Starting phenix.real_space_refine on Sat Feb 7 12:33:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z6r_39802/02_2026/8z6r_39802.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z6r_39802/02_2026/8z6r_39802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z6r_39802/02_2026/8z6r_39802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z6r_39802/02_2026/8z6r_39802.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z6r_39802/02_2026/8z6r_39802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z6r_39802/02_2026/8z6r_39802.map" } resolution = 2.87 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= 0.002 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 164 5.16 5 C 21452 2.51 5 N 5536 2.21 5 O 6402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33554 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8229 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 57, 'TRANS': 993} Chain breaks: 11 Chain: "D" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1419 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 13, 'TRANS': 177} Chain breaks: 4 Chain: "E" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1544 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 10, 'TRANS': 191} Chain breaks: 3 Chain: "F" Number of atoms: 1429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1429 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 13, 'TRANS': 178} Chain breaks: 4 Chain: "G" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1510 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 3 Chain: "H" Number of atoms: 1429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1429 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 13, 'TRANS': 178} Chain breaks: 4 Chain: "I" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1544 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 10, 'TRANS': 191} Chain breaks: 3 Chain: "B" Number of atoms: 8221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8221 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 57, 'TRANS': 992} Chain breaks: 12 Chain: "C" Number of atoms: 8229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8229 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 57, 'TRANS': 993} Chain breaks: 11 Time building chain proxies: 8.32, per 1000 atoms: 0.25 Number of scatterers: 33554 At special positions: 0 Unit cell: (143.528, 140.732, 226.476, 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 164 16.00 O 6402 8.00 N 5536 7.00 C 21452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 742 " - pdb=" SG CYS A 764 " distance=2.03 Simple disulfide: pdb=" SG CYS A 747 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A1036 " - pdb=" SG CYS A1047 " distance=2.03 Simple disulfide: pdb=" SG CYS A1086 " - pdb=" SG CYS A1130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 104 " distance=2.03 Simple disulfide: pdb=" SG CYS D 155 " - pdb=" SG CYS D 214 " distance=2.03 Simple disulfide: pdb=" SG CYS E 155 " - pdb=" SG CYS E 211 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 104 " distance=2.03 Simple disulfide: pdb=" SG CYS F 155 " - pdb=" SG CYS F 214 " distance=2.03 Simple disulfide: pdb=" SG CYS G 155 " - pdb=" SG CYS G 211 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 742 " - pdb=" SG CYS B 764 " distance=2.03 Simple disulfide: pdb=" SG CYS B 747 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B1036 " - pdb=" SG CYS B1047 " distance=2.03 Simple disulfide: pdb=" SG CYS B1086 " - pdb=" SG CYS B1130 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 742 " - pdb=" SG CYS C 764 " distance=2.03 Simple disulfide: pdb=" SG CYS C 747 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C1036 " - pdb=" SG CYS C1047 " distance=2.03 Simple disulfide: pdb=" SG CYS C1086 " - pdb=" SG CYS C1130 " 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 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.4 seconds 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8052 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 77 sheets defined 19.5% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.564A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 741 through 747 Processing helix chain 'A' and resid 750 through 758 removed outlier: 3.556A pdb=" N LEU A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 761 No H-bonds generated for 'chain 'A' and resid 759 through 761' Processing helix chain 'A' and resid 762 through 787 Processing helix chain 'A' and resid 820 through 830 removed outlier: 3.551A pdb=" N LEU A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 828 " --> pdb=" O ASP A 824 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 830 " --> pdb=" O LEU A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 860 Processing helix chain 'A' and resid 870 through 889 Processing helix chain 'A' and resid 890 through 895 removed outlier: 3.744A pdb=" N ALA A 894 " --> pdb=" O TRP A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 913 removed outlier: 3.746A pdb=" N ALA A 907 " --> pdb=" O PRO A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 945 removed outlier: 4.278A pdb=" N LEU A 920 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 926 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 948 No H-bonds generated for 'chain 'A' and resid 946 through 948' Processing helix chain 'A' and resid 949 through 969 Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 980 through 988 removed outlier: 3.510A pdb=" N ILE A 984 " --> pdb=" O VAL A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1037 removed outlier: 3.511A pdb=" N GLU A 994 " --> pdb=" O PRO A 990 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL A 995 " --> pdb=" O PRO A 991 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN A 996 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG A 999 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1150 removed outlier: 3.539A pdb=" N GLU A1148 " --> pdb=" O PRO A1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 removed outlier: 3.561A pdb=" N GLU D 99 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 148 removed outlier: 3.510A pdb=" N ALA D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 208 removed outlier: 3.715A pdb=" N SER D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.722A pdb=" N GLY E 49 " --> pdb=" O PRO E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 72 removed outlier: 3.923A pdb=" N GLN E 72 " --> pdb=" O PRO E 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 69 through 72' Processing helix chain 'E' and resid 95 through 99 removed outlier: 3.504A pdb=" N ASP E 98 " --> pdb=" O LYS E 95 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR E 99 " --> pdb=" O ALA E 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 95 through 99' Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'F' and resid 95 through 99 removed outlier: 3.623A pdb=" N GLU F 99 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 148 Processing helix chain 'F' and resid 202 through 208 Processing helix chain 'G' and resid 69 through 72 removed outlier: 4.071A pdb=" N GLN G 72 " --> pdb=" O PRO G 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 69 through 72' Processing helix chain 'G' and resid 95 through 