Starting phenix.real_space_refine on Sat Jun 21 23:41:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8toa_41441/06_2025/8toa_41441.cif Found real_map, /net/cci-nas-00/data/ceres_data/8toa_41441/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8toa_41441/06_2025/8toa_41441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8toa_41441/06_2025/8toa_41441.map" model { file = "/net/cci-nas-00/data/ceres_data/8toa_41441/06_2025/8toa_41441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8toa_41441/06_2025/8toa_41441.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.23, per 1000 atoms: 0.56 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: 4.19 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.15 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: 5.18 Time building geometry restraints manager: 4.92 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 490 or resid 601 through 602)) selection = (chain 'I' and (resid 1 through 490 or resid 601 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 38.940 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.070 ------------------------------------------------------------------------------- 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 : 12.20 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (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 TRP 0.045 0.003 TRP K 404 HIS 0.020 0.002 HIS I 8 PHE 0.034 0.003 PHE E 103 TYR 0.063 0.003 TYR I 273 ARG 0.017 0.001 ARG D 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 11) link_NAG-ASN : angle 2.03621 ( 33) hydrogen bonds : bond 0.19358 ( 474) hydrogen bonds : angle 8.93884 ( 1269) SS BOND : bond 0.00546 ( 24) SS BOND : angle 1.69208 ( 48) covalent geometry : bond 0.00669 (16918) covalent geometry : angle 1.07522 (22907) Misc. bond : bond 0.26959 ( 2) *********************** 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 : 1.771 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: 0.2832 time to fit residues: 192.7890 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 : 1.881 ------------------------------------------------------------------------------- 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 174 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 187 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 D 1 GLN D 5 GLN D 30 ASN A 1 GLN A 5 GLN A 30 ASN A 39 GLN B 6 GLN B 98 GLN C 7 HIS C 259 GLN ** I 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.128269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.102318 restraints weight = 47872.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.105830 restraints weight = 26362.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.108426 restraints weight = 15896.275| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16955 Z= 0.146 Angle : 0.725 13.429 22988 Z= 0.374 Chirality : 0.044 0.177 2497 Planarity : 0.005 0.100 2996 Dihedral : 6.850 65.648 2531 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.82 % Favored : 94.04 % Rotamer: Outliers : 2.79 % Allowed : 12.43 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.17), residues: 2079 helix: 0.23 (0.28), residues: 324 sheet: -2.06 (0.22), residues: 507 loop : -1.94 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP I 342 HIS 0.012 0.001 HIS I 463 PHE 0.026 0.002 PHE E 57 TYR 0.038 0.002 TYR D 104 ARG 0.006 0.001 ARG A 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 11) link_NAG-ASN : angle 1.92744 ( 33) hydrogen bonds : bond 0.04235 ( 474) hydrogen bonds : angle 6.73855 ( 1269) SS BOND : bond 0.00783 ( 24) SS BOND : angle 2.03523 ( 48) covalent geometry : bond 0.00318 (16918) covalent geometry : angle 0.71705 (22907) Misc. bond : bond 0.00847 ( 2) *********************** 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 405 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 355 time to evaluate : 1.914 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: H 5 GLN cc_start: 0.8814 (tp-100) cc_final: 0.8483 (tm-30) REVERT: H 38 ARG cc_start: 0.7790 (ttp80) cc_final: 0.7579 (ttp80) REVERT: L 9 LEU cc_start: 0.8121 (tp) cc_final: 0.7823 (tt) REVERT: L 23 CYS cc_start: 0.4269 (t) cc_final: 0.3984 (t) REVERT: L 38 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8629 (mt) REVERT: L 94 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7293 (tpt) REVERT: D 93 TYR cc_start: 0.6888 (m-80) cc_final: 0.6483 (m-80) REVERT: E 29 LEU cc_start: 0.6557 (mp) cc_final: 0.6096 (pt) REVERT: E 39 ASP cc_start: 0.8133 (m-30) cc_final: 0.7907 (m-30) REVERT: E 58 ASN cc_start: 0.8304 (t0) cc_final: 0.7990 (t0) REVERT: E 86 GLU cc_start: 0.8354 (pp20) cc_final: 0.7734 (pm20) REVERT: A 4 LEU cc_start: 0.8227 (mt) cc_final: 0.7981 (mt) REVERT: A 5 GLN cc_start: 0.8785 (tp40) cc_final: 0.8144 (tm-30) REVERT: A 47 TRP cc_start: 0.7799 (t60) cc_final: 0.7432 (t60) REVERT: B 78 LEU cc_start: 0.9745 (tp) cc_final: 0.9498 (tp) REVERT: B 95 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7693 (pp30) REVERT: B 97 LEU cc_start: 0.8229 (tt) cc_final: 0.7979 (mp) REVERT: B 100 PRO cc_start: 0.8743 (Cg_exo) cc_final: 0.8405 (Cg_endo) REVERT: C 298 ARG cc_start: 0.7565 (mpt180) cc_final: 0.7324 (mpt180) REVERT: C 330 PHE cc_start: 0.6300 (p90) cc_final: 0.5991 (p90) REVERT: I 111 GLU cc_start: 0.7449 (tp30) cc_final: 0.7232 (tp30) REVERT: I 113 MET cc_start: 0.7493 (ttm) cc_final: 0.7025 (ttm) REVERT: I 256 MET cc_start: 0.6443 (mtp) cc_final: 0.6171 (mmm) REVERT: K 43 SER cc_start: 0.7971 (p) cc_final: 0.7683 (p) REVERT: K 488 MET cc_start: 0.7054 (ttp) cc_final: 0.6745 (ttp) outliers start: 50 outliers final: 28 residues processed: 375 average time/residue: 0.2739 time to fit residues: 155.9866 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 : 2.005 ------------------------------------------------------------------------------- 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 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 94 MET 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 69 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 198 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 138 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 191 optimal weight: 0.0670 chunk 106 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.129020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.102985 restraints weight = 47986.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.106253 restraints weight = 25067.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.108343 restraints weight = 16506.266| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16955 Z= 0.119 Angle : 0.675 11.652 22988 Z= 0.343 Chirality : 0.044 0.297 2497 Planarity : 0.005 0.079 2996 Dihedral : 6.197 58.526 2529 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.44 % Favored : 94.42 % Rotamer: Outliers : 2.29 % Allowed : 16.05 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.17), residues: 2079 helix: 0.60 (0.29), residues: 324 sheet: -2.05 (0.22), residues: 492 loop : -1.87 (0.15), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 40 HIS 0.007 0.001 HIS C 224 PHE 0.019 0.002 PHE E 67 TYR 0.031 0.002 TYR D 104 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 11) link_NAG-ASN : angle 1.60645 ( 33) hydrogen bonds : bond 0.03703 ( 474) hydrogen bonds : angle 6.23476 ( 1269) SS BOND : bond 0.00260 ( 24) SS BOND : angle 1.55288 ( 48) covalent geometry : bond 0.00266 (16918) covalent geometry : angle 0.66990 (22907) Misc. bond : bond 0.00676 ( 2) *********************** 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 379 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 338 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8744 (tp-100) cc_final: 0.8448 (tm-30) REVERT: H 38 ARG cc_start: 0.7802 (ttp80) cc_final: 0.7519 (ttp80) REVERT: H 93 TYR cc_start: 0.6466 (m-10) cc_final: 0.6228 (m-10) REVERT: L 9 LEU cc_start: 0.8201 (tp) cc_final: 0.7876 (tt) REVERT: L 23 CYS cc_start: 0.3626 (t) cc_final: 0.2887 (t) REVERT: L 58 ASN cc_start: 0.8412 (t0) cc_final: 0.8136 (t0) REVERT: L 94 MET cc_start: 0.8027 (tpt) cc_final: 0.7790 (tpp) REVERT: E 58 ASN cc_start: 0.8373 (t0) cc_final: 0.8095 (t0) REVERT: E 86 GLU cc_start: 0.8323 (pp20) cc_final: 0.7769 (pm20) REVERT: A 5 GLN cc_start: 0.8690 (tp40) cc_final: 0.8103 (tm-30) REVERT: B 95 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7610 (pp30) REVERT: C 330 PHE cc_start: 0.6210 (p90) cc_final: 0.5963 (p90) REVERT: I 113 MET cc_start: 0.7359 (ttm) cc_final: 0.6928 (ttm) REVERT: K 43 SER cc_start: 0.7977 (p) cc_final: 0.7762 (p) REVERT: K 435 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8038 (tp30) REVERT: K 488 MET cc_start: 0.7038 (ttp) cc_final: 0.6742 (ttp) outliers start: 41 outliers final: 25 residues processed: 361 average time/residue: 0.2738 time to fit residues: 149.6043 Evaluate side-chains 333 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 307 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 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 38 LEU Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 108 TYR 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 72 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain C residue 313 ASN 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 347 HIS Chi-restraints excluded: chain I residue 445 ARG Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 426 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 194 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 97 optimal weight: 0.0980 chunk 128 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN C 259 GLN ** I 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.125401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.100749 restraints weight = 48330.