planarity : 0.006 0.096 2996 Dihedral : 6.898 64.209 2531 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.87 % Favored : 93.99 % Rotamer: Outliers : 2.84 % Allowed : 12.76 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.17), residues: 2079 helix: 0.23 (0.28), residues: 324 sheet: -2.16 (0.21), residues: 543 loop : -1.91 (0.15), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 97 TYR 0.039 0.002 TYR D 104 PHE 0.028 0.002 PHE E 57 TRP 0.039 0.003 TRP I 342 HIS 0.012 0.001 HIS I 463 Details of bonding type rmsd covalent geometry : bond 0.00356 (16918) covalent geometry : angle 0.72383 (22907) SS BOND : bond 0.00459 ( 24) SS BOND : angle 1.89796 ( 48) hydrogen bonds : bond 0.04223 ( 474) hydrogen bonds : angle 6.71576 ( 1269) Misc. bond : bond 0.00881 ( 2) link_NAG-ASN : bond 0.00224 ( 11) link_NAG-ASN : angle 1.98154 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 353 time to evaluate : 0.472 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: H 5 GLN cc_start: 0.8808 (tp-100) cc_final: 0.8477 (tm-30) REVERT: H 38 ARG cc_start: 0.7731 (ttp80) cc_final: 0.7431 (ttp80) REVERT: L 9 LEU cc_start: 0.8128 (tp) cc_final: 0.7824 (tt) REVERT: L 23 CYS cc_start: 0.4048 (t) cc_final: 0.3654 (t) REVERT: L 38 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8681 (mt) REVERT: L 94 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7167 (tpt) REVERT: D 93 TYR cc_start: 0.6924 (m-80) cc_final: 0.6517 (m-80) REVERT: E 29 LEU cc_start: 0.6581 (mp) cc_final: 0.6112 (pt) REVERT: E 39 ASP cc_start: 0.8114 (m-30) cc_final: 0.7883 (m-30) REVERT: E 86 GLU cc_start: 0.8258 (pp20) cc_final: 0.7642 (pm20) REVERT: A 4 LEU cc_start: 0.8226 (mt) cc_final: 0.7989 (mt) REVERT: A 47 TRP cc_start: 0.7845 (t60) cc_final: 0.7479 (t60) REVERT: B 78 LEU cc_start: 0.9745 (tp) cc_final: 0.9485 (tp) REVERT: B 97 LEU cc_start: 0.8283 (tt) cc_final: 0.7858 (mp) REVERT: C 330 PHE cc_start: 0.6385 (p90) cc_final: 0.5989 (p90) REVERT: I 111 GLU cc_start: 0.7550 (tp30) cc_final: 0.7294 (tp30) REVERT: I 113 MET cc_start: 0.7586 (ttm) cc_final: 0.7083 (ttm) REVERT: I 336 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6710 (mm-30) REVERT: K 43 SER cc_start: 0.7887 (p) cc_final: 0.7609 (p) REVERT: K 154 GLN cc_start: 0.8512 (tt0) cc_final: 0.8302 (tt0) REVERT: K 488 MET cc_start: 0.7046 (ttp) cc_final: 0.6744 (ttp) outliers start: 51 outliers final: 29 residues processed: 373 average time/residue: 0.1103 time to fit residues: 62.8355 Evaluate side-chains 338 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 307 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TRP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 57 PHE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 313 ASN Chi-restraints excluded: chain I residue 401 VAL Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 445 ARG Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 401 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 110 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 76 optimal weight: 0.0770 chunk 185 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 43 GLN E 43 GLN C 259 GLN ** I 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 347 HIS K 425 ASN ** K 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.124904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.100574 restraints weight = 48683.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.102711 restraints weight = 25026.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.105025 restraints weight = 16618.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.105224 restraints weight = 13931.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.105320 restraints weight = 12463.734| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16955 Z= 0.188 Angle : 0.705 10.980 22988 Z= 0.363 Chirality : 0.044 0.238 2497 Planarity : 0.005 0.073 2996 Dihedral : 6.340 56.506 2529 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.59 % Favored : 93.27 % Rotamer: Outliers : 3.23 % Allowed : 15.83 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.17), residues: 2079 helix: 0.55 (0.29), residues: 324 sheet: -2.20 (0.21), residues: 477 loop : -1.88 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.029 0.002 TYR D 104 PHE 0.028 0.002 PHE K 115 TRP 0.036 0.002 TRP I 342 HIS 0.010 0.002 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00416 (16918) covalent geometry : angle 0.69923 (22907) SS BOND : bond 0.00289 ( 24) SS