99 removed outlier: 3.557A pdb=" N ASP G 98 " --> pdb=" O LYS G 95 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR G 99 " --> pdb=" O ALA G 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 95 through 99' Processing helix chain 'G' and resid 171 through 173 No H-bonds generated for 'chain 'G' and resid 171 through 173' Processing helix chain 'H' and resid 95 through 99 removed outlier: 4.252A pdb=" N GLU H 99 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 148 removed outlier: 3.538A pdb=" N ALA H 148 " --> pdb=" O GLU H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 209 removed outlier: 4.070A pdb=" N HIS H 209 " --> pdb=" O GLN H 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 37 Processing helix chain 'I' and resid 69 through 72 removed outlier: 4.074A pdb=" N GLN I 72 " --> pdb=" O PRO I 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 69 through 72' Processing helix chain 'I' and resid 95 through 99 removed outlier: 3.587A pdb=" N ASP I 98 " --> pdb=" O LYS I 95 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR I 99 " --> pdb=" O ALA I 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 95 through 99' Processing helix chain 'I' and resid 171 through 173 No H-bonds generated for 'chain 'I' and resid 171 through 173' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 741 through 747 Processing helix chain 'B' and resid 751 through 758 Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 762 through 787 Processing helix chain 'B' and resid 820 through 830 removed outlier: 3.515A pdb=" N LEU B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 830 " --> pdb=" O LEU B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 859 Processing helix chain 'B' and resid 870 through 889 Processing helix chain 'B' and resid 890 through 895 removed outlier: 3.794A pdb=" N ALA B 894 " --> pdb=" O TRP B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 913 Processing helix chain 'B' and resid 916 through 945 removed outlier: 4.331A pdb=" N LEU B 920 " --> pdb=" O THR B 916 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS B 925 " --> pdb=" O TYR B 921 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU B 926 " --> pdb=" O GLU B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 948 No H-bonds generated for 'chain 'B' and resid 946 through 948' Processing helix chain 'B' and resid 949 through 969 removed outlier: 3.790A pdb=" N VAL B 955 " --> pdb=" O LYS B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 972 No H-bonds generated for 'chain 'B' and resid 970 through 972' Processing helix chain 'B' and resid 980 through 988 Processing helix chain 'B' and resid 989 through 1037 removed outlier: 4.752A pdb=" N VAL B 995 " --> pdb=" O PRO B 991 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN B 996 " --> pdb=" O GLU B 992 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B 999 " --> pdb=" O VAL B 995 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B1000 " --> pdb=" O GLN B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1150 removed outlier: 3.589A pdb=" N GLU B1148 " --> pdb=" O PRO B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 741 through 747 Processing helix chain 'C' and resid 751 through 758 removed outlier: 3.570A pdb=" N LEU C 758 " --> pdb=" O SER C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 761 No H-bonds generated for 'chain 'C' and resid 759 through 761' Processing helix chain 'C' and resid 762 through 787 Processing helix chain 'C' and resid 820 through 830 removed outlier: 3.522A pdb=" N LEU C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 860 Processing helix chain 'C' and resid 870 through 889 Processing helix chain 'C' and resid 890 through 895 removed outlier: 3.893A pdb=" N ALA C 894 " --> pdb=" O TRP C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 914 removed outlier: 3.619A pdb=" N ALA C 907 " --> pdb=" O PRO C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 945 removed outlier: 4.249A pdb=" N LEU C 920 " --> pdb=" O THR C 916 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS C 925 " --> pdb=" O TYR C 921 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU C 926 " --> pdb=" O GLU C 922 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 948 No H-bonds generated for 'chain 'C' and resid 946 through 948' Processing helix chain 'C' and resid 949 through 969 Processing helix chain 'C' and resid 970 through 972 No H-bonds generated for 'chain 'C' and resid 970 through 972' Processing helix chain 'C' and resid 980 through 988 Processing helix chain 'C' and resid 989 through 1037 removed outlier: 4.994A pdb=" N VAL C 995 " --> pdb=" O PRO C 991 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN C 996 " --> pdb=" O GLU C 992 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG C 999 " --> pdb=" O VAL C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1144 through 1150 removed outlier: 3.854A pdb=" N GLU C1148 " --> pdb=" O PRO C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.515A pdb=" N SER A 61 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 8.043A pdb=" N ASN A 62 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR A 269 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 261 " --> pdb=" O HIS A 70 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 56 removed outlier: 6.925A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 85 through 86 removed outlier: 4.169A pdb=" N GLY A 104 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA A 243 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE A 102 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 172 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 168 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.480A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.586A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.115A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.760A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.044A pdb=" N GLU A 654 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR A 700 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 705 through 708 Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 732 removed outlier: 6.713A pdb=" N SER A 715 " --> pdb=" O THR A1080 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR A1080 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA A 717 " --> pdb=" O ASN A1078 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN A1078 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU A1076 " --> pdb=" O PRO A 719 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLY A1063 " --> pdb=" O SER A1059 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER A1059 " --> pdb=" O GLY A1063 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A1065 " --> pdb=" O PRO A1057 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A1067 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER A1055 " --> pdb=" O LEU A1067 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL A1069 " --> pdb=" O LEU A1053 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 739 through 740 Processing sheet with id=AB6, first strand: chain 'A' and resid 791 through 794 removed outlier: 5.550A pdb=" N ILE A 792 " --> pdb=" O ASN C 