Starting phenix.real_space_refine on Thu Aug 6 09:44:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vh5_65056/08_2026/9vh5_65056.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vh5_65056/08_2026/9vh5_65056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vh5_65056/08_2026/9vh5_65056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vh5_65056/08_2026/9vh5_65056.map" model { file = "/net/cci-nas-00/data/ceres_data/9vh5_65056/08_2026/9vh5_65056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vh5_65056/08_2026/9vh5_65056.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 8937 2.51 5 N 2565 2.21 5 O 2760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14328 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2509 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 301} Chain: "B" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1389 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "C" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 878 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "D" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2509 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 301} Chain: "E" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1389 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "F" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 878 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "G" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2509 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 301} Chain: "H" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1389 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "I" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 878 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Time building chain proxies: 2.81, per 1000 atoms: 0.20 Number of scatterers: 14328 At special positions: 0 Unit cell: (126.48, 122.76, 145.08, 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 66 16.00 O 2760 8.00 N 2565 7.00 C 8937 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS B 482 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 155 " distance=2.36 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 30 " - pdb=" SG CYS E 482 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 155 " distance=2.36 Simple disulfide: pdb=" SG CYS D 297 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 30 " - pdb=" SG CYS H 482 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 293 " distance=2.03 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 155 " distance=2.37 Simple disulfide: pdb=" SG CYS G 297 " - pdb=" SG CYS G 321 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 688.8 milliseconds 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3342 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 45 sheets defined 22.1% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 81 through 88 Processing helix chain 'A' and resid 89 through 96 removed outlier: 4.977A pdb=" N GLY A 94 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 96 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 420 through 472 Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 507 through 516 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'D' and resid 81 through 88 Processing helix chain 'D' and resid 89 through 96 removed outlier: 4.976A pdb=" N GLY D 94 " --> pdb=" O GLN D 91 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN D 96 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 132 Processing helix chain 'D' and resid 203 through 212 Processing helix chain 'E' and resid 382 through 399 Processing helix chain 'E' and resid 420 through 472 Processing helix chain 'E' and resid 490 through 499 Processing helix chain 'E' and resid 507 through 516 Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'G' and resid 81 through 88 Processing helix chain 'G' and resid 89 through 96 removed outlier: 4.977A pdb=" N GLY G 94 " --> pdb=" O GLN G 91 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN G 96 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 132 Processing helix chain 'G' and resid 203 through 212 Processing helix chain 'H' and resid 382 through 399 Processing helix chain 'H' and resid 420 through 472 Processing helix chain 'H' and resid 490 through 499 Processing helix chain 'H' and resid 507 through 516 Processing helix chain 'I' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'B' and resid 376 through 382 removed outlier: 3.691A pdb=" N GLY B 376 " --> pdb=" O ASN B 373 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR B 367 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 42 Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA5, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.162A pdb=" N ILE A 67 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N CYS A 293 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 69 " --> pdb=" O CYS A 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 74 through 77 removed outlier: 5.969A pdb=" N PHE A 103 " --> pdb=" O MET A 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 117 removed outlier: 6.997A pdb=" N ASP A 117 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N TRP A 250 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE A 195 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY A 272 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 116 through 117 removed outlier: 6.997A pdb=" N ASP A 117 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N TRP A 250 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE A 195 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AB1, first strand: chain 'A' and resid 152 through 157 removed outlier: 4.714A pdb=" N CYS A 155 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 180 through 185 Processing sheet with id=AB3, first strand: chain 'A' and resid 302 through 304 removed outlier: 4.324A pdb=" N CYS A 297 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS A 321 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN B 405 " --> pdb=" O CYS A 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 2 through 7 removed outlier: 3.542A pdb=" N THR C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.779A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG C 98 " --> pdb=" O ASN C 32 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET C 34 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA C 96 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TRP C 36 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR C 94 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG C 38 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C 92 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE C 107 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.779A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG C 98 " --> pdb=" O ASN C 32 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET C 34 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA C 96 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TRP C 36 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR C 94 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG C 38 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C 92 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 376 through 381 removed outlier: 3.691A pdb=" N GLY E 376 " --> pdb=" O ASN E 373 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 40 through 42 Processing sheet with id=AB9, first strand: chain 'D' and resid 55 through 57 Processing sheet with id=AC1, first strand: chain 'D' and resid 59 through 60 Processing sheet with id=AC2, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.161A pdb=" N ILE D 67 " --> pdb=" O GLY D 291 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N CYS D 293 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP D 69 " --> pdb=" O CYS D 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 74 through 77 removed outlier: 5.969A pdb=" N PHE D 103 " --> pdb=" O MET D 284 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 116 through 117 removed outlier: 6.998A pdb=" N ASP D 117 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N TRP D 250 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE D 195 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY D 272 " --> pdb=" O ILE D 195 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 116 through 117 removed outlier: 6.998A pdb=" N ASP D 117 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N TRP D 250 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE D 195 " --> pdb=" O PRO D 270 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 146 through 147 Processing sheet with id=AC7, first strand: chain 'D' and resid 152 through 157 removed outlier: 4.714A pdb=" N CYS D 155 " --> pdb=" O SER D 162 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 180 through 185 Processing sheet with id=AC9, first strand: chain 'D' and resid 302 through 304 removed outlier: 4.324A pdb=" N CYS D 297 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS D 321 " --> pdb=" O ASN E 405 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN E 405 " --> pdb=" O CYS D 321 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 2 through 7 removed outlier: 3.541A pdb=" N THR F 77 " --> pdb=" O ASP F 72 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 57 through 59 removed outlier: 5.780A pdb=" N LEU F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG F 98 " --> pdb=" O ASN F 32 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N MET F 34 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA F 96 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TRP F 36 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR F 94 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG F 38 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL F 92 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE F 107 " --> pdb=" O ALA F 97 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 57 through 59 removed outlier: 5.780A pdb=" N LEU F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG F 98 " --> pdb=" O ASN F 32 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N MET F 34 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA F 96 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TRP F 36 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR F 94 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG F 38 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL F 92 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 376 through 381 removed outlier: 3.691A pdb=" N GLY H 376 " --> pdb=" O ASN H 373 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 40 through 42 Processing sheet with id=AD6, first strand: chain 'G' and resid 55 through 57 Processing sheet with id=AD7, first strand: chain 'G' and resid 59 through 60 Processing sheet with id=AD8, first strand: chain 'G' and resid 67 through 70 removed outlier: 6.162A pdb=" N ILE G 67 " --> pdb=" O GLY G 291 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N CYS G 293 " --> pdb=" O ILE G 67 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP G 69 " --> pdb=" O CYS G 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'G' and resid 74 through 77 removed outlier: 5.969A pdb=" N PHE G 103 " --> pdb=" O MET G 284 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 116 through 117 removed outlier: 6.998A pdb=" N ASP G 117 " --> pdb=" O ILE G 248 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N TRP G 250 " --> pdb=" O ASP G 117 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE G 195 " --> pdb=" O GLY G 272 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY G 272 " --> pdb=" O ILE G 195 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 116 through 117 removed outlier: 6.998A pdb=" N ASP G 117 " --> pdb=" O ILE G 248 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N TRP G 250 " --> pdb=" O ASP G 117 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE G 195 " --> pdb=" O PRO G 270 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 146 through 147 Processing sheet with id=AE4, first strand: chain 'G' and resid 152 through 157 removed outlier: 4.714A pdb=" N CYS G 155 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 180 through 185 Processing sheet with id=AE6, first strand: chain 'G' and resid 302 through 304 removed outlier: 4.324A pdb=" N CYS G 297 " --> pdb=" O ILE G 304 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS G 321 " --> pdb=" O ASN H 405 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN H 405 " --> pdb=" O CYS G 321 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 2 through 7 removed outlier: 3.542A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.780A pdb=" N LEU I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG I 38 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG I 98 " --> pdb=" O ASN I 32 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N MET I 34 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA I 96 