BOND : angle 1.65675 ( 48) hydrogen bonds : bond 0.03933 ( 474) hydrogen bonds : angle 6.22063 ( 1269) Misc. bond : bond 0.00633 ( 2) link_NAG-ASN : bond 0.00393 ( 11) link_NAG-ASN : angle 1.70091 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 336 time to evaluate : 0.514 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: H 5 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8427 (tp-100) REVERT: H 13 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7598 (mpt90) REVERT: L 9 LEU cc_start: 0.8228 (tp) cc_final: 0.7910 (tt) REVERT: L 23 CYS cc_start: 0.3586 (t) cc_final: 0.2992 (t) REVERT: L 28 SER cc_start: 0.8329 (t) cc_final: 0.7952 (m) REVERT: D 95 CYS cc_start: 0.2501 (p) cc_final: 0.1626 (p) REVERT: E 86 GLU cc_start: 0.8330 (pp20) cc_final: 0.7728 (pm20) REVERT: E 94 MET cc_start: 0.7895 (tpp) cc_final: 0.7586 (mmm) REVERT: A 5 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8210 (tm-30) REVERT: A 59 TYR cc_start: 0.7654 (m-80) cc_final: 0.7282 (m-10) REVERT: B 79 LYS cc_start: 0.9134 (tptt) cc_final: 0.8910 (tptp) REVERT: B 95 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7630 (pp30) REVERT: C 140 MET cc_start: 0.8604 (mmp) cc_final: 0.8210 (mmp) REVERT: I 113 MET cc_start: 0.7413 (ttm) cc_final: 0.6735 (ttm) REVERT: I 336 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6764 (mm-30) REVERT: K 43 SER cc_start: 0.7760 (p) cc_final: 0.7520 (p) REVERT: K 488 MET cc_start: 0.7047 (ttp) cc_final: 0.6729 (ttp) outliers start: 58 outliers final: 40 residues processed: 364 average time/residue: 0.1077 time to fit residues: 60.2562 Evaluate side-chains 347 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 305 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 34 TRP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 57 PHE Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 313 ASN Chi-restraints excluded: chain I residue 347 HIS Chi-restraints excluded: chain I residue 423 MET Chi-restraints excluded: chain I residue 445 ARG Chi-restraints excluded: chain K residue 104 GLU Chi-restraints excluded: chain K residue 221 ILE Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 367 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 30 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** I 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 ASN I 347 HIS ** K 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 400 ASN K 416 ASN ** K 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.114923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.090700 restraints weight = 50068.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.092385 restraints weight = 23522.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.092684 restraints weight = 19542.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.092936 restraints weight = 17023.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.093262 restraints weight = 15721.098| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.092 16955 Z= 0.455 Angle : 0.955 15.715 22988 Z= 0.497 Chirality : 0.052 0.343 2497 Planarity : 0.007 0.065 2996 Dihedral : 7.462 55.786 2529 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 25.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.05 % Favored : 89.80 % Rotamer: Outliers : 5.74 % Allowed : 16.67 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.17), residues: 2079 helix: 0.25 (0.28), residues: 324 sheet: -2.61 (0.20), residues: 504 loop : -2.05 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 346 TYR 0.030 0.003 TYR A 33 PHE 0.024 0.003 PHE L 76 TRP 0.041 0.003 TRP I 342 HIS 0.019 0.003 HIS K 7 Details of bonding type rmsd covalent geometry : bond 0.00986 (16918) covalent geometry : angle 0.94210 (22907) SS BOND : bond 0.00869 ( 24) SS BOND : angle 2.51362 ( 48) hydrogen bonds : bond 0.05068 ( 474) hydrogen bonds : angle 6.72133 ( 1269) Misc. bond : bond 0.00489 ( 2) link_NAG-ASN : bond 0.00726 ( 11) link_NAG-ASN : angle 3.11747 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 320 time to evaluate : 0.566 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: H 13 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.6986 (ttm110) REVERT: L 9 LEU cc_start: 0.8177 (tp) cc_final: 0.7872 (tt) REVERT: L 23 CYS cc_start: 0.3494 (t) cc_final: 0.3078 (t) REVERT: L 24 ARG cc_start: 0.8160 (tmm-80) cc_final: 0.7945 (ttm170) REVERT: L 39 ASP cc_start: 0.7695 (t0) cc_final: 0.7351 (t0) REVERT: D 93 TYR cc_start: 0.7086 (m-80) cc_final: 0.6744 (m-80) REVERT: E 9 LEU cc_start: 0.8335 (tp) cc_final: 0.8073 (tt) REVERT: E 24 ARG cc_start: 0.8402 (tmm-80) cc_final: 0.8033 (ttp-110) REVERT: E 86 GLU cc_start: 0.8351 (pp20) cc_final: 0.7841 (pm20) REVERT: A 5 GLN cc_start: 0.8726 (tp40) cc_final: 0.8516 (tm-30) REVERT: B 95 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8170 (pp30) REVERT: C 91 LYS cc_start: 0.8241 (mmtt) cc_final: 0.8040 (mmmt) REVERT: C 247 ARG cc_start: 0.7875 (mtp180) cc_final: 0.7554 (mtp85) REVERT: C 280 ILE cc_start: 0.7880 (pt) cc_final: 0.7506 (pt) REVERT: I 461 ILE cc_start: 0.0705 (OUTLIER) cc_final: 0.0486 (mp) REVERT: K 423 MET cc_start: 0.8373 (mtm) cc_final: 0.7994 (mtm) REVERT: K 459 PHE cc_start: 0.5739 (m-80) cc_final: 0.5338 (m-80) outliers start: 103 outliers final: 72 residues processed: 380 average time/residue: 0.1131 time to fit residues: 65.4750 Evaluate side-chains 369 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 294 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 34 TRP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 57 PHE Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 57 PHE Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 343 TYR Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 313 ASN Chi-restraints excluded: chain I residue 347 HIS Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 401 VAL Chi-restraints excluded: chain I residue 412 VAL Chi-restraints excluded: chain I residue 423 MET Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 445 ARG Chi-restraints excluded: chain I residue 461 ILE Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 104 GLU Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain K residue 157 LYS Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 221 ILE Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 369 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 32 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 88 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 171 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 157 optimal weight: 0.1980 chunk 73 optimal weight: 0.1980 chunk 175 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 347 HIS ** K 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 363 GLN K 426 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.121280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.095200 restraints weight = 49323.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.098793 restraints weight = 25699.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.099272 restraints weight = 15648.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.099698 restraints weight = 15015.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.099753 restraints weight = 13638.542| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16955 Z= 0.137 Angle : 0.722 11.648 22988 Z= 0.364 Chirality : 0.045 0.277 2497 Planarity : 0.005 0.063 2996 Dihedral : 6.417 53.691 2529 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.92 % Favored : 93.94 % Rotamer: Outliers : 3.57 % Allowed : 21.01 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.17), residues: 2079 helix: 0.89 (0.29), residues: 324 sheet: -2.41 (0.23), residues: 429 loop : -1.85 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 291 TYR 0.033 0.002 TYR K 415 PHE 0.026 0.002 PHE I 330 TRP 0.038 0.002 TRP I 342 HIS 0.006 0.001 HIS I 463 Details of bonding type rmsd covalent geometry : bond 0.00300 (16918) covalent geometry : angle 0.71250 (22907) SS BOND : bond 0.00488 ( 24) SS BOND : angle 1.74658 ( 48) hydrogen bonds : bond 0.03714 ( 474) hydrogen bonds : angle 6.06104 ( 1269) Misc. bond : bond 0.00543 ( 2) link_NAG-ASN : bond 0.00897 ( 11) link_NAG-ASN : angle 2.53930 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 345 time to evaluate : 0.578 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: H 4 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8088 (tp) REVERT: H 5 GLN cc_start: 0.8893 (tp-100) cc_final: 0.8527 (tm-30) REVERT: H 38 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7774 (ttp80) REVERT: L 28 SER cc_start: 0.8608 (t) cc_final: 0.8166 (m) REVERT: L 39 ASP cc_start: 0.8116 (t0) cc_final: 0.7715 (t70) REVERT: L 55 LEU cc_start: 0.7854 (mt) cc_final: 0.7559 (tp) REVERT: D 4 LEU cc_start: 0.8235 (tp) cc_final: 0.8001 (tt) REVERT: D 5 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8417 (tm-30) REVERT: D 93 TYR cc_start: 0.7015 (m-80) cc_final: 0.6621 (m-80) REVERT: E 86 GLU cc_start: 0.8451 (pp20) cc_final: 0.7911 (pm20) REVERT: E 94 MET cc_start: 0.7545 (mmm) cc_final: 0.7130 (mmm) REVERT: A 5 GLN cc_start: 0.8813 (tp40) cc_final: 0.8333 (tm-30) REVERT: A 92 ARG cc_start: 0.7402 (ttt180) cc_final: 0.6985 (ttt180) REVERT: B 24 ARG cc_start: 0.8555 (ttp-110) cc_final: 0.8339 (ttm-80) REVERT: B 79 LYS cc_start: 0.9164 (tptt) cc_final: 0.8951 (tptp) REVERT: B 95 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7781 (pp30) REVERT: C 247 ARG cc_start: 0.7632 (mtp180) cc_final: 0.7383 (mtp85) REVERT: C 423 MET cc_start: 0.6725 (mtp) cc_final: 0.6357 (mtm) REVERT: C 424 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7412 (mm-30) REVERT: I 113 MET cc_start: 0.7232 (ttm) cc_final: 0.6688 (ttm) REVERT: K 423 MET cc_start: 0.8339 (mtm) cc_final: 0.8055 (mtp) outliers start: 64 outliers final: 39 residues processed: 381 average time/residue: 0.1167 time to fit residues: 67.7149 Evaluate side-chains 354 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 313 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 34 TRP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 PHE Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 313 ASN Chi-restraints excluded: chain I residue 347 HIS Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 445 ARG Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 157 LYS Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 426 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 61 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 91 optimal weight: 0.3980 chunk 93 optimal weight: 0.7980 chunk 193 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 ASN I 347 HIS ** K 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 425 ASN K 426 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.119195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.092866 restraints weight = 49598.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.095651 restraints weight = 25298.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.097353 restraints weight = 16116.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.097613 restraints weight = 14347.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.097563 restraints weight = 12653.247| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16955 Z= 0.140 Angle : 0.700 10.273 22988 Z= 0.351 Chirality : 0.044 0.352 2497 Planarity : 0.005 0.065 2996 Dihedral : 6.060 54.970 2529 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.73 % Favored : 93.12 % Rotamer: Outliers : 3.40 % Allowed : 23.19 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.17), residues: 2079 helix: 1.04 (0.29), residues: 324 sheet: -2.35 (0.23), residues: 435 loop : -1.77 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 346 TYR 0.038 0.002 TYR D 33 PHE 0.026 0.002 PHE I 330 TRP 0.038 0.002 TRP I 342 HIS 0.006 0.001 HIS I 463 Details of bonding type rmsd covalent geometry : bond 0.00315 (16918) covalent geometry : angle 0.68452 (22907) SS BOND : bond 0.00383 ( 24) SS BOND : angle 2.66887 ( 48) hydrogen bonds : bond 0.03655 ( 474) hydrogen bonds : angle 5.86855 ( 1269) Misc. bond : bond 0.00561 ( 2) link_NAG-ASN : bond 0.00354 ( 11) link_NAG-ASN : angle 2.31609 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 322 time to evaluate : 0.469 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: H 5 GLN cc_start: 0.8948 (tp-100) cc_final: 0.8623 (tm-30) REVERT: L 28 SER cc_start: 0.8658 (t) cc_final: 0.8276 (m) REVERT: L 39 ASP cc_start: 0.8257 (t0) cc_final: 0.7699 (t70) REVERT: L 55 LEU cc_start: 0.7792 (mt) cc_final: 0.7507 (tp) REVERT: L 87 ASP cc_start: 0.7526 (m-30) cc_final: 0.7016 (m-30) REVERT: D 5 GLN cc_start: 0.9003 (tp-100) cc_final: 0.8471 (tm-30) REVERT: D 93 TYR cc_start: 0.7086 (m-80) cc_final: 0.6607 (m-80) REVERT: E 86 GLU cc_start: 0.8487 (pp20) cc_final: 0.7925 (pm20) REVERT: E 87 ASP cc_start: 0.7537 (m-30) cc_final: 0.6669 (m-30) REVERT: A 4 LEU cc_start: 0.7906 (tp) cc_final: 0.7656 (tp) REVERT: A 5 GLN cc_start: 0.8889 (tp40) cc_final: 0.8591 (tm-30) REVERT: A 92 ARG cc_start: 0.7423 (ttt180) cc_final: 0.7050 (ttt180) REVERT: B 38 LEU cc_start: 0.9395 (tt) cc_final: 0.9100 (tt) REVERT: B 95 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7949 (pp30) REVERT: C 247 ARG cc_start: 0.7581 (mtp180) cc_final: 0.7310 (mtp85) REVERT: C 423 MET cc_start: 0.6960 (mtp) cc_final: 0.6736 (mtm) REVERT: C 424 