707 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1085 through 1086 removed outlier: 4.538A pdb=" N ALA A1091 " --> pdb=" O SER A1127 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1098 through 1101 Processing sheet with id=AB9, first strand: chain 'D' and resid 9 through 14 removed outlier: 6.956A pdb=" N VAL D 11 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU D 127 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY D 13 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN D 43 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 9 through 14 removed outlier: 6.956A pdb=" N VAL D 11 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU D 127 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY D 13 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AC3, first strand: chain 'D' and resid 135 through 139 removed outlier: 3.549A pdb=" N VAL D 154 " --> pdb=" O PHE D 139 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS D 155 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER D 197 " --> pdb=" O CYS D 155 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP D 159 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR D 193 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU D 181 " --> pdb=" O TYR D 198 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 166 through 170 Processing sheet with id=AC5, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.886A pdb=" N GLY E 54 " --> pdb=" O TRP E 41 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 135 through 138 removed outlier: 3.586A pdb=" N VAL E 157 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 193 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP E 159 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N TYR E 191 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 135 through 138 removed outlier: 3.586A pdb=" N VAL E 157 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 193 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP E 159 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N TYR E 191 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 166 through 169 removed outlier: 4.158A pdb=" N THR E 166 " --> pdb=" O ASN E 214 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 9 through 14 removed outlier: 3.515A pdb=" N THR F 125 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLN F 43 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 9 through 14 removed outlier: 3.515A pdb=" N THR F 125 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER F 106 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AD4, first strand: chain 'F' and resid 135 through 139 removed outlier: 3.947A pdb=" N VAL F 154 " --> pdb=" O PHE F 139 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS F 155 " --> pdb=" O SER F 197 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER F 197 " --> pdb=" O CYS F 155 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TYR F 193 " --> pdb=" O ASP F 159 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER F 196 " --> pdb=" O THR F 183 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU F 181 " --> pdb=" O TYR F 198 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 166 through 170 removed outlier: 3.718A pdb=" N SER F 213 " --> pdb=" O LYS F 170 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 20 through 24 removed outlier: 4.037A pdb=" N ILE G 21 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 66 through 67 removed outlier: 3.525A pdb=" N ARG G 66 " --> pdb=" O ILE G 55 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE G 55 " --> pdb=" O ARG G 66 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N TRP G 52 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG G 43 " --> pdb=" O TRP G 52 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY G 54 " --> pdb=" O TRP G 41 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR G 117 " --> pdb=" O ARG G 106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 66 through 67 removed outlier: 3.525A pdb=" N ARG G 66 " --> pdb=" O ILE G 55 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE G 55 " --> pdb=" O ARG G 66 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N TRP G 52 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG G 43 " --> pdb=" O TRP G 52 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY G 54 " --> pdb=" O TRP G 41 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR G 122 " --> pdb=" O TYR G 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 135 through 138 removed outlier: 3.797A pdb=" N ASP G 159 " --> pdb=" O TYR G 191 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR G 191 " --> pdb=" O ASP G 159 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 135 through 138 removed outlier: 3.797A pdb=" N ASP G 159 " --> pdb=" O TYR G 191 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR G 191 " --> pdb=" O ASP G 159 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 165 through 169 Processing sheet with id=AE3, first strand: chain 'H' and resid 9 through 14 removed outlier: 3.659A pdb=" N THR H 125 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN H 43 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU H 52 " --> pdb=" O GLN H 43 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 9 through 14 removed outlier: 3.659A pdb=" N THR H 125 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER H 106 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 19 through 23 Processing sheet with id=AE6, first strand: chain 'H' and resid 135 through 139 removed outlier: 3.676A pdb=" N VAL H 154 " --> pdb=" O PHE H 139 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS H 155 " --> pdb=" O SER H 197 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER H 197 " --> pdb=" O CYS H 155 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP H 159 " --> pdb=" O TYR H 193 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N TYR H 193 " --> pdb=" O ASP H 159 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU H 181 " --> pdb=" O TYR H 198 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 166 through 170 Processing sheet with id=AE8, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.682A pdb=" N ILE I 21 " --> pdb=" O LEU I 89 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 66 through 67 removed outlier: 3.621A pdb=" N MET I 53 " --> pdb=" O TRP I 41 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TRP I 41 " --> pdb=" O MET I 53 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE I 55 " --> pdb=" O ILE I 39 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE I 39 " --> pdb=" O ILE I 55 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 135 through 138 removed outlier: 3.533A pdb=" N SER I 195 " --> pdb=" O CYS I 155 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL I 157 " --> pdb=" O LEU I 193 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU I 193 " --> pdb=" O VAL I 157 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP I 159 " --> pdb=" O TYR I 191 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 135 through 138 removed outlier: 3.533A pdb=" N SER I 195 " --> pdb=" O CYS I 155 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL I 157 " --> pdb=" O LEU I 193 