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.103091 restraints weight = 23977.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.105347 restraints weight = 15985.904| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2860 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= 0.164 Angle : 0.679 10.471 22988 Z= 0.346 Chirality : 0.044 0.247 2497 Planarity : 0.005 0.075 2996 Dihedral : 5.994 55.562 2529 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.92 % Favored : 93.94 % Rotamer: Outliers : 3.07 % Allowed : 17.56 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.17), residues: 2079 helix: 0.75 (0.29), residues: 324 sheet: -1.96 (0.22), residues: 483 loop : -1.82 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 47 HIS 0.010 0.001 HIS I 347 PHE 0.028 0.002 PHE K 115 TYR 0.020 0.002 TYR C 415 ARG 0.005 0.000 ARG B 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 11) link_NAG-ASN : angle 1.62762 ( 33) hydrogen bonds : bond 0.03700 ( 474) hydrogen bonds : angle 5.92065 ( 1269) SS BOND : bond 0.00309 ( 24) SS BOND : angle 1.98114 ( 48) covalent geometry : bond 0.00364 (16918) covalent geometry : angle 0.67080 (22907) Misc. bond : bond 0.00563 ( 2) *********************** 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 391 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 336 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8322 (tm-30) REVERT: H 13 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7609 (mpt90) REVERT: H 22 CYS cc_start: 0.4054 (t) cc_final: 0.3738 (t) REVERT: H 38 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7111 (ttp80) REVERT: H 93 TYR cc_start: 0.6357 (m-10) cc_final: 0.5808 (m-10) REVERT: L 9 LEU cc_start: 0.8127 (tp) cc_final: 0.7785 (tt) REVERT: L 39 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7517 (t70) REVERT: L 55 LEU cc_start: 0.7786 (mt) cc_final: 0.7538 (tp) REVERT: D 20 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8866 (tp) REVERT: D 93 TYR cc_start: 0.7037 (m-80) cc_final: 0.6356 (m-80) REVERT: E 58 ASN cc_start: 0.8502 (t0) cc_final: 0.8101 (t0) REVERT: E 76 PHE cc_start: 0.7224 (m-80) cc_final: 0.6895 (m-10) REVERT: E 94 MET cc_start: 0.7237 (mmm) cc_final: 0.6960 (mmm) REVERT: A 5 GLN cc_start: 0.8746 (tp40) cc_final: 0.8313 (tm-30) REVERT: A 59 TYR cc_start: 0.7607 (m-80) cc_final: 0.7119 (m-10) REVERT: A 92 ARG cc_start: 0.7486 (ttt180) cc_final: 0.7284 (ttt180) REVERT: B 94 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7510 (tpt) REVERT: B 95 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7364 (pp30) REVERT: I 113 MET cc_start: 0.7369 (ttm) cc_final: 0.6724 (ttm) REVERT: K 43 SER cc_start: 0.8055 (p) cc_final: 0.7763 (p) REVERT: K 376 LEU cc_start: 0.8719 (mm) cc_final: 0.8508 (mm) REVERT: K 488 MET cc_start: 0.7056 (ttp) cc_final: 0.6739 (ttp) outliers start: 55 outliers final: 29 residues processed: 357 average time/residue: 0.3789 time to fit residues: 202.4174 Evaluate side-chains 341 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 307 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 L residue 38 LEU Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain D residue 20 LEU 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 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 38 ARG Chi-restraints excluded: chain A residue 72 ASP 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 313 ASN 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 193 VAL Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 313 ASN Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 157 LYS 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 81 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 139 optimal weight: 0.3980 chunk 178 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** I 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 HIS ** 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 416 ASN ** K 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.121966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.098335 restraints weight = 48808.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.099907 restraints weight = 23137.