Starting phenix.real_space_refine on Sun Apr 5 15:14:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nj9_49476/04_2026/9nj9_49476.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nj9_49476/04_2026/9nj9_49476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nj9_49476/04_2026/9nj9_49476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nj9_49476/04_2026/9nj9_49476.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nj9_49476/04_2026/9nj9_49476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nj9_49476/04_2026/9nj9_49476.map" } resolution = 2.6 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= -0.000 sd= 0.021 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 65 5.16 5 C 6997 2.51 5 N 1936 2.21 5 O 2155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11153 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1001 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 8, 'TRANS': 93} Chain breaks: 1 Chain: "P" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 751 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Chain: "Q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 957 Classifications: {'peptide': 124} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 116} Chain: "A" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1962 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 240} Chain: "B" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1962 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 240} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1972 Classifications: {'peptide': 259} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 241} Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 113} Chain: "K" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 701 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.60, per 1000 atoms: 0.23 Number of scatterers: 11153 At special positions: 0 Unit cell: (87.6231, 120.84, 143.175, 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 65 16.00 O 2155 8.00 N 1936 7.00 C 6997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 100E" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 29 " - pdb=" SG CYS P 94 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 181 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 57 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 181 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 57 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 181 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 29 " - pdb=" SG CYS K 94 " 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG G 1 " - " FUC G 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 601 " - " ASN A 197 " " NAG B 601 " - " ASN B 197 " " NAG C 601 " - " ASN C 197 " " NAG D 1 " - " ASN A 145 " " NAG E 1 " - " ASN B 145 " " NAG F 1 " - " ASN C 145 " " NAG G 1 " - " ASN C 233 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 549.5 milliseconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2582 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 34 sheets defined 10.0% alpha, 39.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'P' and resid 85 through 89 Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'Q' and resid 61 through 64 removed outlier: 3.682A pdb=" N GLN Q 64 " --> pdb=" O GLN Q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 61 through 64' Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.656A pdb=" N THR Q 87 " --> pdb=" O PRO Q 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.503A pdb=" N THR A 102 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.726A pdb=" N ALA A 130 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.620A pdb=" N ALA B 130 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 197 through 206 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.749A pdb=" N THR J 87 " --> pdb=" O PRO J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 35 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.537A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.537A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.439A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AA6, first strand: chain 'L' and resid 90 through 92 Processing sheet with id=AA7, first strand: chain 'P' and resid 12 through 13 Processing sheet with id=AA8, first strand: chain 'P' and resid 16 through 17 removed outlier: 3.576A pdb=" N VAL P 17 " --> pdb=" O GLN P 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'P' and resid 51 through 54 removed outlier: 6.552A pdb=" N TRP P 41 " --> pdb=" O VAL P 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.705A pdb=" N ILE Q 34 " --> pdb=" O GLU Q 50 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP Q 36 " --> pdb=" O MET Q 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.775A pdb=" N CYS Q 92 " --> pdb=" O TRP Q 103 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TRP Q 103 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG Q 94 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 100A through 100B removed outlier: 4.625A pdb=" N TRP A 158 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.070A pdb=" N SER A 140 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 13.202A pdb=" N MET A 156 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 267 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL A 190 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 150 through 151 removed outlier: 4.625A pdb=" N TRP A 158 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.070A pdb=" N SER A 140 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 13.202A pdb=" N MET A 156 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 267 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL A 190 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 43 through 44 removed outlier: 5.484A pdb=" N ASN A 43 " --> pdb=" O ALA A 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.926A pdb=" N ARG A 50 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 283 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AB9, first strand: chain 'B' and resid 43 through 44 removed outlier: 5.442A pdb=" N