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TRP I 36 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR I 94 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG I 38 " --> pdb=" O VAL I 92 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL I 92 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE I 107 " --> pdb=" O ALA I 97 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.780A pdb=" N LEU I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG I 38 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG I 98 " --> pdb=" O ASN I 32 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N MET I 34 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA I 96 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TRP I 36 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR I 94 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG I 38 " --> pdb=" O VAL I 92 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL I 92 " --> pdb=" O ARG I 38 " (cutoff:3.500A) 639 hydrogen bonds defined for protein. 1746 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: 3.11 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4841 1.34 - 1.46: 2482 1.46 - 1.58: 7212 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 14625 Sorted by residual: bond pdb=" C CYS D 113 " pdb=" O CYS D 113 " ideal model delta sigma weight residual 1.235 1.219 0.017 1.26e-02 6.30e+03 1.76e+00 bond pdb=" C CYS A 113 " pdb=" O CYS A 113 " ideal model delta sigma weight residual 1.235 1.219 0.017 1.26e-02 6.30e+03 1.75e+00 bond pdb=" C CYS G 113 " pdb=" O CYS G 113 " ideal model delta sigma weight residual 1.235 1.219 0.016 1.26e-02 6.30e+03 1.58e+00 bond pdb=" CB ASP E 364 " pdb=" CG ASP E 364 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.54e+00 bond pdb=" CB ASP H 364 " pdb=" CG ASP H 364 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.52e+00 ... (remaining 14620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 19568 1.93 - 3.86: 205 3.86 - 5.79: 18 5.79 - 7.73: 0 7.73 - 9.66: 6 Bond angle restraints: 19797 Sorted by residual: angle pdb=" CA LEU D 31 " pdb=" CB LEU D 31 " pdb=" CG LEU D 31 " ideal model delta sigma weight residual 116.30 125.96 -9.66 3.50e+00 8.16e-02 7.61e+00 angle pdb=" CA LEU A 31 " pdb=" CB LEU A 31 " pdb=" CG LEU A 31 " ideal model delta sigma weight residual 116.30 125.93 -9.63 3.50e+00 8.16e-02 7.56e+00 angle pdb=" CA LEU G 31 " pdb=" CB LEU G 31 " pdb=" CG LEU G 31 " ideal model delta sigma weight residual 116.30 125.89 -9.59 3.50e+00 8.16e-02 7.51e+00 angle pdb=" CA LEU H 512 " pdb=" CB LEU H 512 " pdb=" CG LEU H 512 " ideal model delta sigma weight residual 116.30 125.36 -9.06 3.50e+00 8.16e-02 6.70e+00 angle pdb=" CA LEU E 512 " pdb=" CB LEU E 512 " pdb=" CG LEU E 512 " ideal model delta sigma weight residual 116.30 125.36 -9.06 3.50e+00 8.16e-02 6.70e+00 ... (remaining 19792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 7738 17.76 - 35.53: 811 35.53 - 53.29: 151 53.29 - 71.06: 42 71.06 - 88.82: 21 Dihedral angle restraints: 8763 sinusoidal: 3537 harmonic: 5226 Sorted by residual: dihedral pdb=" CA CYS G 113 " pdb=" CB CYS G 113 " pdb=" SG CYS G 113 " pdb=" SG CYS G 155 " ideal model delta sinusoidal sigma weight residual 79.00 16.73 62.27 1 2.00e+01 2.50e-03 1.28e+01 dihedral pdb=" CA CYS A 113 " pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " pdb=" SG CYS A 155 " ideal model delta sinusoidal sigma weight residual 79.00 16.80 62.20 1 2.00e+01 2.50e-03 1.28e+01 dihedral pdb=" CA CYS D 113 " pdb=" CB CYS D 113 " pdb=" SG CYS D 113 " pdb=" SG CYS D 155 " ideal model delta sinusoidal sigma weight residual 79.00 16.80 62.20 1 2.00e+01 2.50e-03 1.28e+01 ... (remaining 8760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1667 0.045 - 0.089: 324 0.089 - 0.134: 136 0.134 - 0.178: 3 0.178 - 0.223: 3 Chirality restraints: 2133 Sorted by residual: chirality pdb=" CG LEU H 512 " pdb=" CB LEU H 512 " pdb=" CD1 LEU H 512 " pdb=" CD2 LEU H 512 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CG LEU B 512 " pdb=" CB LEU B 512 " pdb=" CD1 LEU B 512 " pdb=" CD2 LEU B 512 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU E 512 " pdb=" CB LEU E 512 " pdb=" CD1 LEU E 512 " pdb=" CD2 LEU E 512 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2130 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 67 " 0.013 2.00e-02 2.50e+03 1.20e-02 2.53e+00 pdb=" CG PHE C 67 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 67 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE C 67 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 67 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 67 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 67 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 67 " 0.013 2.00e-02 2.50e+03 1.20e-02 2.53e+00 pdb=" CG PHE F 67 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE F 67 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE F 67 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE F 67 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 67 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 67 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 67 " 0.013 2.00e-02 2.50e+03 1.19e-02 2.49e+00 pdb=" CG PHE I 67 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE I 67 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE I 67 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE I 67 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE I 67 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE I 67 " 0.001 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 0.67 - 1.52: 9 1.52 - 2.36: 60 2.36 - 3.21: 12943 3.21 - 4.05: 39000 4.05 - 4.90: 72300 Warning: very small nonbonded interaction distances. Nonbonded interactions: 124312 Sorted by model distance: nonbonded pdb=" OE2 GLU B 476 " pdb=" CZ ARG E 472 " model vdw 0.673 2.616 nonbonded pdb=" CZ ARG B 472 " pdb=" OE2 GLU H 476 " model vdw 0.692 2.616 nonbonded pdb=" OE2 GLU E 476 " pdb=" CZ ARG H 472 " model vdw 0.698 2.616 nonbonded pdb=" OE2 GLU B 476 " pdb=" NE ARG E 472 " model vdw 1.283 3.120 nonbonded pdb=" NE ARG B 472 " pdb=" OE2 GLU H 476 " model vdw 1.286 3.120 ... (remaining 124307 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.600 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:8.