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.100432 restraints weight = 18375.945| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16955 Z= 0.228 Angle : 0.724 10.440 22988 Z= 0.369 Chirality : 0.045 0.231 2497 Planarity : 0.005 0.064 2996 Dihedral : 6.083 52.848 2529 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.36 % Favored : 92.50 % Rotamer: Outliers : 4.07 % Allowed : 18.67 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.17), residues: 2079 helix: 0.82 (0.29), residues: 324 sheet: -2.04 (0.23), residues: 426 loop : -1.84 (0.15), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP I 342 HIS 0.009 0.002 HIS K 7 PHE 0.025 0.002 PHE K 115 TYR 0.023 0.002 TYR K 343 ARG 0.005 0.001 ARG I 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 11) link_NAG-ASN : angle 1.91029 ( 33) hydrogen bonds : bond 0.03921 ( 474) hydrogen bonds : angle 5.88821 ( 1269) SS BOND : bond 0.00704 ( 24) SS BOND : angle 1.95455 ( 48) covalent geometry : bond 0.00499 (16918) covalent geometry : angle 0.71634 (22907) Misc. bond : bond 0.00521 ( 2) *********************** 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 397 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 324 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8900 (tp-100) cc_final: 0.8434 (tm-30) REVERT: H 13 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7612 (mpt90) REVERT: H 38 ARG cc_start: 0.7762 (ttp80) cc_final: 0.6962 (ttp80) REVERT: H 93 TYR cc_start: 0.6549 (m-10) cc_final: 0.6013 (m-10) REVERT: L 9 LEU cc_start: 0.8177 (tp) cc_final: 0.7823 (tt) REVERT: L 28 SER cc_start: 0.8462 (t) cc_final: 0.8141 (m) REVERT: L 39 ASP cc_start: 0.7844 (t0) cc_final: 0.7542 (t70) REVERT: D 20 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9024 (tp) REVERT: D 93 TYR cc_start: 0.6982 (m-80) cc_final: 0.6515 (m-80) REVERT: E 58 ASN cc_start: 0.8684 (t0) cc_final: 0.8191 (t0) REVERT: E 94 MET cc_start: 0.7629 (mmm) cc_final: 0.7230 (mmm) REVERT: A 5 GLN cc_start: 0.8688 (tp40) cc_final: 0.8130 (tm-30) REVERT: A 59 TYR cc_start: 0.7846 (m-80) cc_final: 0.7588 (m-80) REVERT: B 78 LEU cc_start: 0.9718 (tp) cc_final: 0.9413 (tp) REVERT: B 95 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7854 (pp30) REVERT: C 104 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7629 (tt0) REVERT: C 247 ARG cc_start: 0.7688 (mtp180) cc_final: 0.7419 (mtp85) REVERT: I 113 MET cc_start: 0.7477 (ttm) cc_final: 0.6855 (ttm) REVERT: I 336 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6850 (mm-30) REVERT: I 445 ARG cc_start: 0.6477 (ttp80) cc_final: 0.6226 (tmm160) REVERT: K 488 MET cc_start: 0.6997 (ttp) cc_final: 0.6679 (ttp) outliers start: 73 outliers final: 51 residues processed: 365 average time/residue: 0.3538 time to fit residues: 197.2051 Evaluate side-chains 357 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 303 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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 72 ASP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 20 LEU 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 66 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 109 VAL 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 470 MET Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 203 SER 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 307 LEU Chi-restraints excluded: chain I residue 313 ASN Chi-restraints excluded: chain I residue 412 VAL Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 140 MET Chi-restraints excluded: chain K residue 143 LEU 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 205 VAL Chi-restraints excluded: chain K residue 221 ILE Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 369 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 74 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 125 optimal weight: 0.0980 chunk 62 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 58 ASN ** C 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 347 HIS ** 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 = 0.4080 r_free = 0.4080 target = 0.122877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.098435 restraints weight = 48770.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.100687 restraints weight = 24800.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.101590 restraints weight = 16672.459| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16955 Z= 0.157 Angle : 0.697 10.245 22988 Z= 0.349 Chirality : 0.044 0.241 2497 Planarity : 0.005 0.070 2996 Dihedral : 5.902 52.583 2529 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.30 % Favored : 93.55 % Rotamer: Outliers : 3.18 % Allowed : 21.07 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.17), residues: 2079 helix: 0.99 (0.29), residues: 324 sheet: -1.99 (0.24), residues: 411 loop : -1.77 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 342 HIS 0.006 0.001 HIS K 7 PHE 0.030 0.002 PHE L 103 TYR 0.022 0.002 TYR K 343 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 11) link_NAG-ASN : angle 1.74769 ( 33) hydrogen bonds : bond 0.03595 ( 474) hydrogen bonds : angle 5.76049 ( 1269) SS BOND : bond 0.00347 ( 24) SS BOND : angle 2.03252 ( 48) covalent geometry : bond 0.00352 (16918) covalent geometry : angle 0.68864 (22907) Misc. bond : bond 0.00566 ( 2) *********************** 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 371 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 314 time to evaluate : 1.870 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: 0.8830 (tp-100) cc_final: 0.8366 (tm-30) REVERT: H 13 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7598 (mpt90) REVERT: H 38 ARG cc_start: 0.7732 (ttp80) cc_final: 0.6915 (ttp80) REVERT: H 93 TYR cc_start: 0.6511 (m-10) cc_final: 0.5993 (m-10) REVERT: L 39 ASP cc_start: 0.8014 (t0) cc_final: 0.7600 (t70) REVERT: D 93 TYR cc_start: 0.7021 (m-80) cc_final: 0.6548 (m-80) REVERT: E 58 ASN cc_start: 0.8616 (t0) cc_final: 0.8129 (t0) REVERT: E 94 MET cc_start: 0.7841 (mmm) cc_final: 0.7440 (mmm) REVERT: A 5 GLN cc_start: 0.8716 (tp40) cc_final: 0.8360 (tm-30) REVERT: I 113 MET cc_start: 0.7443 (ttm) cc_final: 0.6878 (ttm) REVERT: I 273 TYR cc_start: 0.8007 (m-80) cc_final: 0.7794 (m-10) outliers start: 57 outliers final: 37 residues processed: 350 average time/residue: 0.3513 time to fit residues: 188.6734 Evaluate side-chains 339 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 301 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 16 GLU 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 72 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 86 THR 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 470 MET Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 203 SER 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 313 ASN Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain K residue 3 ILE 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 366 ILE Chi-restraints excluded: chain K residue 369 ILE 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 160 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 171 optimal weight: 0.5980 chunk 82 optimal weight: 0.0770 chunk 153 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.123487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.098245 restraints weight = 49934.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.100496 restraints weight = 25601.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.102689 restraints weight = 16611.436| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3708 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= 0.124 Angle : 0.694 10.389 22988 Z= 0.345 Chirality : 0.043 0.206 2497 Planarity : 0.005 0.071 2996 Dihedral : 5.467 49.861 2526 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.77 % Favored : 94.08 % Rotamer: Outliers : 2.73 % Allowed : 22.19 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2079 helix: 1.12 (0.29), residues: 324 sheet: -1.88 (0.23), residues: 447 loop : -1.72 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 342 HIS 0.004 0.001 HIS I 463 PHE 0.027 0.002 PHE I 330 TYR 0.022 0.002 TYR K 343 ARG 0.003 0.000 ARG L 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 11) link_NAG-ASN : angle 1.54229 ( 33) hydrogen bonds : bond 0.03455 ( 474) hydrogen bonds : angle 5.58688 ( 1269) SS BOND : bond 0.00263 ( 24) SS BOND : angle 2.02011 ( 48) covalent geometry : bond 0.00286 (16918) covalent geometry : angle 0.68692 (22907) Misc. bond : bond 0.00582 ( 2) *********************** 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 373 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 324 time to evaluate : 1.762 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: H 5 GLN cc_start: 0.8769 (tp-100) cc_final: 0.8458 (tm-30) REVERT: H 38 ARG cc_start: 0.7780 (ttp80) cc_final: 0.6973 (ttp80) REVERT: H 93 TYR cc_start: 0.6412 (m-10) cc_final: 0.5925 (m-10) REVERT: L 39 ASP cc_start: 0.7982 (t0) cc_final: 0.7656 (t70) REVERT: D 5 GLN cc_start: 0.8930 (tp40) cc_final: 0.8339 (tm-30) REVERT: D 47 TRP cc_start: 0.8104 (t60) cc_final: 0.7831 (t60) REVERT: D 93 TYR cc_start: 0.6871 (m-80) cc_final: 0.6644 (m-10) REVERT: E 58 ASN cc_start: 0.8640 (t0) cc_final: 0.8161 (t0) REVERT: E 87 ASP cc_start: 0.7559 (m-30) cc_final: 0.6891 (m-30) REVERT: A 4 LEU cc_start: 0.7913 (tp) cc_final: 0.7652 (tp) REVERT: A 5 GLN cc_start: 0.8848 (tp40) cc_final: 0.8535 (tm-30) REVERT: A 92 ARG cc_start: 0.7354 (ttt180) cc_final: 0.6977 (ttt180) REVERT: C 335 TRP cc_start: 0.7207 (OUTLIER) cc_final: 0.6313 (p-90) REVERT: I 113 MET cc_start: 0.7271 (ttm) cc_final: 0.6690 (ttm) REVERT: I 273 TYR cc_start: 0.7988 (m-80) cc_final: 0.7765 (m-10) REVERT: K 43 SER cc_start: 0.8225 (p) cc_final: 0.7909 (p) REVERT: K 423 MET cc_start: 0.7608 (mtm) cc_final: 0.7359 (mtm) REVERT: K 426 