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7635 (mm-30) REVERT: I 113 MET cc_start: 0.7315 (ttm) cc_final: 0.6650 (ttm) REVERT: K 423 MET cc_start: 0.8486 (mtm) cc_final: 0.8232 (mtp) outliers start: 61 outliers final: 48 residues processed: 358 average time/residue: 0.1066 time to fit residues: 58.3614 Evaluate side-chains 352 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 303 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 34 TRP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 57 PHE Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 313 ASN Chi-restraints excluded: chain I residue 347 HIS Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 445 ARG Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 157 LYS Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 425 ASN Chi-restraints excluded: chain K residue 426 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 185 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 144 optimal weight: 0.0000 chunk 15 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 52 optimal weight: 0.0980 chunk 198 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 76 ASN I 347 HIS K 149 ASN ** K 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 425 ASN K 426 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.119978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.092389 restraints weight = 49457.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.095574 restraints weight = 25804.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.097649 restraints weight = 17217.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.098881 restraints weight = 13328.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.099763 restraints weight = 11391.836| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16955 Z= 0.130 Angle : 0.691 10.226 22988 Z= 0.346 Chirality : 0.044 0.415 2497 Planarity : 0.005 0.060 2996 Dihedral : 5.872 54.464 2529 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.20 % Favored : 93.65 % Rotamer: Outliers : 3.29 % Allowed : 23.75 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.18), residues: 2079 helix: 1.15 (0.29), residues: 324 sheet: -2.39 (0.23), residues: 456 loop : -1.66 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.034 0.002 TYR D 33 PHE 0.024 0.002 PHE I 330 TRP 0.040 0.002 TRP I 342 HIS 0.006 0.001 HIS I 463 Details of bonding type rmsd covalent geometry : bond 0.00295 (16918) covalent geometry : angle 0.68013 (22907) SS BOND : bond 0.00461 ( 24) SS BOND : angle 2.24956 ( 48) hydrogen bonds : bond 0.03580 ( 474) hydrogen bonds : angle 5.70958 ( 1269) Misc. bond : bond 0.00562 ( 2) link_NAG-ASN : bond 0.00365 ( 11) link_NAG-ASN : angle 2.12874 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 322 time to evaluate : 0.647 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: H 5 GLN cc_start: 0.8783 (tp-100) cc_final: 0.8325 (tm-30) REVERT: H 98 GLN cc_start: 0.7234 (mp10) cc_final: 0.6867 (mm110) REVERT: L 39 ASP cc_start: 0.8049 (t0) cc_final: 0.7685 (t70) REVERT: L 55 LEU cc_start: 0.7725 (mt) cc_final: 0.7490 (tp) REVERT: L 87 ASP cc_start: 0.7576 (m-30) cc_final: 0.7107 (m-30) REVERT: D 5 GLN cc_start: 0.8909 (tp-100) cc_final: 0.8385 (tm-30) REVERT: D 93 TYR cc_start: 0.6987 (m-80) cc_final: 0.6770 (m-10) REVERT: E 58 ASN cc_start: 0.8741 (t0) cc_final: 0.8246 (t0) REVERT: E 86 GLU cc_start: 0.8339 (pp20) cc_final: 0.7809 (pm20) REVERT: E 87 ASP cc_start: 0.7621 (m-30) cc_final: 0.6780 (m-30) REVERT: E 94 MET cc_start: 0.7429 (mmm) cc_final: 0.6917 (mmm) REVERT: A 5 GLN cc_start: 0.8815 (tp40) cc_final: 0.8540 (tm-30) REVERT: A 92 ARG cc_start: 0.7312 (ttt180) cc_final: 0.7043 (ttp-170) REVERT: C 247 ARG cc_start: 0.7573 (mtp180) cc_final: 0.7321 (mtp85) REVERT: C 335 TRP cc_start: 0.7310 (OUTLIER) cc_final: 0.6895 (p-90) REVERT: C 423 MET cc_start: 0.6943 (mtp) cc_final: 0.6702 (mtm) REVERT: I 113 MET cc_start: 0.7299 (ttm) cc_final: 0.6659 (ttm) REVERT: K 423 MET cc_start: 0.8558 (mtm) cc_final: 0.8235 (mtp) outliers start: 59 outliers final: 46 residues processed: 360 average time/residue: 0.1193 time to fit residues: 65.9665 Evaluate side-chains 354 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 307 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 34 TRP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 PHE Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 335 TRP Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 445 ARG Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 157 LYS Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 426 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 177 optimal weight: 0.5980 chunk 167 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 77 optimal weight: 0.0970 chunk 8 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.119672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.094455 restraints weight = 50598.