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 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 : 0.013 0.807 14646 Z= 1.169 Angle : 0.552 9.657 19833 Z= 0.302 Chirality : 0.042 0.223 2133 Planarity : 0.003 0.036 2604 Dihedral : 15.357 88.821 5367 Min Nonbonded Distance : 0.673 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.06 % Allowed : 13.91 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 1809 helix: 3.08 (0.25), residues: 348 sheet: 0.01 (0.24), residues: 450 loop : -0.16 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.008 0.001 TYR G 211 PHE 0.028 0.001 PHE C 67 TRP 0.010 0.001 TRP E 437 HIS 0.004 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (14625) covalent geometry : angle 0.53673 / 0.30 (19797) SS BOND : bond 0.13638 / 9.21 ( 18) SS BOND : angle 3.02431 / 1.74 ( 36) hydrogen bonds : bond 0.18118 / 11.68 ( 591) hydrogen bonds : angle 8.21364 / 5.77 ( 1746) Misc. bond : bond 0.79414 / 39.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 263 time to evaluate : 0.547 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: E 403 LYS cc_start: 0.7712 (mmtm) cc_final: 0.7506 (mmtm) outliers start: 1 outliers final: 2 residues processed: 264 average time/residue: 0.7451 time to fit residues: 210.7096 Evaluate side-chains 187 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain D residue 50 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN C 3 GLN C 32 ASN C 76 ASN D 213 GLN ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 GLN E 461 ASN F 3 GLN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN G 232 ASN ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 461 ASN I 3 GLN I 76 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.097632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.060385 restraints weight = 26815.994| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.34 r_work: 0.2659 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14646 Z= 0.158 Angle : 0.556 7.422 19833 Z= 0.293 Chirality : 0.043 0.188 2133 Planarity : 0.004 0.042 2604 Dihedral : 4.788 95.575 1987 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.56 % Allowed : 16.03 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1809 helix: 3.03 (0.26), residues: 348 sheet: 0.23 (0.25), residues: 417 loop : -0.18 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 472 TYR 0.021 0.001 TYR B 507 PHE 0.018 0.001 PHE E 348 TRP 0.008 0.001 TRP B 437 HIS 0.003 0.001 HIS G 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (14625) covalent geometry : angle 0.55460 / 0.29 (19797) SS BOND : bond 0.00410 / 0.26 ( 18) SS BOND : angle 1.16884 / 0.71 ( 36) hydrogen bonds : bond 0.03814 / 2.43 ( 591) hydrogen bonds : angle 5.66740 / 3.96 ( 1746) Misc. bond : bond 0.00550 / 0.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 372 GLN cc_start: 0.8306 (tm-30) cc_final: 0.8066 (tm-30) REVERT: B 392 GLN cc_start: 0.9083 (mt0) cc_final: 0.8873 (mt0) REVERT: B 486 TYR cc_start: 0.7563 (m-80) cc_final: 0.7362 (m-80) REVERT: B 496 SER cc_start: 0.9133 (p) cc_final: 0.8884 (t) REVERT: B 508 ARG cc_start: 0.8970 (ttt-90) cc_final: 0.8599 (ttt180) REVERT: C 72 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8137 (p0) REVERT: C 79 TYR cc_start: 0.7438 (m-80) cc_final: 0.7199 (m-10) REVERT: C 103 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.8735 (t0) REVERT: E 372 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8217 (tm-30) REVERT: E 384 LYS cc_start: 0.9063 (mmmm) cc_final: 0.8837 (tppt) REVERT: E 392 GLN cc_start: 0.9065 (mt0) cc_final: 0.8854 (mt0) REVERT: E 403 LYS cc_start: 0.8310 (mmtm) cc_final: 0.8029 (mmtm) REVERT: E 484 LYS cc_start: 0.8623 (tptp) cc_final: 0.8373 (tptp) REVERT: E 496 SER cc_start: 0.9098 (p) cc_final: 0.8851 (t) REVERT: F 72 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8091 (p0) REVERT: H 384 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8814 (tppt) REVERT: H 484 LYS cc_start: 0.8637 (tptp) cc_final: 0.8302 (tptp) REVERT: H 486 TYR cc_start: 0.7640 (m-80) cc_final: 0.7380 (m-80) REVERT: H 496 SER cc_start: 0.9097 (p) cc_final: 0.8818 (t) outliers start: 40 outliers final: 11 residues processed: 237 average time/residue: 0.6604 time to fit residues: 169.4243 Evaluate side-chains 206 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 383 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 145 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN C 3 GLN ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 GLN E 474 ASN F 3 GLN ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 470 GLN H 474 ASN I 3 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.095304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.056706 restraints weight = 27177.986| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.41 r_work: 0.2614 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14646 Z= 0.210 Angle : 0.541 7.901 19833 Z= 0.286 Chirality : 0.044 0.156 2133 Planarity : 0.007 0.244 2604 Dihedral : 6.257 174.440 1985 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.01 % Allowed : 16.09 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.19), residues: 1809 helix: 2.94 (0.26), residues: 348 sheet: 0.19 (0.24), residues: 417 loop : -0.29 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 472 TYR 0.021 0.001 TYR B 507 PHE 0.013 0.001 PHE H 348 TRP 0.007 0.001 TRP H 437 HIS 0.003 0.001 HIS G 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (14625) covalent geometry : angle 0.53994 / 0.29 (19797) SS BOND : bond 0.00404 / 0.25 ( 18) SS BOND : angle 1.01668 / 0.61 ( 36) hydrogen bonds : bond 0.03602 / 2.31 ( 591) hydrogen bonds : angle 5.44105 / 3.81 ( 1746) Misc. bond : bond 0.00450 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 GLU cc_start: 0.8756 (tt0) cc_final: 0.8354 (mt-10) REVERT: B 372 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7985 (tm-30) REVERT: B 384 LYS cc_start: 0.8997 (mmmm) cc_final: 0.8794 (tppt) REVERT: B 496 SER cc_start: 0.9184 (p) cc_final: 0.8869 (t) REVERT: C 79 TYR cc_start: 0.7467 (m-80) cc_final: 0.7243 (m-10) REVERT: C 103 ASN cc_start: 0.9295 (m110) cc_final: 0.8751 (t0) REVERT: D 31 LEU cc_start: 0.8907 (pt) cc_final: 0.8613 (pp) REVERT: E 372 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8084 (tm-30) REVERT: E 384 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8803 (tppt) REVERT: E 496 SER cc_start: 0.9154 (p) cc_final: 0.8861 (t) REVERT: F 38 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7865 (ptp-170) REVERT: F 98 ARG cc_start: 0.8844 (ttp-170) cc_final: 0.8368 (tmm-80) REVERT: F 103 ASN cc_start: 0.9357 (m-40) cc_final: 0.9121 (m-40) REVERT: G 78 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8262 (pm20) REVERT: G 341 GLU cc_start: 0.8751 (tt0) cc_final: 0.8339 (mt-10) REVERT: H 372 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8259 (tm-30) REVERT: H 384 LYS cc_start: 0.9027 (mmmm) cc_final: 0.8797 (tppt) REVERT: H 484 LYS cc_start: 0.8657 (tptp) cc_final: 0.8450 (tptp) REVERT: H 496 SER cc_start: 0.9120 (p) cc_final: 0.8805 (t) REVERT: I 82 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.5868 (mmm) REVERT: I 103 ASN cc_start: 0.9045 (m110) cc_final: 0.8538 (t0) outliers start: 47 outliers final: 17 residues processed: 238 average time/residue: 0.6638 time to fit residues: 171.5073 Evaluate side-chains 215 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 78 GLU Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain H residue 383 LEU Chi-restraints excluded: chain H residue 506 VAL Chi-restraints excluded: chain I residue 82 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 GLN F 3 GLN ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN H 392 GLN H 470 GLN I 3 GLN I 32 ASN I 103 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.057597 restraints weight = 27114.872| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.33 r_work: 0.2662 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14646 Z= 0.192 Angle : 0.532 8.639 19833 Z= 0.281 Chirality : 0.043 0.143 2133 Planarity : 0.005 0.089 2604 Dihedral : 7.297 172.665 1985 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.82 % Allowed : 17.12 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.19), residues: 1809 helix: 2.82 (0.26), residues: 354 sheet: 0.21 (0.24), residues: 417 loop : -0.28 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 472 TYR 0.025 0.001 TYR B 507 PHE 0.010 0.001 PHE H 348 TRP 0.007 0.001 TRP H 437 HIS 0.003 0.001 HIS G 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (14625) covalent geometry : angle 0.53077 / 0.28 (19797) SS BOND : bond 0.00390 / 0.24 ( 18) SS BOND : angle 0.94719 / 0.56 ( 36) hydrogen bonds : bond 0.03442 / 2.20 ( 591) hydrogen bonds : angle 5.33526 / 3.73 ( 1746) Misc. bond : bond 0.00377 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 GLU cc_start: 0.8748 (tt0) cc_final: 0.8335 (mt-10) REVERT: A 342 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8306 (mtmm) REVERT: B 372 GLN cc_start: 0.8414 (tm-30) cc_final: 0.7909 (tm-30) REVERT: B 392 GLN cc_start: 0.9138 (mt0) cc_final: 0.8857 (mt0) REVERT: B 496 SER cc_start: 0.9197 (p) cc_final: 0.8850 (t) REVERT: C 79 TYR cc_start: 0.7540 (m-80) cc_final: 0.7275 (m-10) REVERT: C 103 ASN cc_start: 0.9297 (m110) cc_final: 0.8782 (t0) REVERT: D 31 LEU cc_start: 0.8888 (pt) cc_final: 0.8597 (pp) REVERT: E 372 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8044 (tm-30) REVERT: E 384 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8809 (tppt) REVERT: E 496 SER cc_start: 0.9157 (p) cc_final: 0.8860 (t) REVERT: F 38 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7894 (ptp-170) REVERT: F 99 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8858 (ttpp) REVERT: G 78 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: G 341 GLU cc_start: 0.8760 (tt0) cc_final: 0.8338 (mt-10) REVERT: H 370 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7286 (mtm-85) REVERT: H 372 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8200 (tm-30) REVERT: H 384 LYS cc_start: 0.9047 (mmmm) cc_final: 0.8822 (tppt) REVERT: H 484 LYS cc_start: 0.8620 (tptp) cc_final: 0.8155 (tptp) REVERT: H 496 SER cc_start: 0.9157 (p) cc_final: 0.8795 (t) REVERT: H 508 ARG cc_start: 0.9010 (ttt90) cc_final: 0.8656 (ttt90) REVERT: I 103 ASN cc_start: 0.9204 (m-40) cc_final: 0.8830 (t0) outliers start: 44 outliers final: 17 residues processed: 225 average time/residue: 0.6704 time to fit residues: 162.7362 Evaluate side-chains 219 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 78 GLU Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 383 LEU Chi-restraints excluded: chain H residue 506 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 160 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 110 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN C 3 GLN ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 GLN E 470 GLN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 GLN H 470 GLN I 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.097181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.059708 restraints weight = 27000.729| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.38 r_work: 0.2669 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14646 Z= 0.149 Angle : 0.518 8.369 19833 Z= 0.272 Chirality : 0.042 0.131 2133 Planarity : 0.005 0.100 2604 Dihedral : 8.216 177.848 1985 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.56 % Allowed : 17.76 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1809 helix: 2.95 (0.26), residues: 354 sheet: 0.41 (0.24), residues: 426 loop : -0.28 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 472 TYR 0.024 0.001 TYR E 507 PHE 0.009 0.001 PHE B 369 TRP 0.008 0.001 TRP H 437 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (14625) covalent geometry : angle 0.51710 / 0.27 (19797) SS BOND : bond 0.00341 / 0.21 ( 18) SS BOND : angle 0.88186 / 0.52 ( 36) hydrogen bonds : bond 0.03249 / 2.07 ( 591) hydrogen bonds : angle 5.17059 / 3.62 ( 1746) Misc. bond : bond 0.00250 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 GLU cc_start: 0.8724 (tt0) cc_final: 0.8350 (mt-10) REVERT: A 342 LYS cc_start: 0.8889 (mtmm) cc_final: 0.8301 (mtmm) REVERT: B 372 GLN cc_start: 0.8441 (tm-30) cc_final: 0.7908 (tm-30) REVERT: B 392 GLN cc_start: 0.9117 (mt0) cc_final: 0.8839 (mt0) REVERT: B 496 SER cc_start: 0.9204 (p) cc_final: 0.8866 (t) REVERT: C 72 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8012 (p0) REVERT: C 79 TYR cc_start: 0.7501 (m-80) cc_final: 0.7298 (m-10) REVERT: D 31 LEU cc_start: 0.8881 (pt) cc_final: 0.8612 (pp) REVERT: D 120 ASP cc_start: 0.8928 (t0) cc_final: 0.8710 (t0) REVERT: D 341 GLU cc_start: 0.8736 (tt0) cc_final: 0.8001 (mt-10) REVERT: E 372 GLN cc_start: 0.8465 (tm-30) cc_final: 0.7997 (tm-30) REVERT: E 384 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8825 (tppt) REVERT: E 496 SER cc_start: 0.9167 (p) cc_final: 0.8862 (t) REVERT: E 508 ARG cc_start: 0.9084 (ttt-90) cc_final: 0.8748 (ttt90) REVERT: F 29 PHE cc_start: 0.8909 (m-80) cc_final: 0.8660 (m-10) REVERT: F 38 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7883 (ptp-170) REVERT: F 72 ASP cc_start: 0.8608 (p0) cc_final: 0.7896 (p0) REVERT: F 98 ARG cc_start: 0.8799 (ttp-170) cc_final: 0.8502 (ttp-170) REVERT: F 99 LYS cc_start: 0.9047 (ttpp) cc_final: 0.8816 (ttpp) REVERT: G 78 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: G 341 GLU cc_start: 0.8747 (tt0) cc_final: 0.8357 (mt-10) REVERT: G 342 LYS cc_start: 0.9049 (mtmp) cc_final: 0.8759 (mtmm) REVERT: H 370 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8145 (mtm-85) REVERT: H 372 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8001 (tm-30) REVERT: H 384 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8816 (tppt) REVERT: H 484 LYS cc_start: 0.8616 (tptp) cc_final: 0.8298 (tptp) REVERT: H 496 SER cc_start: 0.9172 (p) cc_final: 0.8816 (t) REVERT: H 508 ARG cc_start: 0.9055 (ttt90) cc_final: 0.8713 (ttt90) REVERT: I 72 ASP cc_start: 0.8522 (p0) cc_final: 0.6900 (p0) REVERT: I 79 TYR cc_start: 0.7267 (m-10) cc_final: 0.6892 (m-10) REVERT: I 103 ASN cc_start: 0.9269 (m-40) cc_final: 0.8896 (t0) outliers start: 40 outliers final: 17 residues processed: 225 average time/residue: 0.7491 time to fit residues: 181.5907 Evaluate side-chains 220 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain G residue 78 GLU Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 383 LEU Chi-restraints excluded: chain H residue 506 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 57 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 57 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 138 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN C 3 GLN ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 GLN E 470 GLN F 3 GLN H 387 GLN H 392 GLN H 470 GLN H 474 ASN I 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.096496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.058562 restraints weight = 26870.997| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.38 r_work: 0.2647 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14646 Z= 0.207 Angle : 0.544 7.659 19833 Z= 0.285 Chirality : 0.043 0.130 2133 Planarity : 0.005 0.103 2604 Dihedral : 8.192 175.864 1985 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.14 % Allowed : 17.63 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1809 helix: 2.97 (0.26), residues: 354 sheet: 0.42 (0.24), residues: 426 loop : -0.34 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 472 TYR 0.030 0.001 TYR B 507 PHE 0.010 0.001 PHE E 369 TRP 0.006 0.001 TRP H 437 HIS 0.003 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (14625) covalent geometry : angle 0.54285 / 0.28 (19797) SS BOND : bond 0.00404 / 0.25 ( 18) SS BOND : angle 0.84341 / 0.50 ( 36) hydrogen bonds : bond 0.03422 / 2.19 ( 591) hydrogen bonds : angle 5.25068 / 3.67 ( 1746) Misc. bond : bond 0.00411 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8402 (mtmm) REVERT: B 372 GLN cc_start: 0.8439 (tm-30) cc_final: 0.7816 (tm-30) REVERT: B 385 SER cc_start: 0.9224 (m) cc_final: 0.8851 (p) REVERT: B 392 GLN cc_start: 0.9155 (mt0) cc_final: 0.8918 (mt0) REVERT: B 496 SER cc_start: 0.9203 (p) cc_final: 0.8859 (t) REVERT: C 66 ARG cc_start: 0.7074 (ttt90) cc_final: 0.6847 (ttt180) REVERT: C 79 TYR cc_start: 0.7524 (m-80) cc_final: 0.7307 (m-80) REVERT: D 31 LEU cc_start: 0.8877 (pt) cc_final: 0.8599 (pp) REVERT: D 341 GLU cc_start: 0.8773 (tt0) cc_final: 0.8490 (mt-10) REVERT: E 372 GLN cc_start: 0.8464 (tm-30) cc_final: 0.7948 (tm-30) REVERT: E 384 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8829 (tppt) REVERT: E 496 SER cc_start: 0.9162 (p) cc_final: 0.8857 (t) REVERT: E 508 ARG cc_start: 0.9128 (ttt-90) cc_final: 0.8844 (ttt90) REVERT: F 38 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7852 (ptp-170) REVERT: F 66 ARG cc_start: 0.7403 (ttt90) cc_final: 0.5831 (tpt170) REVERT: F 72 ASP cc_start: 0.8649 (p0) cc_final: 0.8074 (p0) REVERT: F 99 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8818 (ttpp) REVERT: G 78 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8265 (pm20) REVERT: G 341 GLU cc_start: 0.8760 (tt0) cc_final: 0.8378 (mt-10) REVERT: G 342 LYS cc_start: 0.9047 (mtmp) cc_final: 0.8773 (mtmm) REVERT: H 370 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8188 (mtm-85) REVERT: H 372 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8011 (tm-30) REVERT: H 384 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8848 (tppt) REVERT: H 484 LYS cc_start: 0.8616 (tptp) cc_final: 0.8322 (tptp) REVERT: H 496 SER cc_start: 0.9177 (p) cc_final: 0.8787 (t) REVERT: H 508 ARG cc_start: 0.9105 (ttt90) cc_final: 0.8731 (ttt90) REVERT: I 103 ASN cc_start: 0.9264 (m-40) cc_final: 0.8903 (t0) outliers start: 49 outliers final: 22 residues processed: 225 average time/residue: 0.6926 time to fit residues: 168.2853 Evaluate side-chains 212 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 78 GLU Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 383 LEU Chi-restraints excluded: chain H residue 506 VAL Chi-restraints excluded: chain I residue 57 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 140 optimal weight: 0.1980 chunk 129 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 GLN E 470 GLN E 474 ASN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 GLN H 470 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.096347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.058441 restraints weight = 26819.180| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 2.36 r_work: 0.2643 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14646 Z= 0.218 Angle : 0.555 7.766 19833 Z= 0.292 Chirality : 0.043 0.144 2133 Planarity : 0.005 0.101 2604 Dihedral : 7.932 175.750 1983 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.69 % Allowed : 18.72 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.19), residues: 1809 helix: 2.97 (0.26), residues: 354 sheet: 0.38 (0.24), residues: 426 loop : -0.36 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 472 TYR 0.029 0.002 TYR B 507 PHE 0.010 0.001 PHE H 369 TRP 0.006 0.001 TRP H 437 HIS 0.003 0.001 HIS G 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (14625) covalent geometry : angle 0.55454 / 0.29 (19797) SS BOND : bond 0.00415 / 0.26 ( 18) SS BOND : angle 0.79945 / 0.48 ( 36) hydrogen bonds : bond 0.03458 / 2.22 ( 591) hydrogen bonds : angle 5.28929 / 3.70 ( 1746) Misc. bond : bond 0.00308 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 GLU cc_start: 0.8698 (tt0) cc_final: 0.8012 (mt-10) REVERT: A 342 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8381 (mtmm) REVERT: B 372 GLN cc_start: 0.8497 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 385 SER cc_start: 0.9210 (m) cc_final: 0.8821 (p) REVERT: B 496 SER cc_start: 0.9193 (p) cc_final: 0.8855 (t) REVERT: C 66 ARG cc_start: 0.7146 (ttt90) cc_final: 0.6826 (ttt180) REVERT: D 31 LEU cc_start: 0.8890 (pt) cc_final: 0.8631 (pp) REVERT: D 341 GLU cc_start: 0.8738 (tt0) cc_final: 0.8487 (mt-10) REVERT: E 372 GLN cc_start: 0.8249 (tm-30) cc_final: 0.8003 (tm-30) REVERT: E 384 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8837 (tppt) REVERT: E 496 SER cc_start: 0.9154 (p) cc_final: 0.8855 (t) REVERT: E 508 ARG cc_start: 0.9107 (ttt-90) cc_final: 0.8833 (ttt90) REVERT: F 99 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8843 (ttpp) REVERT: G 78 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: G 341 GLU cc_start: 0.8732 (tt0) cc_final: 0.7975 (mt-10) REVERT: G 342 LYS cc_start: 0.9006 (mtmp) cc_final: 0.8726 (mtmm) REVERT: H 370 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8180 (mtm-85) REVERT: H 372 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8083 (tm-30) REVERT: H 384 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8860 (tppt) REVERT: H 496 SER cc_start: 0.9181 (p) cc_final: 0.8788 (t) REVERT: H 508 ARG cc_start: 0.9084 (ttt90) cc_final: 0.8701 (ttt90) REVERT: I 103 ASN cc_start: 0.9262 (m-40) cc_final: 0.8901 (t0) outliers start: 42 outliers final: 21 residues processed: 214 average time/residue: 0.7158 time to fit residues: 165.4217 Evaluate side-chains 213 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 78 GLU Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 383 LEU Chi-restraints excluded: chain H residue 506 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 19 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 85 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 GLN E 470 GLN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 HIS G 24 ASN H 392 GLN H 470 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.095281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.057214 restraints weight = 26594.808| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.34 r_work: 0.2561 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14646 Z= 0.186 Angle : 0.558 10.157 19833 Z= 0.290 Chirality : 0.043 0.135 2133 Planarity : 0.005 0.095 2604 Dihedral : 7.903 174.568 1983 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.12 % Allowed : 19.55 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1809 helix: 3.00 (0.26), residues: 354 sheet: 0.37 (0.24), residues: 426 loop : -0.35 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 399 TYR 0.031 0.001 TYR B 507 PHE 0.010 0.001 PHE H 369 TRP 0.007 0.001 TRP H 437 HIS 0.003 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (14625) covalent geometry : angle 0.55766 / 0.29 (19797) SS BOND : bond 0.00369 / 0.23 ( 18) SS BOND : angle 0.79195 / 0.47 ( 36) hydrogen bonds : bond 0.03373 / 2.16 ( 591) hydrogen bonds : angle 5.24069 / 3.66 ( 1746) Misc. bond : bond 0.00259 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 GLU cc_start: 0.8651 (tt0) cc_final: 0.7993 (mt-10) REVERT: A 342 LYS cc_start: 0.8938 (mtmm) cc_final: 0.8373 (mtmm) REVERT: B 372 GLN cc_start: 0.8523 (tm-30) cc_final: 0.7956 (tm-30) REVERT: B 385 SER cc_start: 0.9186 (m) cc_final: 0.8853 (p) REVERT: B 478 MET cc_start: 0.8551 (mtp) cc_final: 0.8282 (mtm) REVERT: B 496 SER cc_start: 0.9172 (p) cc_final: 0.8827 (t) REVERT: D 31 LEU cc_start: 0.8865 (pt) cc_final: 0.8596 (pp) REVERT: D 120 ASP cc_start: 0.8939 (t0) cc_final: 0.8730 (t0) REVERT: D 341 GLU cc_start: 0.8778 (tt0) cc_final: 0.8251 (mt-10) REVERT: E 372 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7991 (tm-30) REVERT: E 384 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8838 (tmmm) REVERT: E 496 SER cc_start: 0.9141 (p) cc_final: 0.8827 (t) REVERT: E 508 ARG cc_start: 0.9091 (ttt-90) cc_final: 0.8826 (ttt90) REVERT: F 98 ARG cc_start: 0.8776 (ttp-170) cc_final: 0.8388 (tmm-80) REVERT: F 99 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8744 (ttpp) REVERT: G 78 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8260 (pm20) REVERT: G 341 GLU cc_start: 0.8721 (tt0) cc_final: 0.7890 (mt-10) REVERT: G 342 LYS cc_start: 0.8992 (mtmp) cc_final: 0.8705 (mtmm) REVERT: H 370 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7327 (mtm-85) REVERT: H 372 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8096 (tm-30) REVERT: H 384 LYS cc_start: 0.9057 (mmmm) cc_final: 0.8848 (tppt) REVERT: H 478 MET cc_start: 0.8764 (mtm) cc_final: 0.8563 (mtp) REVERT: H 496 SER cc_start: 0.9162 (p) cc_final: 0.8760 (t) REVERT: H 508 ARG cc_start: 0.9127 (ttt90) cc_final: 0.8762 (ttt90) REVERT: I 66 ARG cc_start: 0.7419 (ttt90) cc_final: 0.7154 (tpt170) REVERT: I 103 ASN cc_start: 0.9260 (m-40) cc_final: 0.8908 (t0) outliers start: 33 outliers final: 19 residues processed: 212 average time/residue: 0.7492 time to fit residues: 171.2709 Evaluate side-chains 210 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 78 GLU Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 383 LEU Chi-restraints excluded: chain H residue 506 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 117 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN D 343 GLN ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 GLN E 470 GLN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 HIS ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 GLN H 470 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.095964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.057782 restraints weight = 26806.710| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.39 r_work: 0.2577 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14646 Z= 0.152 Angle : 0.548 8.769 19833 Z= 0.286 Chirality : 0.042 0.144 2133 Planarity : 0.005 0.090 2604 Dihedral : 7.859 174.192 1983 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.67 % Allowed : 20.45 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1809 helix: 3.18 (0.25), residues: 351 sheet: 0.37 (0.24), residues: 420 loop : -0.35 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 399 TYR 0.029 0.001 TYR B 507 PHE 0.009 0.001 PHE E 369 TRP 0.008 0.001 TRP H 437 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (14625) covalent geometry : angle 0.54782 / 0.29 (19797) SS BOND : bond 0.00318 / 0.20 ( 18) SS BOND : angle 0.79570 / 0.47 ( 36) hydrogen bonds : bond 0.03225 / 2.06 ( 591) hydrogen bonds : angle 5.14702 / 3.59 ( 1746) Misc. bond : bond 0.00246 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 GLU cc_start: 0.8601 (tt0) cc_final: 0.8181 (mt-10) REVERT: A 342 LYS cc_start: 0.8935 (mtmm) cc_final: 0.8343 (mtmm) REVERT: B 372 GLN cc_start: 0.8498 (tm-30) cc_final: 0.7930 (tm-30) REVERT: B 385 SER cc_start: 0.9187 (m) cc_final: 0.8805 (p) REVERT: B 469 LYS cc_start: 0.8940 (mttm) cc_final: 0.8734 (mmtp) REVERT: B 496 SER cc_start: 0.9163 (p) cc_final: 0.8812 (t) REVERT: D 31 LEU cc_start: 0.8854 (pt) cc_final: 0.8590 (pp) REVERT: D 120 ASP cc_start: 0.8932 (t0) cc_final: 0.8725 (t0) REVERT: D 341 GLU cc_start: 0.8802 (tt0) cc_final: 0.8348 (mt-10) REVERT: E 372 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7918 (tm-30) REVERT: E 384 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8840 (tmmm) REVERT: E 496 SER cc_start: 0.9137 (p) cc_final: 0.8822 (t) REVERT: E 508 ARG cc_start: 0.9116 (ttt-90) cc_final: 0.8838 (ttt90) REVERT: F 98 ARG cc_start: 0.8651 (ttp-170) cc_final: 0.8331 (tmm-80) REVERT: G 78 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: G 206 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8594 (t0) REVERT: G 341 GLU cc_start: 0.8702 (tt0) cc_final: 0.8091 (mt-10) REVERT: H 362 MET cc_start: 0.9113 (ttp) cc_final: 0.8830 (ttp) REVERT: H 370 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8131 (mtm-85) REVERT: H 372 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8060 (tm-30) REVERT: H 384 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8847 (tppt) REVERT: H 496 SER cc_start: 0.9136 (p) cc_final: 0.8739 (t) REVERT: H 508 ARG cc_start: 0.9148 (ttt90) cc_final: 0.8800 (ttt90) REVERT: I 66 ARG cc_start: 0.7213 (ttt90) cc_final: 0.5604 (tpt170) REVERT: I 103 ASN cc_start: 0.9252 (m-40) cc_final: 0.8891 (t0) outliers start: 26 outliers final: 12 residues processed: 208 average time/residue: 0.7595 time to fit residues: 170.1090 Evaluate side-chains 205 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain G residue 78 GLU Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 506 VAL Chi-restraints excluded: chain I residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 129 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 75 optimal weight: 0.0570 chunk 96 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN C 3 GLN ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 GLN E 470 GLN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 GLN H 470 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.096666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.059290 restraints weight = 26673.158| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.33 r_work: 0.2608 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14646 Z= 0.123 Angle : 0.554 9.046 19833 Z= 0.288 Chirality : 0.042 0.158 2133 Planarity : 0.005 0.086 2604 Dihedral : 7.812 174.776 1983 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.03 % Allowed : 21.35 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1809 helix: 3.30 (0.25), residues: 351 sheet: 0.38 (0.24), residues: 420 loop : -0.34 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 399 TYR 0.028 0.001 TYR B 507 PHE 0.008 0.001 PHE E 369 TRP 0.009 0.001 TRP H 437 HIS 0.004 0.001 HIS G 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (14625) covalent geometry : angle 0.55310 / 0.29 (19797) SS BOND : bond 0.00267 / 0.17 ( 18) SS BOND : angle 0.80223 / 0.48 ( 36) hydrogen bonds : bond 0.03099 / 1.97 ( 591) hydrogen bonds : angle 5.00359 / 3.50 ( 1746) Misc. bond : bond 0.00234 / 0.12 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 GLU cc_start: 0.8563 (tt0) cc_final: 0.8220 (mt-10) REVERT: A 342 LYS cc_start: 0.8905 (mtmm) cc_final: 0.8674 (mppt) REVERT: B 372 GLN cc_start: 0.8452 (tm-30) cc_final: 0.7850 (tm-30) REVERT: B 385 SER cc_start: 0.9130 (m) cc_final: 0.8843 (p) REVERT: B 469 LYS cc_start: 0.8910 (mttp) cc_final: 0.8702 (mmtp) REVERT: B 496 SER cc_start: 0.9165 (p) cc_final: 0.8802 (t) REVERT: C 32 ASN cc_start: 0.8850 (t0) cc_final: 0.8625 (t0) REVERT: D 31 LEU cc_start: 0.8839 (pt) cc_final: 0.8616 (pp) REVERT: D 120 ASP cc_start: 0.8897 (t0) cc_final: 0.8688 (t0) REVERT: D 341 GLU cc_start: 0.8745 (tt0) cc_final: 0.8459 (mt-10) REVERT: E 372 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7886 (tm-30) REVERT: E 496 SER cc_start: 0.9196 (p) cc_final: 0.8872 (t) REVERT: E 508 ARG cc_start: 0.9120 (ttt-90) cc_final: 0.8857 (ttt90) REVERT: F 98 ARG cc_start: 0.8594 (ttp-170) cc_final: 0.8306 (tmm-80) REVERT: G 78 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8240 (pm20) REVERT: G 341 GLU cc_start: 0.8666 (tt0) cc_final: 0.8124 (mt-10) REVERT: H 370 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8130 (mtm-85) REVERT: H 372 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8019 (tm-30) REVERT: H 496 SER cc_start: 0.9159 (p) cc_final: 0.8761 (t) REVERT: H 508 ARG cc_start: 0.9157 (ttt90) cc_final: 0.8818 (ttt90) REVERT: I 103 ASN cc_start: 0.9247 (m-40) cc_final: 0.8922 (t0) outliers start: 16 outliers final: 8 residues processed: 201 average time/residue: 0.7100 time to fit residues: 153.5374 Evaluate side-chains 198 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 78 GLU Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 159 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN B 504 HIS ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 GLN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 GLN H 470 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.053982 restraints weight = 27128.753| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 2.34 r_work: 0.2512 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2380 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 14646 Z= 0.368 Angle : 0.647 9.812 19833 Z= 0.335 Chirality : 0.047 0.175 2133 Planarity : 0.005 0.100 2604 Dihedral : 7.991 173.885 1983 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.41 % Allowed : 20.96 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 1809 helix: 2.96 (0.26), residues: 351 sheet: 0.23 (0.24), residues: 426 loop : -0.43 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 399 TYR 0.035 0.002 TYR B 507 PHE 0.014 0.002 PHE H 369 TRP 0.009 0.001 TRP F 100 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00853 / 0.37 (14625) covalent geometry : angle 0.64688 / 0.34 (19797) SS BOND : bond 0.00608 / 0.38 ( 18) SS BOND : angle 0.82945 / 0.52 ( 36) hydrogen bonds : bond 0.03854 / 2.48 ( 591) hydrogen bonds : angle 5.39476 / 3.78 ( 1746) Misc. bond : bond 0.00273 / 0.14 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6235.05 seconds wall clock time: 107 minutes 6.06 seconds (6426.06 seconds total)