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6535 (mp10) outliers start: 49 outliers final: 36 residues processed: 355 average time/residue: 0.2795 time to fit residues: 150.5938 Evaluate side-chains 344 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 306 time to evaluate : 1.749 ------------------------------------------------------------------------------- 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 L residue 38 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 72 ASP 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 E residue 111 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 VAL 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 425 ASN Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 235 THR 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 313 ASN Chi-restraints excluded: chain K residue 3 ILE 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 307 LEU Chi-restraints excluded: chain K residue 366 ILE 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 73 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 20 optimal weight: 0.0050 chunk 191 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 133 optimal weight: 0.3980 chunk 202 optimal weight: 2.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN C 427 HIS ** K 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 363 GLN K 425 ASN K 426 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.124573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.101250 restraints weight = 47090.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.103359 restraints weight = 22452.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.104133 restraints weight = 16064.872| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3858 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= 0.140 Angle : 0.684 10.337 22988 Z= 0.343 Chirality : 0.043 0.222 2497 Planarity : 0.005 0.068 2996 Dihedral : 5.475 50.175 2526 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.11 % Favored : 93.75 % Rotamer: Outliers : 3.07 % Allowed : 22.07 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.17), residues: 2079 helix: 1.25 (0.29), residues: 324 sheet: -1.90 (0.24), residues: 447 loop : -1.71 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 342 HIS 0.005 0.001 HIS K 7 PHE 0.026 0.002 PHE I 330 TYR 0.021 0.002 TYR K 343 ARG 0.006 0.000 ARG E 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 11) link_NAG-ASN : angle 1.58942 ( 33) hydrogen bonds : bond 0.03483 ( 474) hydrogen bonds : angle 5.57753 ( 1269) SS BOND : bond 0.00295 ( 24) SS BOND : angle 1.78137 ( 48) covalent geometry : bond 0.00320 (16918) covalent geometry : angle 0.67757 (22907) Misc. bond : bond 0.00555 ( 2) *********************** 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 380 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 325 time to evaluate : 1.851 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: H 5 GLN cc_start: 0.8671 (tp-100) cc_final: 0.8179 (tm-30) REVERT: H 38 ARG cc_start: 0.7713 (ttp80) cc_final: 0.6537 (ttp80) REVERT: H 46 GLU cc_start: 0.7667 (pp20) cc_final: 0.7410 (pp20) REVERT: H 93 TYR cc_start: 0.6399 (m-10) cc_final: 0.5912 (m-10) REVERT: L 39 ASP cc_start: 0.7968 (t0) cc_final: 0.7668 (t70) REVERT: D 5 GLN cc_start: 0.8918 (tp40) cc_final: 0.8306 (tm-30) REVERT: D 47 TRP cc_start: 0.8090 (t60) cc_final: 0.7781 (t60) REVERT: D 93 TYR cc_start: 0.6771 (m-80) cc_final: 0.6514 (m-10) REVERT: E 58 ASN cc_start: 0.8636 (t0) cc_final: 0.8197 (t0) REVERT: E 86 GLU cc_start: 0.8410 (pp20) cc_final: 0.7746 (pm20) REVERT: E 87 ASP cc_start: 0.7588 (m-30) cc_final: 0.6610 (m-30) REVERT: A 4 LEU cc_start: 0.7923 (tp) cc_final: 0.7701 (tp) REVERT: A 5 GLN cc_start: 0.8799 (tp40) cc_final: 0.8510 (tm-30) REVERT: B 38 LEU cc_start: 0.9117 (tt) cc_final: 0.8566 (mt) REVERT: C 222 ASP cc_start: 0.7241 (m-30) cc_final: 0.7028 (m-30) REVERT: C 335 TRP cc_start: 0.7305 (OUTLIER) cc_final: 0.6391 (p-90) REVERT: I 113 MET cc_start: 0.7293 (ttm) cc_final: 0.6712 (ttm) REVERT: K 43 SER cc_start: 0.8270 (p) cc_final: 0.7946 (p) REVERT: K 149 ASN cc_start: 0.8655 (t0) cc_final: 0.8416 (t0) REVERT: K 367 ASP cc_start: 0.8704 (m-30) cc_final: 0.8414 (p0) REVERT: K 423 MET cc_start: 0.7930 (mtm) cc_final: 0.7558 (mtm) REVERT: K 426 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6892 (mt0) outliers start: 55 outliers final: 42 residues processed: 362 average time/residue: 0.2767 time to fit residues: 151.6209 Evaluate side-chains 352 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 308 time to evaluate : 1.948 ------------------------------------------------------------------------------- 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 72 ASP Chi-restraints