ASN B 43 " --> pdb=" O ALA B 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AC2, first strand: chain 'B' and resid 116 through 119 removed outlier: 7.369A pdb=" N VAL B 190 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE B 267 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 13.148A pdb=" N MET B 156 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER B 140 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TRP B 158 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 150 through 151 removed outlier: 4.510A pdb=" N TRP B 158 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER B 140 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 13.148A pdb=" N MET B 156 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE B 267 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL B 190 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 173 through 177 Processing sheet with id=AC5, first strand: chain 'C' and resid 41 through 44 removed outlier: 8.023A pdb=" N PHE C 41 " --> pdb=" O GLY C 291 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA C 293 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN C 43 " --> pdb=" O ALA C 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AC7, first strand: chain 'C' and resid 116 through 119 removed outlier: 7.281A pdb=" N VAL C 190 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE C 267 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TRP C 158 " --> pdb=" O GLY C 138 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AC9, first strand: chain 'C' and resid 140 through 144 removed outlier: 3.599A pdb=" N GLY C 151 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 173 through 177 Processing sheet with id=AD2, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'J' and resid 56 through 59 removed outlier: 5.226A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 56 through 59 removed outlier: 5.226A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AD6, first strand: chain 'K' and resid 16 through 17 removed outlier: 6.619A pdb=" N TRP K 41 " --> pdb=" O VAL K 53 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 16 through 17 426 hydrogen bonds defined for protein. 1023 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: 1.83 Time building geometry restraints manager: 1.30 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: 3615 1.34 - 1.46: 2464 1.46 - 1.58: 5233 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 11401 Sorted by residual: bond pdb=" CA SER L 27 " pdb=" C SER L 27 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.80e-02 3.09e+03 2.46e+00 bond pdb=" C LYS A 272 " pdb=" N VAL A 273 " ideal model delta sigma weight residual 1.335 1.316 0.019 1.41e-02 5.03e+03 1.80e+00 bond pdb=" CA GLY B 192 " pdb=" C GLY B 192 " ideal model delta sigma weight residual 1.515 1.503 0.012 1.00e-02 1.00e+04 1.55e+00 bond pdb=" CA VAL B 177 " pdb=" C VAL B 177 " ideal model delta sigma weight residual 1.528 1.519 0.008 7.70e-03 1.69e+04 1.21e+00 bond pdb=" CB GLN A 234 " pdb=" CG GLN A 234 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.91e-01 ... (remaining 11396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 14872 1.34 - 2.68: 466 2.68 - 4.02: 99 4.02 - 5.36: 19 5.36 - 6.70: 3 Bond angle restraints: 15459 Sorted by residual: angle pdb=" C ILE P 54 " pdb=" N TYR P 55 " pdb=" CA TYR P 55 " ideal model delta sigma weight residual 121.81 115.79 6.02 1.83e+00 2.99e-01 1.08e+01 angle pdb=" CA TYR P 55 " pdb=" CB TYR P 55 " pdb=" CG TYR P 55 " ideal model delta sigma weight residual 113.90 119.19 -5.29 1.80e+00 3.09e-01 8.63e+00 angle pdb=" C PRO B 70 " pdb=" N LYS B 71 " pdb=" CA LYS B 71 " ideal model delta sigma weight residual 121.54 126.57 -5.03 1.91e+00 2.74e-01 6.94e+00 angle pdb=" CA TYR K 55 " pdb=" CB TYR K 55 " pdb=" CG TYR K 55 " ideal model delta sigma weight residual 113.90 118.55 -4.65 1.80e+00 3.09e-01 6.68e+00 angle pdb=" C ASP L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 126.40 -4.86 1.91e+00 2.74e-01 6.47e+00 ... (remaining 15454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 6574 17.75 - 35.50: 314 35.50 - 53.25: 57 53.25 - 70.99: 14 70.99 - 88.74: 7 Dihedral angle restraints: 6966 sinusoidal: 2899 harmonic: 4067 Sorted by residual: dihedral pdb=" CB CYS H 100 " pdb=" SG CYS H 100 " pdb=" SG CYS H 100E" pdb=" CB CYS H 100E" ideal model delta sinusoidal sigma weight residual 93.00 129.94 -36.94 1 1.00e+01 1.00e-02 1.93e+01 dihedral pdb=" CA THR B 170 " pdb=" C THR B 170 " pdb=" N ASN B 171 " pdb=" CA ASN B 171 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " pdb=" SG CYS C 143 " pdb=" CB CYS C 143 " ideal model delta sinusoidal sigma weight residual 93.00 125.14 -32.14 1 1.00e+01 1.00e-02 1.47e+01 ... (remaining 6963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1038 0.034 - 0.068: 455 0.068 - 0.102: 154 0.102 - 0.136: 76 0.136 - 0.170: 7 Chirality restraints: 1730 Sorted by residual: chirality pdb=" CA TYR P 55 " pdb=" N TYR P 55 " pdb=" C TYR P 55 " pdb=" CB TYR P 55 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA ILE P 54 " pdb=" N ILE P 54 " pdb=" C ILE P 54 " pdb=" CB ILE P 54 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA ILE C 97 " pdb=" N ILE C 97 " pdb=" C ILE C 97 " pdb=" CB ILE C 97 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 1727 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR P 55 " 0.018 2.00e-02 2.50e+03 1.22e-02 2.96e+00 pdb=" CG TYR P 55 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR P 55 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR P 55 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR P 55 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR P 55 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR P 55 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR P 55 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 287 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO C 288 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 288 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 288 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 88 