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096134 restraints weight = 26306.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.096487 restraints weight = 18514.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.097743 restraints weight = 16816.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.097789 restraints weight = 14861.977| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16955 Z= 0.190 Angle : 0.716 9.976 22988 Z= 0.359 Chirality : 0.045 0.457 2497 Planarity : 0.005 0.068 2996 Dihedral : 5.794 51.865 2526 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.22 % Favored : 92.64 % Rotamer: Outliers : 3.34 % Allowed : 23.86 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.18), residues: 2079 helix: 1.08 (0.29), residues: 324 sheet: -2.36 (0.22), residues: 462 loop : -1.70 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.030 0.002 TYR D 33 PHE 0.020 0.002 PHE I 330 TRP 0.043 0.002 TRP I 342 HIS 0.008 0.001 HIS K 7 Details of bonding type rmsd covalent geometry : bond 0.00420 (16918) covalent geometry : angle 0.70631 (22907) SS BOND : bond 0.00502 ( 24) SS BOND : angle 2.06537 ( 48) hydrogen bonds : bond 0.03716 ( 474) hydrogen bonds : angle 5.66519 ( 1269) Misc. bond : bond 0.00506 ( 2) link_NAG-ASN : bond 0.00344 ( 11) link_NAG-ASN : angle 2.20798 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 312 time to evaluate : 0.595 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: H 5 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8461 (tm-30) REVERT: L 28 SER cc_start: 0.8471 (t) cc_final: 0.8080 (m) REVERT: L 39 ASP cc_start: 0.7993 (t0) cc_final: 0.7626 (t70) REVERT: L 55 LEU cc_start: 0.7823 (mt) cc_final: 0.7567 (tp) REVERT: L 87 ASP cc_start: 0.7416 (m-30) cc_final: 0.6888 (m-30) REVERT: D 93 TYR cc_start: 0.6950 (m-80) cc_final: 0.6735 (m-10) REVERT: E 86 GLU cc_start: 0.8362 (pp20) cc_final: 0.7811 (pm20) REVERT: E 87 ASP cc_start: 0.7605 (m-30) cc_final: 0.6884 (m-30) REVERT: A 5 GLN cc_start: 0.8851 (tp40) cc_final: 0.8437 (tm-30) REVERT: A 92 ARG cc_start: 0.7357 (ttt180) cc_final: 0.7101 (ttp-170) REVERT: C 247 ARG cc_start: 0.7741 (mtp180) cc_final: 0.7467 (mtp85) REVERT: C 335 TRP cc_start: 0.7466 (OUTLIER) cc_final: 0.7088 (p-90) REVERT: C 336 GLU cc_start: 0.8142 (tp30) cc_final: 0.7776 (mm-30) REVERT: C 423 MET cc_start: 0.6838 (mtp) cc_final: 0.6563 (mtm) REVERT: I 113 MET cc_start: 0.7254 (ttm) cc_final: 0.6649 (ttm) REVERT: K 423 MET cc_start: 0.8378 (mtm) cc_final: 0.8149 (mtp) outliers start: 60 outliers final: 52 residues processed: 346 average time/residue: 0.1110 time to fit residues: 58.6858 Evaluate side-chains 355 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 302 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 34 TRP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 PHE Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 335 TRP Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 313 ASN Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 412 VAL Chi-restraints excluded: chain I residue 423 MET Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 445 ARG Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 157 LYS Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 426 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 56 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN K 149 ASN ** K 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 426 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.119904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.093294 restraints weight = 50317.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.096531 restraints weight = 26203.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.098697 restraints weight = 16319.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.098899 restraints weight = 13931.