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU I 193 " --> pdb=" O VAL I 157 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP I 159 " --> pdb=" O TYR I 191 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 165 through 169 removed outlier: 3.608A pdb=" N THR I 166 " --> pdb=" O ASN I 214 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 24 through 32 removed outlier: 3.657A pdb=" N SER B 61 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 91 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 49 through 56 removed outlier: 4.124A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.753A pdb=" N SER B 172 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE B 168 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 141 through 144 Processing sheet with id=AF8, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.354A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.539A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.547A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AG3, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.501A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.026A pdb=" N GLU B 654 " --> pdb=" O ALA B 698 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR B 700 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 705 through 708 removed outlier: 6.786A pdb=" N ALA B 705 " --> pdb=" O ILE C 792 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LYS C 794 " --> pdb=" O ALA B 705 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ASN B 707 " --> pdb=" O LYS C 794 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'B' and resid 715 through 732 removed outlier: 6.778A pdb=" N SER B 715 " --> pdb=" O THR B1080 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR B1080 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA B 717 " --> pdb=" O ASN B1078 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN B1078 " --> pdb=" O ALA B 717 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU B1076 " --> pdb=" O PRO B 719 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR B1071 " --> pdb=" O HIS B1052 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS B1052 " --> pdb=" O TYR B1071 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 739 through 740 Processing sheet with id=AG8, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 4.521A pdb=" N ALA B1091 " --> pdb=" O SER B1127 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 1098 through 1101 Processing sheet with id=AH1, first strand: chain 'C' and resid 24 through 32 removed outlier: 3.510A pdb=" N SER C 61 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASN C 62 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR C 269 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 261 " --> pdb=" O HIS C 70 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 48 through 56 removed outlier: 3.736A pdb=" N VAL C 48 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AH4, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.562A pdb=" N LEU C 241 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLY C 104 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA C 243 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE C 102 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE C 168 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.437A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.597A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.128A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AH9, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.527A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.930A pdb=" N GLU C 654 " --> pdb=" O ALA C 698 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N THR C 700 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 715 through 732 removed outlier: 6.766A pdb=" N SER C 715 " --> pdb=" O THR C1080 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR C1080 " --> pdb=" O SER C 715 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA C 717 " --> pdb=" O ASN C1078 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN C1078 " --> pdb=" O ALA C 717 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU C1076 " --> pdb=" O PRO C 719 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLY C1063 " --> pdb=" O SER C1059 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N SER C1059 " --> pdb=" O GLY C1063 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C1065 " --> pdb=" O PRO C1057 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU C1067 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER C1055 " --> pdb=" O LEU C1067 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL C1069 " --> pdb=" O LEU C1053 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 739 through 740 Processing sheet with id=AI4, first strand: chain 'C' and resid 1124 through 1129 removed outlier: 3.540A pdb=" N SER C1127 " --> pdb=" O ALA C1091 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA C1091 " --> pdb=" O SER C1127 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 1098 through 1101 1292 hydrogen bonds defined for protein. 3474 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: 10.03 Time building geometry restraints manager: 3.90 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: 10588 1.34 - 1.46: 6497 1.46 - 1.58: 17054 1.58 - 1.70: 0 1.70 - 1.82: 211 Bond restraints: 34350 Sorted by residual: bond pdb=" C SER C 490 " pdb=" N PRO C 491 " ideal model delta sigma weight residual 1.334 1.377 -0.043 8.40e-03 1.42e+04 2.64e+01 bond pdb=" CA PRO C 491 " pdb=" C PRO C 491 " ideal model delta sigma weight residual 1.520 1.485 0.036 9.50e-03 1.11e+04 1.42e+01 bond pdb=" CA PRO C 491 " pdb=" CB PRO C 491 " ideal model delta sigma weight residual 1.536 1.497 0.039 1.39e-02 5.18e+03 7.96e+00 bond pdb=" C PRO C 491 " pdb=" N LEU C 492 " ideal model delta sigma weight residual 1.332 1.301 0.030 1.35e-02 5.49e+03 5.08e+00 bond pdb=" N ASN C 481 " pdb=" CA ASN C 481 " ideal model delta sigma weight residual 1.457 1.430 0.028 1.29e-02 6.01e+03 4.64e+00 ... (remaining 34345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 46275 1.81 - 3.63: 414 3.63 - 5.44: 37 5.44 - 7.25: 4 7.25 - 9.07: 2 Bond angle restraints: 46732 Sorted by residual: angle pdb=" C SER C 490 " pdb=" N PRO C 491 " pdb=" CA PRO C 491 " ideal model delta sigma weight residual 120.83 112.64 8.19 1.02e+00 9.61e-01 6.45e+01 angle pdb=" N VAL A 341 " pdb=" CA VAL A 341 " pdb=" C VAL A 341 " ideal model delta sigma weight residual 113.53 109.66 3.87 9.80e-01 1.04e+00 1.56e+01 angle pdb=" N VAL A 483 " pdb=" CA VAL A 483 " pdb=" C VAL A 483 " ideal model delta sigma weight residual 106.72 112.99 -6.27 1.59e+00 3.96e-01 1.56e+01 angle pdb=" N VAL A 733 " pdb=" CA VAL A 733 " pdb=" C VAL A 733 " ideal model delta sigma weight residual 112.96 109.59 3.37 1.00e+00 1.00e+00 1.13e+01 angle pdb=" C PRO C 491 " pdb=" CA PRO C 491 " pdb=" CB PRO C 491 " ideal model delta sigma weight residual 110.52 106.16 4.36 1.36e+00 5.41e-01 1.03e+01 ... (remaining 46727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 19826 17.38 - 34.76: 495 34.76 - 52.14: 68 52.14 - 69.52: 2 69.52 - 86.90: 2 Dihedral angle restraints: 20393 sinusoidal: 7866 harmonic: 