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO A 89 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " 0.021 5.00e-02 4.00e+02 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 6229 3.01 - 3.49: 10390 3.49 - 3.96: 18220 3.96 - 4.43: 21892 4.43 - 4.90: 36167 Nonbonded interactions: 92898 Sorted by model distance: nonbonded pdb=" C SER A 215 " pdb=" OG SER A 215 " model vdw 2.543 2.616 nonbonded pdb=" N THR B 214 " pdb=" OG1 THR B 214 " model vdw 2.593 2.496 nonbonded pdb=" N PHE C 152 " pdb=" O PHE C 152 " model vdw 2.598 2.496 nonbonded pdb=" N PHE A 152 " pdb=" O PHE A 152 " model vdw 2.605 2.496 nonbonded pdb=" N PHE B 152 " pdb=" O PHE B 152 " model vdw 2.605 2.496 ... (remaining 92893 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 41 through 601) } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'E' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) } ncs_group { reference = chain 'J' selection = (chain 'Q' and resid 2 through 109) } ncs_group { reference = chain 'K' selection = (chain 'P' and (resid 9 through 18 or resid 23 through 82 or resid 89 through 11 \ 1)) } 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: 15.270 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: 0.030 Set scattering table: 0.010 Process input model: 11.110 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.005 0.049 11431 Z= 0.239 Angle : 0.612 6.698 15530 Z= 0.328 Chirality : 0.046 0.170 1730 Planarity : 0.005 0.040 1989 Dihedral : 11.228 88.742 4327 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.09 % Allowed : 6.01 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -0.07 (0.23), residues: 1418 helix: -1.17 (0.58), residues: 78 sheet: 0.30 (0.25), residues: 443 loop : -0.04 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 265 TYR 0.029 0.002 TYR P 55 PHE 0.014 0.002 PHE C 193 TRP 0.010 0.002 TRP Q 47 HIS 0.005 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00547 (11401) covalent geometry : angle 0.60513 (15459) SS BOND : bond 0.00224 ( 19) SS BOND : angle 1.07089 ( 38) hydrogen bonds : bond 0.12868 ( 367) hydrogen bonds : angle 8.10620 ( 1023) link_BETA1-4 : bond 0.00153 ( 3) link_BETA1-4 : angle 1.53000 ( 9) link_BETA1-6 : bond 0.00315 ( 1) link_BETA1-6 : angle 1.51611 ( 3) link_NAG-ASN : bond 0.00202 ( 7) link_NAG-ASN : angle 1.93171 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7612 (mm-30) REVERT: H 75 LYS cc_start: 0.9144 (mmtt) cc_final: 0.8809 (mmtm) REVERT: H 100 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8125 (m) REVERT: L 61 ARG cc_start: 0.7905 (ttp-110) cc_final: 0.7687 (ttp80) REVERT: L 85 ASP cc_start: 0.7941 (m-30) cc_final: 0.7616 (p0) REVERT: P 40 SER cc_start: 0.7587 (OUTLIER) cc_final: 0.6704 (m) REVERT: Q 38 ARG cc_start: 0.8385 (ttt-90) cc_final: 0.8183 (tmm-80) REVERT: Q 46 GLU cc_start: 0.8544 (tt0) cc_final: 0.8013 (tm-30) REVERT: Q 72 ASP cc_start: 0.7367 (t70) cc_final: 0.7140 (t70) REVERT: Q 100 LYS cc_start: 0.8070 (mttp) cc_final: 0.7824 (mtmt) REVERT: A 48 LYS cc_start: 0.8016 (mttt) cc_final: 0.7784 (tmtt) REVERT: B 84 LEU cc_start: 0.7901 (tp) cc_final: 0.7611 (tm) REVERT: B 140 SER cc_start: 0.7812 (t) cc_final: 0.7480 (p) REVERT: C 64 ASP cc_start: 0.7838 (m-30) cc_final: 0.7195 (m-30) REVERT: C 92 SER cc_start: 0.8478 (t) cc_final: 0.8074 (m) REVERT: C 163 ASN cc_start: 0.7943 (m-40) cc_final: 0.7261 (p0) REVERT: C 196 ASP cc_start: 0.7767 (t0) cc_final: 0.7477 (t70) REVERT: C 218 ASN cc_start: 0.8649 (t0) cc_final: 0.8199 (t0) REVERT: C 255 SER cc_start: 0.8223 (p) cc_final: 0.7791 (t) REVERT: J 3 GLN cc_start: 0.8765 (tt0) cc_final: 0.8544 (tt0) REVERT: J 38 ARG cc_start: 0.8385 (ptm160) cc_final: 0.7833 (ptm160) REVERT: J 46 GLU cc_start: 0.8369 (tt0) cc_final: 0.7786 (tt0) REVERT: J 72 ASP cc_start: 0.7448 (t70) cc_final: 0.6847 (t70) REVERT: K 43 ARG cc_start: 0.8800 (ttp80) cc_final: 0.8481 (ttp-170) outliers start: 25 outliers final: 9 residues processed: 233 average time/residue: 0.4846 time to fit residues: 123.1514 Evaluate side-chains 196 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 40 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain J residue 63 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN B 223 HIS B 253 GLN B 297 HIS C 59 ASN C 218 ASN C 223 HIS C 271 GLN K 13 GLN K 75 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.147646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.102465 restraints weight = 13613.293| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.62 r_work: 0.3167 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11431 Z= 0.162 Angle : 0.604 20.062 15530 Z= 0.300 Chirality : 0.046 0.354 1730 Planarity : 0.005 0.060 1989 Dihedral : 5.808 59.124 1788 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.00 % Allowed : 12.18 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: 0.05 (0.23), residues: 1418 helix: -0.68 (0.59), residues: 84 sheet: 0.41 (0.25), residues: 445 loop : -0.01 (0.22), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 279 TYR 0.025 0.002 TYR P 55 PHE 0.015 0.002 PHE H 27 TRP 0.009 0.001 TRP Q 47 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00372 (11401) covalent geometry : angle 0.55539 (15459) SS BOND : bond 0.00212 ( 19) SS BOND : angle 0.87708 ( 38) hydrogen bonds : bond 0.03532 ( 367) hydrogen bonds : angle 6.54846 ( 1023) link_BETA1-4 : bond 0.00333 ( 3) link_BETA1-4 : angle 1.46226 ( 9) link_BETA1-6 : bond 0.00735 ( 1) link_BETA1-6 : angle 1.41987 ( 3) link_NAG-ASN : bond 0.00727 ( 7) link_NAG-ASN : angle 6.32752 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: H 46 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7307 (mm-30) REVERT: H 75 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8621 (mmtm) REVERT: L 61 ARG cc_start: 0.7505 (ttp-110) cc_final: 0.7260 (ttp80) REVERT: L 85 ASP cc_start: 0.7902 (m-30) cc_final: 0.7306 (p0) REVERT: P 9 GLU cc_start: 0.7140 (mp0) cc_final: 0.6883 (pm20) REVERT: P 17 VAL cc_start: 0.7988 (t) cc_final: 0.7633 (m) REVERT: P 37 ARG cc_start: 0.7431 (mpp80) cc_final: 0.7197 (mpp80) REVERT: P 40 SER cc_start: 0.6959 (OUTLIER) cc_final: 0.6234 (m) REVERT: Q 38 ARG cc_start: 