excluded: chain E residue 5 THR 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 E residue 111 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 VAL 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 60 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 235 THR 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 313 ASN Chi-restraints excluded: chain K residue 3 ILE 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 366 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 191 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 100 optimal weight: 0.2980 chunk 175 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** C 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.121255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.096332 restraints weight = 49705.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.098761 restraints weight = 23521.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.099134 restraints weight = 17619.515| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.746 16955 Z= 0.393 Angle : 1.019 65.599 22988 Z= 0.530 Chirality : 0.048 0.871 2497 Planarity : 0.006 0.189 2996 Dihedral : 5.476 50.173 2526 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.16 % Favored : 93.70 % Rotamer: Outliers : 2.62 % Allowed : 22.85 % Favored : 74.53 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.17), residues: 2079 helix: 1.23 (0.29), residues: 324 sheet: -1.90 (0.24), residues: 447 loop : -1.70 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP I 342 HIS 0.005 0.001 HIS K 7 PHE 0.025 0.002 PHE I 330 TYR 0.025 0.002 TYR I 273 ARG 0.047 0.001 ARG B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 11) link_NAG-ASN : angle 1.59028 ( 33) hydrogen bonds : bond 0.03526 ( 474) hydrogen bonds : angle 5.58352 ( 1269) SS BOND : bond 0.09055 ( 24) SS BOND : angle 7.66274 ( 48) covalent geometry : bond 0.00961 (16918) covalent geometry : angle 0.95709 (22907) Misc. bond : bond 0.00554 ( 2) *********************** 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 355 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 308 time to evaluate : 1.738 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: H 5 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8240 (tm-30) REVERT: H 38 ARG cc_start: 0.7857 (ttp80) cc_final: 0.6615 (ttp80) REVERT: H 46 GLU cc_start: 0.7713 (pp20) cc_final: 0.7448 (pp20) REVERT: H 93 TYR cc_start: 0.6468 (m-10) cc_final: 0.5943 (m-10) REVERT: L 39 ASP cc_start: 0.8115 (t0) cc_final: 0.7675 (t70) REVERT: D 5 GLN cc_start: 0.8923 (tp40) cc_final: 0.8375 (tm-30) REVERT: D 47 TRP cc_start: 0.8123 (t60) cc_final: 0.7799 (t60) REVERT: D 93 TYR cc_start: 0.6870 (m-80) cc_final: 0.6576 (m-10) REVERT: E 58 ASN cc_start: 0.8646 (t0) cc_final: 0.8187 (t0) REVERT: E 86 GLU cc_start: 0.8503 (pp20) cc_final: 0.7835 (pm20) REVERT: E 87 ASP cc_start: 0.7603 (m-30) cc_final: 0.6604 (m-30) REVERT: A 5 GLN cc_start: 0.8886 (tp40) cc_final: 0.8612 (tm-30) REVERT: B 38 LEU cc_start: 0.9144 (tt) cc_final: 0.8610 (mt) REVERT: C 335 TRP cc_start: 0.7212 (OUTLIER) cc_final: 0.6285 (p-90) REVERT: I 113 MET cc_start: 0.7330 (ttm) cc_final: 0.6735 (ttm) REVERT: K 43 SER cc_start: 0.8414 (p) cc_final: 0.8087 (p) REVERT: K 149 ASN cc_start: 0.8739 (t0) cc_final: 0.8512 (t0) REVERT: K 367 ASP cc_start: 0.8857 (m-30) cc_final: 0.8525 (p0) REVERT: K 423 MET cc_start: 0.7963 (mtm) cc_final: 0.7645 (mtm) outliers start: 47 outliers final: 45 residues processed: 337 average time/residue: 0.2792 time to fit residues: 141.8452 Evaluate side-chains 352 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 306 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 72 ASP 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 E residue 111 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 VAL 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 60 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 372 LYS Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 203 SER 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 313 ASN Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 4 CYS 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 366 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 34 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 425 ASN ** K 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.122635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.099029 restraints weight = 48143.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.100743 restraints weight = 23013.