12527 Sorted by residual: dihedral pdb=" CB CYS C 747 " pdb=" SG CYS C 747 " pdb=" SG CYS C 753 " pdb=" CB CYS C 753 " ideal model delta sinusoidal sigma weight residual -86.00 -59.16 -26.84 1 1.00e+01 1.00e-02 1.03e+01 dihedral pdb=" CA ILE B 101 " pdb=" C ILE B 101 " pdb=" N ILE B 102 " pdb=" CA ILE B 102 " ideal model delta harmonic sigma weight residual -180.00 -164.30 -15.70 0 5.00e+00 4.00e-02 9.86e+00 dihedral pdb=" C PRO C 491 " pdb=" N PRO C 491 " pdb=" CA PRO C 491 " pdb=" CB PRO C 491 " ideal model delta harmonic sigma weight residual -120.70 -112.89 -7.81 0 2.50e+00 1.60e-01 9.77e+00 ... (remaining 20390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3319 0.027 - 0.055: 1198 0.055 - 0.082: 289 0.082 - 0.109: 408 0.109 - 0.137: 74 Chirality restraints: 5288 Sorted by residual: chirality pdb=" CB ILE B 410 " pdb=" CA ILE B 410 " pdb=" CG1 ILE B 410 " pdb=" CG2 ILE B 410 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CB ILE C 410 " pdb=" CA ILE C 410 " pdb=" CG1 ILE C 410 " pdb=" CG2 ILE C 410 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ASN A 487 " pdb=" N ASN A 487 " pdb=" C ASN A 487 " pdb=" CB ASN A 487 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 5285 not shown) Planarity restraints: 5974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 472 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C ILE C 472 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE C 472 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR C 473 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 485 " 0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO B 486 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 486 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 486 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 490 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO C 491 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 491 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 491 " 0.030 5.00e-02 4.00e+02 ... (remaining 5971 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5196 2.77 - 3.30: 30789 3.30 - 3.83: 55064 3.83 - 4.37: 62726 4.37 - 4.90: 113064 Nonbonded interactions: 266839 Sorted by model distance: nonbonded pdb=" OH TYR B 760 " pdb=" OD1 ASP B 998 " model vdw 2.232 3.040 nonbonded pdb=" OG SER A 888 " pdb=" OG1 THR A 891 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR A 760 " pdb=" OD1 ASP A 998 " model vdw 2.237 3.040 nonbonded pdb=" OG SER C 888 " pdb=" OG1 THR C 891 " model vdw 2.243 3.040 nonbonded pdb=" O VAL A 367 " pdb=" ND2 ASN A 370 " model vdw 2.252 3.120 ... (remaining 266834 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' and (resid 18 through 486 or resid 488 through 1150)) selection = chain 'B' selection = (chain 'C' and (resid 18 through 486 or resid 488 through 1150)) } ncs_group { reference = chain 'D' selection = (chain 'F' and (resid 2 through 208 or resid 212 through 219)) selection = (chain 'H' and (resid 2 through 208 or resid 212 through 219)) } ncs_group { reference = (chain 'E' and resid 5 through 226) selection = chain 'G' selection = (chain 'I' and resid 5 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 35.290 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 : 0.002 0.043 34401 Z= 0.098 Angle : 0.425 9.067 46834 Z= 0.235 Chirality : 0.040 0.137 5288 Planarity : 0.004 0.051 5974 Dihedral : 7.146 86.895 12188 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.95 % Rotamer: Outliers : 1.89 % Allowed : 4.40 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.56 (0.12), residues: 4201 helix: 0.42 (0.19), residues: 709 sheet: -0.57 (0.15), residues: 1127 loop : -1.79 (0.11), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1023 TYR 0.011 0.001 TYR A 489 PHE 0.006 0.001 PHE A1099 TRP 0.006 0.000 TRP I 52 HIS 0.002 0.000 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00159 (34350) covalent geometry : angle 0.42522 (46732) SS BOND : bond 0.00127 ( 51) SS BOND : angle 0.47782 ( 102) hydrogen bonds : bond 0.22785 ( 1238) hydrogen bonds : angle 8.52125 ( 3474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 548 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 80 LYS cc_start: 0.7581 (mmmm) cc_final: 0.7018 (mptt) REVERT: D 193 TYR cc_start: 0.7043 (m-80) cc_final: 0.6519 (m-80) REVERT: E 144 LYS cc_start: 0.0074 (mttt) cc_final: -0.0548 (mtpt) REVERT: E 146 THR cc_start: 0.2442 (p) cc_final: 0.2005 (t) REVERT: G 113 ILE cc_start: 0.7772 (tp) cc_final: 0.7555 (tp) REVERT: I 41 TRP cc_start: 0.5751 (m100) cc_final: 0.5524 (m100) REVERT: I 144 LYS cc_start: 0.1416 (mttt) cc_final: 0.0814 (mtmt) outliers start: 71 outliers final: 14 residues processed: 609 average time/residue: 0.6736 time to fit residues: 488.6635 Evaluate side-chains 271 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 257 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 197 optimal weight: 40.0000 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 3.9990 chunk 155 optimal weight: 50.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 343 ASN A 613 GLN A 641 ASN A 876 GLN ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN D 6 GLN D 95 GLN D 149 ASN E 44 GLN E 179 HIS F 6 GLN F 95 GLN G 179 HIS H 6 GLN H 95 GLN I 3 GLN I 179 HIS B 207 HIS B 239 GLN B 519 HIS B 613 GLN B 641 ASN B 876 GLN B1015 GLN B1129 ASN C 138 ASN C 207 HIS C 239 GLN C 519 HIS C 641 ASN C 781 ASN C 876 GLN C1015 GLN C1075 GLN C1129 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.090634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.055668 restraints weight = 112090.132| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 4.12 r_work: 0.2884 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 34401 Z= 0.259 Angle : 0.654 9.446 46834 Z= 0.337 Chirality : 0.046 0.187 5288 Planarity : 0.005 0.063 5974 Dihedral : 3.677 35.407 4613 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.48 % Allowed : 10.27 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.12), residues: 4201 helix: 1.36 (0.20), residues: 708 sheet: -0.33 (0.14), residues: 1197 loop : -1.30 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 646 TYR 0.026 0.002 TYR A 501 PHE 0.022 0.002 PHE B 157 TRP 0.021 0.002 TRP G 52 HIS 0.009 0.001 HIS G 90 Details of bonding type rmsd covalent geometry : bond 0.00585 (34350) covalent geometry : angle 0.65039 (46732) SS BOND : bond 0.00348 ( 51) SS BOND : angle 1.67860 ( 102) hydrogen bonds : bond 0.04641 ( 1238) hydrogen bonds : angle 6.26956 ( 3474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 271 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.7885 (m-40) cc_final: 0.7044 (p0) REVERT: A 153 MET cc_start: 0.7827 (mpp) cc_final: 0.7542 (ptp) REVERT: A 460 LYS cc_start: 0.9287 (mmmm) cc_final: 0.8969 (mmmm) REVERT: A 991 PRO cc_start: 0.8736 (Cg_exo) cc_final: 0.8456 (Cg_endo) REVERT: A 1006 GLN cc_start: 0.9108 (tt0) cc_final: 0.8806 (tp40) REVERT: D 42 TYR cc_start: 0.7193 (m-80) cc_final: 0.6709 (m-80) REVERT: D 80 LYS cc_start: 0.8114 (mmmm) cc_final: 0.7706 (mptt) REVERT: D 161 TYR cc_start: 0.7686 (t80) cc_final: 0.7172 (t80) REVERT: D 193 TYR cc_start: 0.8028 (m-80) cc_final: 0.7749 (m-80) REVERT: D 219 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: E 115 LEU