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.098904 restraints weight = 12558.437| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16955 Z= 0.153 Angle : 0.711 10.497 22988 Z= 0.355 Chirality : 0.045 0.481 2497 Planarity : 0.005 0.062 2996 Dihedral : 5.735 52.089 2526 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.97 % Favored : 92.88 % Rotamer: Outliers : 3.01 % Allowed : 24.47 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.18), residues: 2079 helix: 1.13 (0.29), residues: 324 sheet: -2.23 (0.24), residues: 432 loop : -1.68 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.032 0.002 TYR D 33 PHE 0.018 0.002 PHE I 330 TRP 0.048 0.003 TRP I 342 HIS 0.006 0.001 HIS K 7 Details of bonding type rmsd covalent geometry : bond 0.00345 (16918) covalent geometry : angle 0.70078 (22907) SS BOND : bond 0.00380 ( 24) SS BOND : angle 2.12104 ( 48) hydrogen bonds : bond 0.03608 ( 474) hydrogen bonds : angle 5.62778 ( 1269) Misc. bond : bond 0.00512 ( 2) link_NAG-ASN : bond 0.00326 ( 11) link_NAG-ASN : angle 2.10985 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 316 time to evaluate : 0.438 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: H 5 GLN cc_start: 0.8755 (tp-100) cc_final: 0.8271 (tm-30) REVERT: H 38 ARG cc_start: 0.8266 (ttp80) cc_final: 0.8030 (ttp80) REVERT: L 28 SER cc_start: 0.8473 (t) cc_final: 0.8059 (m) REVERT: L 39 ASP cc_start: 0.8043 (t0) cc_final: 0.7665 (t70) REVERT: L 55 LEU cc_start: 0.7778 (mt) cc_final: 0.7526 (tp) REVERT: L 87 ASP cc_start: 0.7434 (m-30) cc_final: 0.7009 (m-30) REVERT: D 93 TYR cc_start: 0.6964 (m-80) cc_final: 0.6754 (m-10) REVERT: E 58 ASN cc_start: 0.8760 (t0) cc_final: 0.8238 (t0) REVERT: E 86 GLU cc_start: 0.8356 (pp20) cc_final: 0.7826 (pm20) REVERT: E 87 ASP cc_start: 0.7590 (m-30) cc_final: 0.6854 (m-30) REVERT: E 94 MET cc_start: 0.7300 (mmm) cc_final: 0.6948 (mmm) REVERT: A 5 GLN cc_start: 0.8899 (tp40) cc_final: 0.8532 (tm-30) REVERT: A 92 ARG cc_start: 0.7382 (ttt180) cc_final: 0.7139 (ttp-170) REVERT: B 38 LEU cc_start: 0.9387 (tt) cc_final: 0.9171 (tt) REVERT: C 247 ARG cc_start: 0.7688 (mtp180) cc_final: 0.7421 (mtp85) REVERT: C 335 TRP cc_start: 0.7492 (OUTLIER) cc_final: 0.7141 (p-90) REVERT: C 423 MET cc_start: 0.6874 (mtp) cc_final: 0.6444 (mtm) REVERT: I 113 MET cc_start: 0.7253 (ttm) cc_final: 0.6671 (ttm) REVERT: I 433 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.6867 (t70) REVERT: K 367 ASP cc_start: 0.8687 (m-30) cc_final: 0.8421 (p0) REVERT: K 423 MET cc_start: 0.8403 (mtm) cc_final: 0.8171 (mtp) outliers start: 54 outliers final: 48 residues processed: 349 average time/residue: 0.1116 time to fit residues: 59.1982 Evaluate side-chains 359 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 309 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 34 TRP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 PHE Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 335 TRP Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 313 ASN Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 433 ASP Chi-restraints excluded: chain I residue 445 ARG Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 157 LYS Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 426 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 189 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 76 ASN K 149 ASN ** K 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 426 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.119024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.094772 restraints weight = 49937.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.095555 restraints weight = 22983.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.096615 restraints weight = 19354.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096672 restraints weight = 16834.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.097837 restraints weight = 15087.935| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16955 Z= 0.154 Angle : 0.737 13.652 22988 Z= 0.366 Chirality : 0.046 0.493 2497 Planarity : 0.005 0.064 2996 Dihedral : 5.733 52.051 2526 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.07 % Favored : 92.78 % Rotamer: Outliers : 3.18 % Allowed : 24.58 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.18), residues: 2079 helix: 1.12 (0.29), residues: 324 sheet: -2.27 (0.22), residues: 477 loop : -1.71 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.031 0.002 TYR D 33 PHE 0.018 0.002 PHE L 76 TRP 0.051 0.002 TRP I 342 HIS 0.006 0.001 HIS K 7 Details of bonding type rmsd covalent geometry : bond 0.00348 (16918) covalent geometry : angle 0.72157 (22907) SS BOND : bond 