0.8067 (ttt-90) cc_final: 0.7536 (tmm-80) REVERT: Q 46 GLU cc_start: 0.8187 (tt0) cc_final: 0.7409 (tt0) REVERT: Q 72 ASP cc_start: 0.7183 (t70) cc_final: 0.6833 (t70) REVERT: A 48 LYS cc_start: 0.8192 (mttt) cc_final: 0.7788 (tmtt) REVERT: B 84 LEU cc_start: 0.7912 (tp) cc_final: 0.7682 (tm) REVERT: C 64 ASP cc_start: 0.7680 (m-30) cc_final: 0.7128 (m-30) REVERT: C 92 SER cc_start: 0.8366 (t) cc_final: 0.7993 (m) REVERT: C 163 ASN cc_start: 0.7897 (m-40) cc_final: 0.7209 (p0) REVERT: C 196 ASP cc_start: 0.7798 (t0) cc_final: 0.7479 (t70) REVERT: J 3 GLN cc_start: 0.8763 (tt0) cc_final: 0.8491 (tt0) REVERT: J 38 ARG cc_start: 0.7942 (ptm160) cc_final: 0.7411 (ptm160) REVERT: J 46 GLU cc_start: 0.7633 (tt0) cc_final: 0.7256 (tt0) REVERT: J 62 LYS cc_start: 0.7654 (mtpp) cc_final: 0.7406 (mtpt) REVERT: J 72 ASP cc_start: 0.7193 (t70) cc_final: 0.6451 (t70) REVERT: K 37 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7461 (mtp85) REVERT: K 43 ARG cc_start: 0.8410 (ttp80) cc_final: 0.8023 (ttp-170) REVERT: K 95 GLN cc_start: 0.8970 (tm-30) cc_final: 0.7915 (tt0) outliers start: 36 outliers final: 15 residues processed: 209 average time/residue: 0.5058 time to fit residues: 115.3193 Evaluate side-chains 197 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain P residue 40 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 103 optimal weight: 0.0030 chunk 104 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 0.0970 chunk 74 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 12 optimal weight: 0.1980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN C 59 ASN C 218 ASN K 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.150394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.105398 restraints weight = 13647.451| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.62 r_work: 0.3303 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11431 Z= 0.102 Angle : 0.522 14.522 15530 Z= 0.265 Chirality : 0.045 0.477 1730 Planarity : 0.004 0.054 1989 Dihedral : 5.263 58.134 1783 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.42 % Allowed : 14.10 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: 0.18 (0.23), residues: 1418 helix: -0.24 (0.60), residues: 84 sheet: 0.54 (0.25), residues: 442 loop : 0.01 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 279 TYR 0.020 0.001 TYR P 55 PHE 0.018 0.001 PHE H 27 TRP 0.010 0.001 TRP Q 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00226 (11401) covalent geometry : angle 0.49878 (15459) SS BOND : bond 0.00137 ( 19) SS BOND : angle 0.75024 ( 38) hydrogen bonds : bond 0.02949 ( 367) hydrogen bonds : angle 6.03410 ( 1023) link_BETA1-4 : bond 0.00390 ( 3) link_BETA1-4 : angle 1.43003 ( 9) link_BETA1-6 : bond 0.00663 ( 1) link_BETA1-6 : angle 1.26851 ( 3) link_NAG-ASN : bond 0.00721 ( 7) link_NAG-ASN : angle 4.01186 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7631 (mp0) REVERT: H 46 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7260 (mm-30) REVERT: H 75 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8629 (mmtm) REVERT: H 100 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7667 (m) REVERT: L 85 ASP cc_start: 0.7884 (m-30) cc_final: 0.7273 (p0) REVERT: P 17 VAL cc_start: 0.7984 (t) cc_final: 0.7663 (m) REVERT: P 87 MET cc_start: 0.8627 (ptm) cc_final: 0.8145 (ppp) REVERT: Q 38 ARG cc_start: 0.8034 (ttt-90) cc_final: 0.7693 (tmm-80) REVERT: Q 46 GLU cc_start: 0.8158 (tt0) cc_final: 0.7506 (tt0) REVERT: Q 72 ASP cc_start: 0.7115 (t70) cc_final: 0.6730 (t70) REVERT: A 48 LYS cc_start: 0.8363 (mttt) cc_final: 0.7970 (tmtt) REVERT: B 84 LEU cc_start: 0.7877 (tp) cc_final: 0.7627 (tm) REVERT: B 175 VAL cc_start: 0.8625 (m) cc_final: 0.8423 (p) REVERT: C 64 ASP cc_start: 0.7564 (m-30) cc_final: 0.7052 (m-30) REVERT: C 92 SER cc_start: 0.8398 (t) cc_final: 0.8049 (m) REVERT: C 163 ASN cc_start: 0.7864 (m-40) cc_final: 0.7179 (p0) REVERT: C 196 ASP cc_start: 0.7800 (t0) cc_final: 0.7498 (t70) REVERT: J 3 GLN cc_start: 0.8741 (tt0) cc_final: 0.8469 (tt0) REVERT: J 21 SER cc_start: 0.8130 (t) cc_final: 0.7895 (m) REVERT: J 38 ARG cc_start: 0.7878 (ptm160) cc_final: 0.7231 (ptm160) REVERT: J 46 GLU cc_start: 0.7582 (tt0) cc_final: 0.6785 (tt0) REVERT: J 62 LYS cc_start: 0.7668 (mtpp) cc_final: 0.7448 (mtpt) REVERT: J 72 ASP cc_start: 0.7113 (t70) cc_final: 0.6350 (t70) REVERT: K 37 ARG cc_start: 0.7772 (mtt90) cc_final: 0.7442 (mtp85) REVERT: K 43 ARG cc_start: 0.8300 (ttp80) cc_final: 0.8056 (ttp-170) outliers start: 29 outliers final: 16 residues processed: 209 average time/residue: 0.4904 time to fit residues: 111.8667 Evaluate side-chains 196 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 40 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 70 optimal weight: 0.0010 chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN B 253 GLN C 40 HIS C 59 ASN C 242 GLN K 75 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.146846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.101445 restraints weight = 13862.037| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.66 r_work: 0.3139 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11431 Z= 0.245 Angle : 0.610 11.402 15530 Z= 0.313 Chirality : 0.049 0.510 1730 Planarity : 0.005 0.059 1989 Dihedral : 5.628 58.568 1781 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.92 % Allowed : 14.26 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -0.00 (0.23), residues: 1418 helix: -0.52 (0.58), residues: 84 sheet: 0.46 (0.25), residues: 461 loop : -0.14 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 67 TYR 0.026 0.002 TYR P 55 PHE 0.018 0.002 PHE H 27 TRP 0.012 0.002 TRP Q 47 HIS 0.007 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00579 (11401) covalent geometry : angle 0.59377 (15459) SS BOND : bond 0.00301 ( 19) SS BOND : angle 1.06672 ( 38) hydrogen bonds : bond 0.03483 ( 367) hydrogen bonds : angle 6.26553 ( 1023) link_BETA1-4 : bond 0.00092 ( 3) link_BETA1-4 : angle 1.52038 ( 9) link_BETA1-6 : bond 0.00395 ( 1) link_BETA1-6 : angle 1.45758 ( 3) link_NAG-ASN : bond 0.00588 ( 7) link_NAG-ASN : angle 3.44374 