cc_start: 0.6376 (OUTLIER) cc_final: 0.6108 (mp) REVERT: E 144 LYS cc_start: -0.0027 (mttt) cc_final: -0.0786 (mtpt) REVERT: E 146 THR cc_start: 0.2089 (p) cc_final: 0.1701 (t) REVERT: E 224 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6738 (pttp) REVERT: F 53 MET cc_start: 0.8694 (ttp) cc_final: 0.8336 (ptt) REVERT: F 55 TYR cc_start: 0.8207 (p90) cc_final: 0.7748 (p90) REVERT: F 56 ASP cc_start: 0.8031 (m-30) cc_final: 0.7046 (p0) REVERT: F 75 ARG cc_start: 0.8837 (ptt90) cc_final: 0.8110 (ptt90) REVERT: F 98 ASP cc_start: 0.4911 (p0) cc_final: 0.4652 (p0) REVERT: G 41 TRP cc_start: 0.7764 (m100) cc_final: 0.7295 (m100) REVERT: G 53 MET cc_start: 0.6498 (mtm) cc_final: 0.6018 (mtm) REVERT: G 81 ASP cc_start: 0.7098 (m-30) cc_final: 0.6625 (m-30) REVERT: G 88 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.8175 (m-10) REVERT: G 113 ILE cc_start: 0.7449 (tp) cc_final: 0.7222 (tp) REVERT: H 56 ASP cc_start: 0.6573 (p0) cc_final: 0.6315 (p0) REVERT: H 123 MET cc_start: 0.8389 (ppp) cc_final: 0.8133 (ppp) REVERT: I 24 LYS cc_start: 0.8986 (mptp) cc_final: 0.8780 (mppt) REVERT: I 41 TRP cc_start: 0.6839 (m100) cc_final: 0.5962 (m100) REVERT: I 144 LYS cc_start: 0.1073 (mttt) cc_final: 0.0235 (mtmt) REVERT: B 498 ARG cc_start: 0.9057 (mtt90) cc_final: 0.8753 (ttm-80) REVERT: B 661 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8672 (tm-30) REVERT: B 1021 GLU cc_start: 0.9283 (tt0) cc_final: 0.8980 (tp30) REVERT: C 126 ASN cc_start: 0.8518 (m-40) cc_final: 0.7647 (p0) REVERT: C 129 ILE cc_start: 0.9237 (mt) cc_final: 0.9022 (mp) REVERT: C 471 GLU cc_start: 0.8835 (pt0) cc_final: 0.8450 (pp20) REVERT: C 641 ASN cc_start: 0.7081 (OUTLIER) cc_final: 0.6667 (p0) REVERT: C 661 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8739 (tm-30) REVERT: C 784 GLU cc_start: 0.9257 (mt-10) cc_final: 0.9017 (mt-10) REVERT: C 1129 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8074 (p0) outliers start: 93 outliers final: 32 residues processed: 348 average time/residue: 0.5868 time to fit residues: 247.8154 Evaluate side-chains 258 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain G residue 88 TYR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1129 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 45 optimal weight: 4.9990 chunk 329 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 chunk 402 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN I 44 GLN B 207 HIS B 613 GLN C 207 HIS C 641 ASN C1129 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.090048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.054772 restraints weight = 112627.505| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.16 r_work: 0.2864 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 34401 Z= 0.201 Angle : 0.604 10.957 46834 Z= 0.307 Chirality : 0.045 0.179 5288 Planarity : 0.004 0.060 5974 Dihedral : 3.803 35.277 4606 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.51 % Allowed : 11.20 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.13), residues: 4201 helix: 1.86 (0.20), residues: 691 sheet: -0.21 (0.14), residues: 1187 loop : -1.14 (0.12), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 106 TYR 0.031 0.001 TYR A 501 PHE 0.034 0.001 PHE C 157 TRP 0.031 0.001 TRP E 41 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00456 (34350) covalent geometry : angle 0.60034 (46732) SS BOND : bond 0.00302 ( 51) SS BOND : angle 1.48538 ( 102) hydrogen bonds : bond 0.04043 ( 1238) hydrogen bonds : angle 5.89332 ( 3474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 236 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.7959 (m-40) cc_final: 0.7046 (p0) REVERT: A 357 ARG cc_start: 0.8728 (ttp80) cc_final: 0.8103 (ttt-90) REVERT: A 991 PRO cc_start: 0.8677 (Cg_exo) cc_final: 0.8304 (Cg_endo) REVERT: A 992 GLU cc_start: 0.8636 (mp0) cc_final: 0.8214 (mp0) REVERT: D 55 TYR cc_start: 0.8535 (p90) cc_final: 0.7659 (p90) REVERT: D 56 ASP cc_start: 0.8224 (m-30) cc_final: 0.7531 (p0) REVERT: D 161 TYR cc_start: 0.7729 (t80) cc_final: 0.7273 (t80) REVERT: D 193 TYR cc_start: 0.8120 (m-80) cc_final: 0.7755 (m-80) REVERT: D 219 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7217 (pm20) REVERT: E 41 TRP cc_start: 0.7019 (m100) cc_final: 0.6279 (m100) REVERT: E 66 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.5547 (mmt180) REVERT: E 146 THR cc_start: 0.2053 (p) cc_final: 0.1677 (t) REVERT: E 224 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6978 (pttp) REVERT: F 56 ASP cc_start: 0.8036 (m-30) cc_final: 0.7061 (p0) REVERT: F 103 TYR cc_start: 0.7899 (m-80) cc_final: 0.7390 (m-80) REVERT: G 41 TRP cc_start: 0.7861 (m100) cc_final: 0.7318 (m100) REVERT: G 53 MET cc_start: 0.6557 (mtm) cc_final: 0.6068 (mtm) REVERT: G 81 ASP cc_start: 0.7309 (m-30) cc_final: 0.6860 (m-30) REVERT: G 88 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.8411 (m-10) REVERT: G 106 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7528 (ttp80) REVERT: G 113 ILE cc_start: 0.7427 (tp) cc_final: 0.7095 (tt) REVERT: G 114 LEU cc_start: 0.5942 (OUTLIER) cc_final: 0.5707 (tm) REVERT: I 23 CYS cc_start: 0.9101 (p) cc_final: 0.8429 (t) REVERT: I 41 TRP cc_start: 0.6784 (m100) cc_final: 0.5779 (m100) REVERT: I 144 LYS cc_start: 0.0862 (mttt) cc_final: 0.0067 (mtmt) REVERT: B 314 GLN cc_start: 0.8965 (tt0) cc_final: 0.8179 (tm-30) REVERT: B 498 ARG cc_start: 0.9056 (mtt90) cc_final: 0.8593 (mtp85) REVERT: B 661 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8764 (tm-30) REVERT: B 744 MET cc_start: 0.9446 (ttp) cc_final: 0.9107 (tpp) REVERT: B 1021 GLU cc_start: 0.9312 (tt0) cc_final: 0.9053 (tm-30) REVERT: B 1111 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8907 (mtt90) REVERT: C 138 ASN cc_start: 0.6802 (t0) cc_final: 0.6400 (t0) REVERT: C 460 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9123 (mmtp) REVERT: C 471 GLU cc_start: 0.8925 (pt0) cc_final: 0.8439 (pp20) REVERT: C 641 ASN cc_start: 0.7233 (OUTLIER) cc_final: 0.6858 (p0) REVERT: C 780 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.8513 (tmmm) REVERT: C 992 GLU cc_start: 0.8733 (mp0) cc_final: 0.8477 (pm20) outliers start: 94 outliers final: 41 residues processed: 314 average time/residue: 0.6359 time to fit residues: 242.4248 Evaluate side-chains 260 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain G residue 88 TYR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 938 ILE Chi-restraints excluded: chain B residue 1111 ARG Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 780 LYS Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 230 optimal weight: 10.0000 chunk 336 optimal weight: 9.9990 chunk 340 optimal weight: 9.9990 chunk 183 optimal weight: 30.0000 chunk 367 optimal weight: 9.9990 chunk 156 optimal weight: 50.0000 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 155 optimal weight: 50.0000 chunk 271 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 781 ASN D 149 ASN ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 GLN ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 613 GLN C 138 ASN ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.086529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.050751 restraints weight = 113036.469| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 4.10 r_work: 0.2756 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 34401 Z= 0.391 Angle : 0.734 12.289 46834 Z= 0.372 Chirality : 0.048 0.205 5288 Planarity : 0.005 0.065 5974 Dihedral : 4.426 36.317 4605 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.91 % Allowed : 11.68 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.13), residues: 4201 helix: 1.59 (0.20), residues: 727 sheet: -0.37 (0.14), residues: 1222 loop : -1.15 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 190 TYR 0.027 0.002 TYR A 501 PHE 0.021 0.002 PHE I 161 TRP 0.022 0.002 TRP G 52 HIS 0.009 0.001 HIS B1062 Details of bonding type rmsd covalent geometry : bond 0.00885 (34350) covalent geometry : angle 0.73055 (46732) SS BOND : bond 0.00401 ( 51) SS BOND : angle 1.61057 ( 102) hydrogen bonds : bond 0.04634 ( 1238) hydrogen bonds : angle 5.92952 ( 3474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 204 time to evaluate : 2.