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.101379 restraints weight = 17431.605| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16955 Z= 0.181 Angle : 0.746 12.886 22988 Z= 0.374 Chirality : 0.045 0.256 2497 Planarity : 0.005 0.070 2996 Dihedral : 5.558 50.082 2526 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.12 % Favored : 92.78 % Rotamer: Outliers : 2.68 % Allowed : 23.02 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.18), residues: 2079 helix: 1.27 (0.29), residues: 324 sheet: -1.89 (0.23), residues: 453 loop : -1.73 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP I 342 HIS 0.009 0.001 HIS K 7 PHE 0.026 0.002 PHE B 103 TYR 0.042 0.002 TYR I 273 ARG 0.010 0.001 ARG B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 11) link_NAG-ASN : angle 1.75095 ( 33) hydrogen bonds : bond 0.03609 ( 474) hydrogen bonds : angle 5.62544 ( 1269) SS BOND : bond 0.00371 ( 24) SS BOND : angle 1.85381 ( 48) covalent geometry : bond 0.00408 (16918) covalent geometry : angle 0.73993 (22907) Misc. bond : bond 0.00519 ( 2) ********************** 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: 48 poor density : 320 time to evaluate : 2.906 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: H 5 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8335 (tm-30) REVERT: H 38 ARG cc_start: 0.7775 (ttp80) cc_final: 0.6633 (ttp80) REVERT: H 46 GLU cc_start: 0.7720 (pp20) cc_final: 0.7431 (pp20) REVERT: H 93 TYR cc_start: 0.6435 (m-10) cc_final: 0.5935 (m-10) REVERT: L 39 ASP cc_start: 0.7984 (t0) cc_final: 0.7742 (t70) REVERT: D 5 GLN cc_start: 0.8811 (tp40) cc_final: 0.8312 (tm-30) REVERT: D 47 TRP cc_start: 0.8171 (t60) cc_final: 0.7865 (t60) REVERT: D 93 TYR cc_start: 0.6744 (m-80) cc_final: 0.6489 (m-10) REVERT: D 95 CYS cc_start: 0.3445 (p) cc_final: 0.3118 (p) REVERT: E 58 ASN cc_start: 0.8597 (t0) cc_final: 0.8093 (t0) REVERT: E 86 GLU cc_start: 0.8416 (pp20) cc_final: 0.7762 (pm20) REVERT: E 87 ASP cc_start: 0.7621 (m-30) cc_final: 0.6603 (m-30) REVERT: A 5 GLN cc_start: 0.8798 (tp40) cc_final: 0.8381 (tm-30) REVERT: B 38 LEU cc_start: 0.9081 (tt) cc_final: 0.8605 (mt) REVERT: C 335 TRP cc_start: 0.7369 (OUTLIER) cc_final: 0.6308 (p-90) REVERT: I 113 MET cc_start: 0.7312 (ttm) cc_final: 0.6690 (ttm) REVERT: K 43 SER cc_start: 0.8348 (p) cc_final: 0.8043 (p) REVERT: K 149 ASN cc_start: 0.8699 (t0) cc_final: 0.8467 (t0) REVERT: K 367 ASP cc_start: 0.8771 (m-30) cc_final: 0.8468 (p0) REVERT: K 423 MET cc_start: 0.7989 (mtm) cc_final: 0.7650 (mtm) outliers start: 48 outliers final: 42 residues processed: 350 average time/residue: 0.3580 time to fit residues: 193.7547 Evaluate side-chains 357 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 314 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 72 ASP 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 109 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 86 THR 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 327 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 194 THR Chi-restraints excluded: chain I residue 203 SER 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 313 ASN 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 425 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 85 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 161 optimal weight: 0.0770 chunk 188 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN A 58 ASN ** K 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 425 ASN K 426 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.122252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.097967 restraints weight = 48429.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.100083 restraints weight = 22507.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.100581 restraints weight = 17086.842| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4117 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= 0.139 Angle : 0.735 14.211 22988 Z= 0.362 Chirality : 0.043 0.213 2497 Planarity : 0.005 0.069 2996 Dihedral : 5.471 49.977 2526 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.06 % Favored : 93.84 % Rotamer: Outliers : 2.34 % Allowed : 23.58 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.18), residues: 2079 helix: 1.39 (0.29), residues: 324 sheet: -1.82 (0.24), residues: 453 loop : -1.68 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP I 342 HIS 0.006 0.001 HIS L 37 PHE 0.024 0.002 PHE L 76 TYR 0.036 0.002 TYR I 273 ARG 0.011 0.000 ARG B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 11) link_NAG-ASN : angle 1.57661 ( 33) hydrogen bonds : bond 0.03490 ( 474) hydrogen bonds : angle 5.49871 ( 1269) SS BOND : bond 0.00307 ( 24) SS BOND : angle 1.71226 ( 48) covalent geometry : bond 0.00319 (16918) covalent geometry : angle 0.72959 (22907) Misc. bond : bond 0.00568 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8608.97 seconds wall clock time: 156 minutes 22.82 seconds (9382.82 seconds total)