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: H 46 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7313 (mm-30) REVERT: H 75 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8608 (mmtm) REVERT: H 100 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.7667 (m) REVERT: L 61 ARG cc_start: 0.7453 (ttp-110) cc_final: 0.7147 (ttp80) REVERT: L 85 ASP cc_start: 0.7863 (m-30) cc_final: 0.7266 (p0) REVERT: P 43 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7220 (ttm170) REVERT: P 87 MET cc_start: 0.8582 (ptm) cc_final: 0.8177 (ppp) REVERT: Q 38 ARG cc_start: 0.8002 (ttt-90) cc_final: 0.7619 (tmm-80) REVERT: Q 46 GLU cc_start: 0.8170 (tt0) cc_final: 0.7507 (tt0) REVERT: Q 72 ASP cc_start: 0.7188 (t70) cc_final: 0.6797 (t70) REVERT: A 48 LYS cc_start: 0.8273 (mttt) cc_final: 0.7854 (tmtt) REVERT: B 84 LEU cc_start: 0.7934 (tp) cc_final: 0.7673 (tm) REVERT: B 176 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8392 (mp0) REVERT: C 64 ASP cc_start: 0.7682 (m-30) cc_final: 0.7051 (m-30) REVERT: C 92 SER cc_start: 0.8380 (t) cc_final: 0.7974 (m) REVERT: C 163 ASN cc_start: 0.7897 (m-40) cc_final: 0.7198 (p0) REVERT: C 196 ASP cc_start: 0.7851 (t0) cc_final: 0.7491 (t70) REVERT: J 3 GLN cc_start: 0.8756 (tt0) cc_final: 0.8421 (tt0) REVERT: J 38 ARG cc_start: 0.7874 (ptm160) cc_final: 0.7157 (ptm160) REVERT: J 46 GLU cc_start: 0.7823 (tt0) cc_final: 0.6978 (tt0) REVERT: J 52 ILE cc_start: 0.6910 (OUTLIER) cc_final: 0.6701 (mp) REVERT: J 72 ASP cc_start: 0.7187 (t70) cc_final: 0.6390 (t70) REVERT: K 37 ARG cc_start: 0.7710 (mtt90) cc_final: 0.7380 (mtp85) REVERT: K 43 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7920 (ttp-170) REVERT: K 95 GLN cc_start: 0.8913 (tm-30) cc_final: 0.7909 (tt0) outliers start: 47 outliers final: 24 residues processed: 211 average time/residue: 0.4745 time to fit residues: 109.6696 Evaluate side-chains 210 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 43 ARG Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 40 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 18 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN C 242 GLN K 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.148451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.103459 restraints weight = 13545.111| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.62 r_work: 0.3169 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11431 Z= 0.156 Angle : 0.550 9.896 15530 Z= 0.283 Chirality : 0.046 0.446 1730 Planarity : 0.005 0.057 1989 Dihedral : 5.540 59.880 1781 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.17 % Allowed : 14.60 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: 0.09 (0.23), residues: 1418 helix: -0.32 (0.59), residues: 84 sheet: 0.58 (0.25), residues: 452 loop : -0.13 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 37 TYR 0.023 0.002 TYR P 55 PHE 0.020 0.002 PHE H 27 TRP 0.011 0.001 TRP Q 47 HIS 0.004 0.001 HIS K 91 Details of bonding type rmsd covalent geometry : bond 0.00360 (11401) covalent geometry : angle 0.53647 (15459) SS BOND : bond 0.00218 ( 19) SS BOND : angle 0.83509 ( 38) hydrogen bonds : bond 0.03118 ( 367) hydrogen bonds : angle 6.09819 ( 1023) link_BETA1-4 : bond 0.00308 ( 3) link_BETA1-4 : angle 1.44854 ( 9) link_BETA1-6 : bond 0.00560 ( 1) link_BETA1-6 : angle 1.43721 ( 3) link_NAG-ASN : bond 0.00868 ( 7) link_NAG-ASN : angle 3.02918 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7272 (mm-30) REVERT: H 75 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8610 (mmtm) REVERT: H 100 SER cc_start: 0.8130 (OUTLIER) cc_final: 0.7613 (m) REVERT: P 43 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7165 (ttm170) REVERT: P 87 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8152 (ppp) REVERT: Q 38 ARG cc_start: 0.8025 (ttt-90) cc_final: 0.7635 (tmm-80) REVERT: Q 46 GLU cc_start: 0.8163 (tt0) cc_final: 0.7503 (tt0) REVERT: Q 72 ASP cc_start: 0.7203 (t70) cc_final: 0.6817 (t70) REVERT: A 48 LYS cc_start: 0.8247 (mttt) cc_final: 0.7841 (tmtt) REVERT: A 245 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7579 (mtt-85) REVERT: B 84 LEU cc_start: 0.7858 (tp) cc_final: 0.7629 (tm) REVERT: C 64 ASP cc_start: 0.7565 (m-30) cc_final: 0.6969 (m-30) REVERT: C 92 SER cc_start: 0.8360 (t) cc_final: 0.7974 (m) REVERT: C 163 ASN cc_start: 0.7886 (m-40) cc_final: 0.7197 (p0) REVERT: C 196 ASP cc_start: 0.7827 (t0) cc_final: 0.7497 (t70) REVERT: J 3 GLN cc_start: 0.8728 (tt0) cc_final: 0.8384 (tt0) REVERT: J 21 SER cc_start: 0.8103 (t) cc_final: 0.7879 (m) REVERT: J 38 ARG cc_start: 0.7846 (ptm160) cc_final: 0.7126 (ptm160) REVERT: J 46 GLU cc_start: 0.7708 (tt0) cc_final: 0.6881 (tt0) REVERT: J 52 ILE cc_start: 0.6808 (OUTLIER) cc_final: 0.6570 (mp) REVERT: J 72 ASP cc_start: 0.7172 (t70) cc_final: 0.6370 (t70) REVERT: K 37 ARG cc_start: 0.7706 (mtt90) cc_final: 0.7389 (mtp85) REVERT: K 43 ARG cc_start: 0.8209 (ttp80) cc_final: 0.7913 (ttp-170) REVERT: K 95 GLN cc_start: 0.8882 (tm-30) cc_final: 0.7854 (tt0) outliers start: 50 outliers final: 28 residues processed: 211 average time/residue: 0.5061 time to fit residues: 116.6190 Evaluate side-chains 209 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 43 ARG Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 87 MET Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 40 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 132 optimal weight: 9.9990 chunk 98 optimal weight: 0.0770 chunk 130 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 128 optimal weight: 0.0670 chunk 117 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN K 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.149490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104512 restraints weight = 13792.848| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.65 r_work: 0.3183 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11431 Z= 0.136 Angle : 0.557 10.949 15530 Z= 0.282 Chirality : 0.046 0.412 1730 Planarity : 0.005 0.058 1989 Dihedral : 6.658 87.582 1781 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.24 % Favored : 96.69 % Rotamer: Outliers : 4.17 % Allowed : 15.10 