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8480 (m-40) cc_final: 0.7444 (p0) REVERT: A 558 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8890 (mmmt) REVERT: A 992 GLU cc_start: 0.8786 (mp0) cc_final: 0.8555 (mp0) REVERT: A 1111 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8921 (mtt90) REVERT: D 193 TYR cc_start: 0.8384 (m-80) cc_final: 0.8164 (m-80) REVERT: D 219 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: E 66 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.5660 (mmt180) REVERT: E 146 THR cc_start: 0.2366 (p) cc_final: 0.1963 (t) REVERT: E 224 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.7043 (pttp) REVERT: F 42 TYR cc_start: 0.8145 (m-10) cc_final: 0.7901 (m-10) REVERT: F 56 ASP cc_start: 0.8275 (m-30) cc_final: 0.7341 (p0) REVERT: F 103 TYR cc_start: 0.7966 (m-80) cc_final: 0.7619 (m-80) REVERT: G 41 TRP cc_start: 0.7964 (m100) cc_final: 0.7431 (m100) REVERT: G 53 MET cc_start: 0.6767 (mtm) cc_final: 0.6269 (mtm) REVERT: G 88 TYR cc_start: 0.8780 (OUTLIER) cc_final: 0.8540 (m-10) REVERT: G 106 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7707 (ttp80) REVERT: G 113 ILE cc_start: 0.7497 (tp) cc_final: 0.7150 (tt) REVERT: H 55 TYR cc_start: 0.8423 (p90) cc_final: 0.8188 (p90) REVERT: H 56 ASP cc_start: 0.6633 (p0) cc_final: 0.5273 (p0) REVERT: H 66 LYS cc_start: 0.7903 (mttp) cc_final: 0.7682 (ptpp) REVERT: H 123 MET cc_start: 0.8563 (tmm) cc_final: 0.7805 (ppp) REVERT: H 215 GLN cc_start: 0.7394 (pt0) cc_final: 0.6992 (pp30) REVERT: I 23 CYS cc_start: 0.8919 (p) cc_final: 0.8231 (t) REVERT: I 144 LYS cc_start: 0.0797 (mttt) cc_final: -0.0108 (mtmt) REVERT: B 126 ASN cc_start: 0.8853 (m-40) cc_final: 0.7629 (p0) REVERT: B 314 GLN cc_start: 0.9074 (tt0) cc_final: 0.8367 (tm-30) REVERT: B 498 ARG cc_start: 0.9004 (mtt90) cc_final: 0.8555 (mtp85) REVERT: B 744 MET cc_start: 0.9527 (ttp) cc_final: 0.9199 (tpp) REVERT: B 983 ASP cc_start: 0.9213 (OUTLIER) cc_final: 0.8559 (t0) REVERT: B 1021 GLU cc_start: 0.9412 (tt0) cc_final: 0.9084 (tm-30) REVERT: B 1111 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8819 (mtt90) REVERT: C 126 ASN cc_start: 0.8754 (m-40) cc_final: 0.8366 (t0) REVERT: C 138 ASN cc_start: 0.7283 (t0) cc_final: 0.6819 (t0) REVERT: C 153 MET cc_start: 0.6427 (mpt) cc_final: 0.6071 (mpp) REVERT: C 460 LYS cc_start: 0.9507 (OUTLIER) cc_final: 0.9262 (mmtp) REVERT: C 471 GLU cc_start: 0.9005 (pt0) cc_final: 0.8477 (pp20) REVERT: C 780 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.8654 (tmmm) REVERT: C 992 GLU cc_start: 0.8748 (mp0) cc_final: 0.8482 (pm20) outliers start: 109 outliers final: 45 residues processed: 295 average time/residue: 0.5977 time to fit residues: 214.7866 Evaluate side-chains 247 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 192 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 1111 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 161 PHE Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 55 TYR Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain G residue 88 TYR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 938 ILE Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1111 ARG Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 780 LYS Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 25 optimal weight: 0.9990 chunk 111 optimal weight: 30.0000 chunk 90 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 326 optimal weight: 20.0000 chunk 330 optimal weight: 5.9990 chunk 375 optimal weight: 3.9990 chunk 415 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 322 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 905 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.088579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.053059 restraints weight = 112318.251| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 4.01 r_work: 0.2820 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34401 Z= 0.137 Angle : 0.589 9.591 46834 Z= 0.297 Chirality : 0.045 0.335 5288 Planarity : 0.004 0.064 5974 Dihedral : 4.154 37.052 4605 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.32 % Allowed : 12.72 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.13), residues: 4201 helix: 1.98 (0.20), residues: 721 sheet: -0.16 (0.15), residues: 1206 loop : -1.04 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 75 TYR 0.025 0.001 TYR A 501 PHE 0.024 0.001 PHE A 400 TRP 0.040 0.001 TRP E 41 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00311 (34350) covalent geometry : angle 0.58596 (46732) SS BOND : bond 0.00232 ( 51) SS BOND : angle 1.35751 ( 102) hydrogen bonds : bond 0.03767 ( 1238) hydrogen bonds : angle 5.59224 ( 3474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 210 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8255 (m-40) cc_final: 0.7209 (p0) REVERT: A 357 ARG cc_start: 0.8923 (ttp80) cc_final: 0.8229 (ttt-90) REVERT: A 983 ASP cc_start: 0.9339 (m-30) cc_final: 0.8803 (t0) REVERT: A 992 GLU cc_start: 0.8744 (mp0) cc_final: 0.8450 (mp0) REVERT: D 161 TYR cc_start: 0.7874 (t80) cc_final: 0.7411 (t80) REVERT: D 192 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7356 (tptp) REVERT: D 219 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: E 41 TRP cc_start: 0.7034 (m100) cc_final: 0.6646 (m100) REVERT: E 72 GLN cc_start: 0.8800 (pm20) cc_final: 0.8508 (mp10) REVERT: E 224 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6906 (pttp) REVERT: F 53 MET cc_start: 0.7368 (tpt) cc_final: 0.6864 (tpt) REVERT: F 56 ASP cc_start: 0.8255 (m-30) cc_final: 0.7373 (p0) REVERT: F 103 TYR cc_start: 0.8041 (m-80) cc_final: 0.7706 (m-80) REVERT: G 41 TRP cc_start: 0.7661 (m100) cc_final: 0.7209 (m100) REVERT: G 53 MET cc_start: 0.6791 (mtm) cc_final: 0.6245 (mtm) REVERT: G 81 ASP cc_start: 0.7459 (m-30) cc_final: 0.7062 (m-30) REVERT: G 88 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.8519 (m-10) REVERT: G 106 ARG cc_start: 0.8405 (ttp80) cc_final: 0.7765 (ttp80) REVERT: H 55 TYR cc_start: 0.8251 (p90) cc_final: 0.7934 (p90) REVERT: H 56 ASP cc_start: 0.6578 (p0) cc_final: 0.5001 (p0) REVERT: H 123 MET cc_start: 0.8588 (tmm) cc_final: 0.7831 (ppp) REVERT: I 23 CYS cc_start: 0.8678 (p) cc_final: 0.8181 (t) REVERT: I 53 MET cc_start: 0.7557 (mpp) cc_final: 0.6811 (mpp) REVERT: I 144 LYS