0.00345 ( 24) SS BOND : angle 2.88157 ( 48) hydrogen bonds : bond 0.03624 ( 474) hydrogen bonds : angle 5.66695 ( 1269) Misc. bond : bond 0.00537 ( 2) link_NAG-ASN : bond 0.00332 ( 11) link_NAG-ASN : angle 2.09506 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 311 time to evaluate : 0.447 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: H 5 GLN cc_start: 0.8842 (tp-100) cc_final: 0.8490 (tm-30) REVERT: H 98 GLN cc_start: 0.7292 (mp10) cc_final: 0.6871 (mm110) REVERT: L 3 VAL cc_start: 0.7867 (t) cc_final: 0.7645 (m) REVERT: L 28 SER cc_start: 0.8540 (t) cc_final: 0.8161 (m) REVERT: L 39 ASP cc_start: 0.8170 (t0) cc_final: 0.7700 (t70) REVERT: L 55 LEU cc_start: 0.7740 (mt) cc_final: 0.7493 (tp) REVERT: L 87 ASP cc_start: 0.7455 (m-30) cc_final: 0.6959 (m-30) REVERT: D 93 TYR cc_start: 0.7010 (m-80) cc_final: 0.6766 (m-10) REVERT: E 58 ASN cc_start: 0.8736 (t0) cc_final: 0.8203 (t0) REVERT: E 86 GLU cc_start: 0.8384 (pp20) cc_final: 0.7864 (pm20) REVERT: E 87 ASP cc_start: 0.7597 (m-30) cc_final: 0.6859 (m-30) REVERT: E 94 MET cc_start: 0.7569 (mmm) cc_final: 0.7207 (mmm) REVERT: A 5 GLN cc_start: 0.8953 (tp40) cc_final: 0.8559 (tm-30) REVERT: A 92 ARG cc_start: 0.7397 (ttt180) cc_final: 0.7168 (ttp-170) REVERT: B 38 LEU cc_start: 0.9396 (tt) cc_final: 0.9186 (tt) REVERT: C 247 ARG cc_start: 0.7666 (mtp180) cc_final: 0.7389 (mtp85) REVERT: C 335 TRP cc_start: 0.7465 (OUTLIER) cc_final: 0.7032 (p-90) REVERT: I 113 MET cc_start: 0.7298 (ttm) cc_final: 0.6664 (ttm) REVERT: I 433 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.6937 (t70) REVERT: K 155 MET cc_start: 0.8071 (mtp) cc_final: 0.7819 (mtm) REVERT: K 222 ASP cc_start: 0.7645 (m-30) cc_final: 0.7312 (m-30) REVERT: K 367 ASP cc_start: 0.8750 (m-30) cc_final: 0.8470 (p0) outliers start: 57 outliers final: 45 residues processed: 347 average time/residue: 0.1141 time to fit residues: 61.0598 Evaluate side-chains 354 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 307 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 34 TRP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 PHE Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 335 TRP Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 313 ASN Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 412 VAL Chi-restraints excluded: chain I residue 433 ASP Chi-restraints excluded: chain I residue 445 ARG Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 157 LYS Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 369 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 131 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 180 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 188 optimal weight: 0.2980 chunk 118 optimal weight: 4.9990 chunk 160 optimal weight: 20.0000 chunk 101 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN C 259 GLN C 427 HIS ** K 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.122621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.098471 restraints weight = 48129.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.100620 restraints weight = 24136.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.101388 restraints weight = 16280.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.101674 restraints weight = 14775.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.101893 restraints weight = 13837.951| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16955 Z= 0.133 Angle : 0.728 10.655 22988 Z= 0.362 Chirality : 0.046 0.501 2497 Planarity : 0.005 0.065 2996 Dihedral : 5.626 52.533 2526 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.40 % Favored : 93.46 % Rotamer: Outliers : 2.90 % Allowed : 25.36 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.18), residues: 2079 helix: 1.25 (0.29), residues: 324 sheet: -2.06 (0.24), residues: 447 loop : -1.70 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 38 TYR 0.031 0.002 TYR D 33 PHE 0.017 0.002 PHE I 330 TRP 0.050 0.002 TRP I 342 HIS 0.005 0.001 HIS I 463 Details of bonding type rmsd covalent geometry : bond 0.00304 (16918) covalent geometry : angle 0.71618 (22907) SS BOND : bond 0.00293 ( 24) SS BOND : angle 2.46682 ( 48) hydrogen bonds : bond 0.03585 ( 474) hydrogen bonds : angle 5.55177 ( 1269) Misc. bond : bond 0.00552 ( 2) link_NAG-ASN : bond 0.00321 ( 11) link_NAG-ASN : angle 1.99542 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2987.91 seconds wall clock time: 52 minutes 27.28 seconds (3147.28 seconds total)