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: 0.15 (0.23), residues: 1418 helix: -0.20 (0.60), residues: 84 sheet: 0.63 (0.25), residues: 451 loop : -0.09 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 67 TYR 0.026 0.002 TYR K 93 PHE 0.022 0.002 PHE H 27 TRP 0.011 0.001 TRP Q 47 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00310 (11401) covalent geometry : angle 0.54439 (15459) SS BOND : bond 0.00190 ( 19) SS BOND : angle 0.73299 ( 38) hydrogen bonds : bond 0.02995 ( 367) hydrogen bonds : angle 6.02859 ( 1023) link_BETA1-4 : bond 0.00369 ( 3) link_BETA1-4 : angle 1.42006 ( 9) link_BETA1-6 : bond 0.00431 ( 1) link_BETA1-6 : angle 1.29027 ( 3) link_NAG-ASN : bond 0.00294 ( 7) link_NAG-ASN : angle 3.02164 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7226 (mm-30) REVERT: H 75 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8620 (mmtm) REVERT: H 100 SER cc_start: 0.8165 (OUTLIER) cc_final: 0.7582 (m) REVERT: P 9 GLU cc_start: 0.7337 (mp0) cc_final: 0.7106 (pm20) REVERT: P 37 ARG cc_start: 0.7383 (mpp80) cc_final: 0.7105 (mtp85) REVERT: P 43 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7164 (ttm170) REVERT: P 87 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8161 (ppp) REVERT: Q 38 ARG cc_start: 0.8048 (ttt-90) cc_final: 0.7667 (tmm-80) REVERT: Q 46 GLU cc_start: 0.8186 (tt0) cc_final: 0.7539 (tt0) REVERT: Q 72 ASP cc_start: 0.7227 (t70) cc_final: 0.6833 (t70) REVERT: A 48 LYS cc_start: 0.8245 (mttt) cc_final: 0.7841 (tmtt) REVERT: A 245 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7609 (mtt-85) REVERT: B 84 LEU cc_start: 0.7850 (tp) cc_final: 0.7624 (tm) REVERT: B 175 VAL cc_start: 0.8628 (m) cc_final: 0.8387 (p) REVERT: B 234 GLN cc_start: 0.7974 (mt0) cc_final: 0.7767 (mt0) REVERT: C 64 ASP cc_start: 0.7575 (m-30) cc_final: 0.6999 (m-30) REVERT: C 92 SER cc_start: 0.8376 (t) cc_final: 0.8003 (m) REVERT: C 128 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: C 163 ASN cc_start: 0.7867 (m-40) cc_final: 0.7187 (p0) REVERT: C 196 ASP cc_start: 0.7829 (t0) cc_final: 0.7498 (t70) REVERT: C 267 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8417 (tp) REVERT: J 3 GLN cc_start: 0.8741 (tt0) cc_final: 0.8408 (tt0) REVERT: J 21 SER cc_start: 0.8146 (t) cc_final: 0.7918 (m) REVERT: J 38 ARG cc_start: 0.7800 (ptm160) cc_final: 0.7253 (ptm160) REVERT: J 46 GLU cc_start: 0.7525 (tt0) cc_final: 0.7150 (tt0) REVERT: J 52 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6616 (mp) REVERT: J 72 ASP cc_start: 0.7168 (t70) cc_final: 0.6381 (t70) REVERT: K 37 ARG cc_start: 0.7725 (mtt90) cc_final: 0.7414 (mtp85) REVERT: K 43 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7937 (ttp-170) REVERT: K 95 GLN cc_start: 0.8882 (tm-30) cc_final: 0.7859 (tt0) outliers start: 50 outliers final: 31 residues processed: 211 average time/residue: 0.4924 time to fit residues: 113.4601 Evaluate side-chains 211 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 43 ARG Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 87 MET Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 26 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 104 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 HIS C 59 ASN K 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.141595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096284 restraints weight = 13861.381| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.65 r_work: 0.3140 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11431 Z= 0.232 Angle : 0.628 12.750 15530 Z= 0.321 Chirality : 0.047 0.180 1730 Planarity : 0.005 0.060 1989 Dihedral : 6.092 58.099 1781 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.25 % Allowed : 15.18 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: 0.00 (0.23), residues: 1418 helix: -0.56 (0.58), residues: 82 sheet: 0.53 (0.25), residues: 462 loop : -0.17 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 67 TYR 0.026 0.002 TYR P 55 PHE 0.022 0.002 PHE H 27 TRP 0.012 0.002 TRP Q 47 HIS 0.006 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00546 (11401) covalent geometry : angle 0.61606 (15459) SS BOND : bond 0.00281 ( 19) SS BOND : angle 1.03323 ( 38) hydrogen bonds : bond 0.03468 ( 367) hydrogen bonds : angle 6.27181 ( 1023) link_BETA1-4 : bond 0.00058 ( 3) link_BETA1-4 : angle 1.49961 ( 9) link_BETA1-6 : bond 0.00428 ( 1) link_BETA1-6 : angle 1.51381 ( 3) link_NAG-ASN : bond 0.00806 ( 7) link_NAG-ASN : angle 3.04969 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7301 (mm-30) REVERT: H 75 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8582 (mmtm) REVERT: H 100 SER cc_start: 0.8131 (OUTLIER) cc_final: 0.7633 (m) REVERT: L 61 ARG cc_start: 0.7457 (ttp-110) cc_final: 0.7095 (ttp80) REVERT: P 40 SER cc_start: 0.6971 (OUTLIER) cc_final: 0.6294 (m) REVERT: P 43 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7151 (ttm170) REVERT: P 87 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8093 (ppp) REVERT: Q 38 ARG cc_start: 0.8018 (ttt-90) cc_final: 0.7602 (tmm-80) REVERT: Q 46 GLU cc_start: 0.8165 (tt0) cc_final: 0.7504 (tt0) REVERT: Q 72 ASP cc_start: 0.7195 (t70) cc_final: 0.6782 (t70) REVERT: A 48 LYS cc_start: 0.8200 (mttt) cc_final: 0.7782 (tmtt) REVERT: A 245 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7521 (mtt-85) REVERT: B 84 LEU cc_start: 0.7898 (tp) cc_final: 0.7666 (tm) REVERT: C 64 ASP cc_start: 0.7672 (m-30) cc_final: 0.7003 (m-30) REVERT: C 92 SER cc_start: 0.8384 (t) cc_final: 0.7982 (m) REVERT: C 128 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: C 163 ASN cc_start: 0.7887 (m-40) cc_final: 0.7002 (p0) REVERT: C 196 ASP cc_start: 0.7857 (t0) cc_final: 0.7510 (t70) REVERT: J 3 GLN cc_start: 0.8749 (tt0) cc_final: 0.8411 (tt0) REVERT: J 38 ARG cc_start: 0.7809 (ptm160) cc_final: 0.7179 (ptm160) REVERT: J 46 GLU cc_start: 0.7770 (tt0) cc_final: 0.6881 (tt0) REVERT: J 52 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6701 (mp) REVERT: J 72 ASP cc_start: 0.7203 (t70) cc_final: 0.6388 (t70) REVERT: K 37 ARG cc_start: 0.7686 (mtt90) cc_final: 0.7349 (mtp85) REVERT: K 43 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7936 (ttp-170) REVERT: K 95 GLN cc_start: 0.8922 (tm-30) cc_final: 0.7751 (tt0) outliers start: 51 outliers final: 30 residues processed: 206 average time/residue: 0.5237 time to fit residues: 117.3296 Evaluate side-chains 211 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 40 SER Chi-restraints excluded: chain P residue 43 ARG Chi-restraints excluded: chain P residue 87 MET Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 40 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 67 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN C 59 ASN K 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.149574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104723 restraints weight = 13721.605| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.65 r_work: 0.3191 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11431 Z= 0.136 Angle : 0.575 11.855 15530 Z= 0.291 Chirality : 0.046 0.473 1730 Planarity : 0.005 0.060 1989 Dihedral : 7.031 102.050 1781 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.42 % Allowed : 16.43 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: 0.13 (0.23), residues: 1418 helix: -0.08 (0.63), residues: 76 sheet: 0.63 (0.25), residues: 452 loop : -0.13 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 67 TYR 0.027 0.002 TYR K 93 PHE 0.020 0.002 PHE H 27 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00305 (11401) covalent geometry : angle 0.56370 (15459) SS BOND : bond 0.00184 ( 19) SS BOND : angle 0.74246 ( 38) hydrogen bonds : bond 0.03004 ( 367) hydrogen bonds : angle 6.04435 ( 1023) link_BETA1-4 : bond 0.00316 ( 3) link_BETA1-4 : angle 1.41474 ( 9) link_BETA1-6 : bond 0.00519 ( 1) link_BETA1-6 : angle 1.33879 ( 3) link_NAG-ASN : bond 0.01330 ( 7) link_NAG-ASN : angle 2.92135 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.8726 (m-80) cc_final: 0.8359 (m-80) REVERT: H 46 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7321 (mm-30) REVERT: H 75 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8608 (mmtm) REVERT: H 100 TYR cc_start: 0.8539 (m-80) cc_final: 0.8332 (m-80) REVERT: H 100 SER cc_start: 0.8158 (OUTLIER) cc_final: 0.7575 (m) REVERT: L 61 ARG cc_start: 0.7437 (ttp-110) cc_final: 0.7088 (ttp80) REVERT: P 37 ARG cc_start: 0.7269 (mpp80) cc_final: 0.7030 (mtp85) REVERT: P 87 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7991 (ppp) REVERT: Q 38 ARG cc_start: 0.8063 (ttt-90) cc_final: 0.7681 (tmm-80) REVERT: Q 46 GLU cc_start: 0.8194 (tt0) cc_final: 0.7556 (tt0) REVERT: Q 72 ASP cc_start: 0.7215 (t70) cc_final: 0.6833 (t70) REVERT: A 48 LYS cc_start: 0.8228 (mttt) cc_final: 0.7795 (tmtt) REVERT: A 284 LYS cc_start: 0.8704 (mttm) cc_final: 0.8389 (mtpm) REVERT: B 84 LEU cc_start: 0.7879 (tp) cc_final: 0.7624 (tm) REVERT: B 175 VAL cc_start: 0.8637 (m) cc_final: 0.8397 (p) REVERT: C 64 ASP cc_start: 0.7567 (m-30) cc_final: 0.6987 (m-30) REVERT: C 92 SER cc_start: 0.8385 (t) cc_final: 0.8025 (m) REVERT: C 128 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: C 163 ASN cc_start: 0.7856 (m-40) cc_final: 0.6961 (p0) REVERT: C 196 ASP cc_start: 0.7796 (t0) cc_final: 0.7481 (t70) REVERT: C 267 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8387 (tp) REVERT: J 3 GLN cc_start: 0.8745 (tt0) cc_final: 0.8482 (tt0) REVERT: J 21 SER cc_start: 0.8113 (t) cc_final: 0.7889 (m) REVERT: J 38 ARG cc_start: 0.7831 (ptm160) cc_final: 0.7288 (ptm160) REVERT: J 46 GLU cc_start: 0.7723 (tt0) cc_final: 0.6921 (tt0) REVERT: J 72 ASP cc_start: 0.7195 (t70) cc_final: 0.6391 (t70) REVERT: K 37 ARG cc_start: 0.7726 (mtt90) cc_final: 0.7408 (mtp85) REVERT: K 43 ARG cc_start: 0.8203 (ttp80) cc_final: 0.8000 (ttp-170) REVERT: K 95 GLN cc_start: 0.8890 (tm-30) cc_final: 0.7806 (tt0) outliers start: 41 outliers final: 27 residues processed: 212 average time/residue: 0.4886 time to fit residues: 113.2154 Evaluate side-chains 210 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 87 MET Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 40 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 GLN C 59 ASN K 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.150147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105446 restraints weight = 13683.146| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.65 r_work: 0.3199 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11431 Z= 0.131 Angle : 0.558 9.465 15530 Z= 0.285 Chirality : 0.045 0.323 1730 Planarity : 0.005 0.062 1989 Dihedral : 7.158 114.370 1781 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.34 % Allowed : 16.93 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: 0.15 (0.23), residues: 1418 helix: -0.49 (0.59), residues: 84 sheet: 0.61 (0.25), residues: 448 loop : -0.04 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 67 TYR 0.027 0.002 TYR K 93 PHE 0.020 0.002 PHE H 27 TRP 0.012 0.001 TRP Q 47 HIS 0.004 0.001 HIS K 91 Details of bonding type rmsd covalent geometry : bond 0.00302 (11401) covalent geometry : angle 0.54764 (15459) SS BOND : bond 0.00179 ( 19) SS BOND : angle 0.73916 ( 38) hydrogen bonds : bond 0.02909 ( 367) hydrogen bonds : angle 5.93725 ( 1023) link_BETA1-4 : bond 0.00360 ( 3) link_BETA1-4 : angle 1.43292 ( 9) link_BETA1-6 : bond 0.00508 ( 1) link_BETA1-6 : angle 1.32464 ( 3) link_NAG-ASN : bond 0.01034 ( 7) link_NAG-ASN : angle 2.75732 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7539 (mp0) REVERT: H 32 TYR cc_start: 0.8731 (m-80) cc_final: 0.8318 (m-80) REVERT: H 46 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7256 (mm-30) REVERT: H 75 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8610 (mmtm) REVERT: H 100 SER cc_start: 0.8157 (OUTLIER) cc_final: 0.7524 (m) REVERT: L 61 ARG cc_start: 0.7423 (ttp-110) cc_final: 0.7068 (ttp80) REVERT: P 37 ARG cc_start: 0.7256 (mpp80) cc_final: 0.7052 (mtp85) REVERT: P 87 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7982 (ppp) REVERT: Q 38 ARG cc_start: 0.8056 (ttt-90) cc_final: 0.7666 (tmm-80) REVERT: Q 46 GLU cc_start: 0.8154 (tt0) cc_final: 0.7499 (tt0) REVERT: Q 72 ASP cc_start: 0.7212 (t70) cc_final: 0.6834 (t70) REVERT: A 48 LYS cc_start: 0.8234 (mttt) cc_final: 0.7815 (tmtt) REVERT: B 175 VAL cc_start: 0.8629 (m) cc_final: 0.8412 (p) REVERT: C 64 ASP cc_start: 0.7555 (m-30) cc_final: 0.6983 (m-30) REVERT: C 92 SER cc_start: 0.8396 (t) cc_final: 0.8034 (m) REVERT: C 128 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: C 163 ASN cc_start: 0.7852 (m-40) cc_final: 0.7169 (p0) REVERT: C 196 ASP cc_start: 0.7780 (t0) cc_final: 0.7461 (t70) REVERT: J 3 GLN cc_start: 0.8737 (tt0) cc_final: 0.8396 (tt0) REVERT: J 21 SER cc_start: 0.8174 (t) cc_final: 0.7950 (m) REVERT: J 38 ARG cc_start: 0.7832 (ptm160) cc_final: 0.7144 (ptm160) REVERT: J 46 GLU cc_start: 0.7750 (tt0) cc_final: 0.6995 (tt0) REVERT: J 52 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6570 (mp) REVERT: J 72 ASP cc_start: 0.7167 (t70) cc_final: 0.6365 (t70) REVERT: K 37 ARG cc_start: 0.7724 (mtt90) cc_final: 0.7407 (mtp85) REVERT: K 95 GLN cc_start: 0.8902 (tm-30) cc_final: 0.7774 (tt0) outliers start: 40 outliers final: 26 residues processed: 207 average time/residue: 0.5054 time to fit residues: 114.1480 Evaluate side-chains 204 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 87 MET Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 40 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 110 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 12 optimal weight: 0.0270 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 ASN K 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.144369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099442 restraints weight = 13799.268| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.66 r_work: 0.3195 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11431 Z= 0.147 Angle : 0.575 11.613 15530 Z= 0.294 Chirality : 0.046 0.384 1730 Planarity : 0.005 0.063 1989 Dihedral : 7.416 112.279 1781 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.84 % Allowed : 17.26 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: 0.13 (0.23), residues: 1418 helix: -0.56 (0.59), residues: 84 sheet: 0.64 (0.25), residues: 443 loop : -0.07 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 67 TYR 0.026 0.002 TYR K 93 PHE 0.019 0.002 PHE H 27 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00342 (11401) covalent geometry : angle 0.56686 (15459) SS BOND : bond 0.00197 ( 19) SS BOND : angle 0.79723 ( 38) hydrogen bonds : bond 0.03038 ( 367) hydrogen bonds : angle 5.98431 ( 1023) link_BETA1-4 : bond 0.00311 ( 3) link_BETA1-4 : angle 1.42710 ( 9) link_BETA1-6 : bond 0.00580 ( 1) link_BETA1-6 : angle 1.38745 ( 3) link_NAG-ASN : bond 0.01005 ( 7) link_NAG-ASN : angle 2.45629 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7509 (mp0) REVERT: H 32 TYR cc_start: 0.8699 (m-80) cc_final: 0.8284 (m-80) REVERT: H 46 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7232 (mm-30) REVERT: H 75 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8592 (mmtm) REVERT: H 100 SER cc_start: 0.8143 (OUTLIER) cc_final: 0.7535 (m) REVERT: L 61 ARG cc_start: 0.7394 (ttp-110) cc_final: 0.7036 (ttp80) REVERT: P 87 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7968 (ppp) REVERT: Q 38 ARG cc_start: 0.8032 (ttt-90) cc_final: 0.7628 (tmm-80) REVERT: Q 46 GLU cc_start: 0.8133 (tt0) cc_final: 0.7456 (tt0) REVERT: Q 72 ASP cc_start: 0.7198 (t70) cc_final: 0.6811 (t70) REVERT: A 48 LYS cc_start: 0.8191 (mttt) cc_final: 0.7765 (tmtt) REVERT: A 196 ASP cc_start: 0.6882 (t0) cc_final: 0.6421 (t70) REVERT: B 175 VAL cc_start: 0.8601 (m) cc_final: 0.8381 (p) REVERT: C 64 ASP cc_start: 0.7517 (m-30) cc_final: 0.6917 (m-30) REVERT: C 92 SER cc_start: 0.8363 (t) cc_final: 0.7991 (m) REVERT: C 128 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: C 163 ASN cc_start: 0.7854 (m-40) cc_final: 0.7161 (p0) REVERT: C 196 ASP cc_start: 0.7827 (t0) cc_final: 0.7500 (t70) REVERT: J 3 GLN cc_start: 0.8736 (tt0) cc_final: 0.8397 (tt0) REVERT: J 21 SER cc_start: 0.8140 (t) cc_final: 0.7920 (m) REVERT: J 38 ARG cc_start: 0.7810 (ptm160) cc_final: 0.7146 (ptm160) REVERT: J 46 GLU cc_start: 0.7789 (tt0) cc_final: 0.7035 (tt0) REVERT: J 72 ASP cc_start: 0.7143 (t70) cc_final: 0.6325 (t70) REVERT: K 37 ARG cc_start: 0.7690 (mtt90) cc_final: 0.7363 (mtp85) REVERT: K 95 GLN cc_start: 0.8908 (tm-30) cc_final: 0.7726 (tt0) outliers start: 34 outliers final: 27 residues processed: 202 average time/residue: 0.4866 time to fit residues: 107.4311 Evaluate side-chains 209 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 87 MET Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 40 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 75 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 131 optimal weight: 6.9990 chunk 92 optimal weight: 0.0870 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 GLN C 59 ASN K 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.150886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106189 restraints weight = 13758.581| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.66 r_work: 0.3207 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11431 Z= 0.131 Angle : 0.562 12.462 15530 Z= 0.286 Chirality : 0.045 0.271 1730 Planarity : 0.005 0.062 1989 Dihedral : 7.144 105.470 1781 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.92 % Allowed : 17.35 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: 0.17 (0.23), residues: 1418 helix: -0.66 (0.57), residues: 90 sheet: 0.71 (0.25), residues: 447 loop : -0.05 (0.22), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 67 TYR 0.025 0.002 TYR K 93 PHE 0.019 0.001 PHE H 27 TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS K 91 Details of bonding type rmsd covalent geometry : bond 0.00303 (11401) covalent geometry : angle 0.55496 (15459) SS BOND : bond 0.00188 ( 19) SS BOND : angle 0.73312 ( 38) hydrogen bonds : bond 0.02898 ( 367) hydrogen bonds : angle 5.91097 ( 1023) link_BETA1-4 : bond 0.00339 ( 3) link_BETA1-4 : angle 1.41322 ( 9) link_BETA1-6 : bond 0.00504 ( 1) link_BETA1-6 : angle 1.29893 ( 3) link_NAG-ASN : bond 0.00933 ( 7) link_NAG-ASN : angle 2.27164 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5645.30 seconds wall clock time: 96 minutes 46.33 seconds (5806.33 seconds total)