cc_start: 0.0900 (mttt) cc_final: -0.0027 (mtmt) REVERT: B 126 ASN cc_start: 0.8678 (m-40) cc_final: 0.7466 (p0) REVERT: B 173 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7003 (tm-30) REVERT: B 206 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8820 (ptmm) REVERT: B 314 GLN cc_start: 0.9026 (tt0) cc_final: 0.8359 (tm-30) REVERT: B 498 ARG cc_start: 0.8966 (mtt90) cc_final: 0.8548 (mtp85) REVERT: B 553 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8710 (p) REVERT: B 744 MET cc_start: 0.9459 (ttp) cc_final: 0.9085 (tpp) REVERT: B 983 ASP cc_start: 0.9176 (OUTLIER) cc_final: 0.8530 (t0) REVERT: B 1021 GLU cc_start: 0.9368 (tt0) cc_final: 0.9044 (tm-30) REVERT: B 1111 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8558 (mtt90) REVERT: C 54 ASP cc_start: 0.8857 (t0) cc_final: 0.8577 (t0) REVERT: C 126 ASN cc_start: 0.8610 (m-40) cc_final: 0.8203 (t0) REVERT: C 153 MET cc_start: 0.6440 (mpt) cc_final: 0.6097 (mpp) REVERT: C 780 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.8564 (tmmm) REVERT: C 908 TYR cc_start: 0.9082 (m-10) cc_final: 0.8881 (m-10) REVERT: C 992 GLU cc_start: 0.8767 (mp0) cc_final: 0.8438 (pm20) outliers start: 87 outliers final: 40 residues processed: 284 average time/residue: 0.7232 time to fit residues: 246.3756 Evaluate side-chains 240 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 190 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain F residue 42 TYR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 55 TYR Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain G residue 88 TYR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain B residue 938 ILE Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1111 ARG Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 780 LYS Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 80 optimal weight: 1.9990 chunk 270 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 378 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 266 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 215 GLN I 44 GLN I 170 ASN B 138 ASN B 207 HIS ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.086899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.051276 restraints weight = 113241.078| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.98 r_work: 0.2775 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 34401 Z= 0.287 Angle : 0.655 13.011 46834 Z= 0.330 Chirality : 0.046 0.200 5288 Planarity : 0.004 0.065 5974 Dihedral : 4.314 37.364 4605 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.56 % Allowed : 13.09 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.13), residues: 4201 helix: 1.94 (0.20), residues: 723 sheet: -0.17 (0.15), residues: 1205 loop : -1.01 (0.13), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 567 TYR 0.023 0.001 TYR A 501 PHE 0.027 0.002 PHE A 400 TRP 0.029 0.002 TRP G 52 HIS 0.008 0.001 HIS G 90 Details of bonding type rmsd covalent geometry : bond 0.00650 (34350) covalent geometry : angle 0.65137 (46732) SS BOND : bond 0.00327 ( 51) SS BOND : angle 1.62853 ( 102) hydrogen bonds : bond 0.04123 ( 1238) hydrogen bonds : angle 5.62603 ( 3474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 185 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8413 (m-40) cc_final: 0.8118 (t0) REVERT: A 558 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8914 (mmmt) REVERT: A 992 GLU cc_start: 0.8786 (mp0) cc_final: 0.8476 (mp0) REVERT: E 41 TRP cc_start: 0.7037 (m100) cc_final: 0.6753 (m100) REVERT: E 66 ARG cc_start: 0.6635 (OUTLIER) cc_final: 0.5819 (mmt180) REVERT: E 224 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6995 (pttp) REVERT: F 56 ASP cc_start: 0.8253 (m-30) cc_final: 0.7356 (p0) REVERT: G 41 TRP cc_start: 0.7775 (m100) cc_final: 0.7413 (m100) REVERT: G 53 MET cc_start: 0.6848 (mtm) cc_final: 0.6320 (mtm) REVERT: G 88 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.8552 (m-10) REVERT: G 106 ARG cc_start: 0.8403 (ttp80) cc_final: 0.7849 (ttp80) REVERT: H 80 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8341 (tptm) REVERT: H 123 MET cc_start: 0.8636 (tmm) cc_final: 0.7860 (ppp) REVERT: H 215 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7038 (pp30) REVERT: I 23 CYS cc_start: 0.8740 (p) cc_final: 0.8106 (t) REVERT: I 53 MET cc_start: 0.7792 (mpp) cc_final: 0.7119 (mpp) REVERT: I 144 LYS cc_start: 0.0772 (mttt) cc_final: -0.0225 (mtmt) REVERT: B 126 ASN cc_start: 0.8871 (m-40) cc_final: 0.8292 (t0) REVERT: B 173 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: B 206 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8806 (ptmm) REVERT: B 553 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8678 (p) REVERT: B 744 MET cc_start: 0.9500 (ttp) cc_final: 0.9135 (tpp) REVERT: B 983 ASP cc_start: 0.9222 (OUTLIER) cc_final: 0.8566 (t0) REVERT: B 1021 GLU cc_start: 0.9388 (tt0) cc_final: 0.9061 (tm-30) REVERT: C 54 ASP cc_start: 0.8908 (t0) cc_final: 0.8605 (t0) REVERT: C 126 ASN cc_start: 0.8710 (m-40) cc_final: 0.8282 (t0) REVERT: C 153 MET cc_start: 0.6455 (mpt) cc_final: 0.6097 (mpp) REVERT: C 414 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: C 780 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.8612 (tmmm) REVERT: C 992 GLU cc_start: 0.8751 (mp0) cc_final: 0.8409 (pm20) REVERT: C 1032 LYS cc_start: 0.9621 (OUTLIER) cc_final: 0.9412 (mttm) outliers start: 96 outliers final: 47 residues processed: 267 average time/residue: 0.6756 time to fit residues: 218.4948 Evaluate side-chains 239 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 179 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain G residue 88 TYR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 215 GLN Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 938 ILE Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 780 LYS Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1095 ARG Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 13 optimal weight: 8.9990 chunk 357 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 395 optimal weight: 0.8980 chunk 260 optimal weight: 0.0870 chunk 182 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 251 optimal weight: 9.9990 chunk 270 optimal weight: 7.9990 overall best weight: 2.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN B 207 HIS B 613 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.088104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.052578 restraints weight = 112323.703| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 4.02 r_work: 0.2805 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34401 Z= 0.153 Angle : 0.608 13.000 46834 Z= 0.307 Chirality : 0.045 0.233 5288 Planarity : 0.004 0.065 5974 Dihedral : 4.224 38.769 4604 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.24 % Allowed : 13.73 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.13), residues: 4201 helix: 2.04 (0.20), residues: 723 sheet: -0.10 (0.15), residues: 1195 loop : -0.98 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 75 TYR 0.022 0.001 TYR A 501 PHE 0.022 0.001 PHE A 400 TRP 0.031 0.001 TRP G 52 HIS 0.009 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00350 (34350) covalent geometry : angle 0.60526 (46732) SS BOND : bond 0.00245 ( 51) SS BOND : angle 1.42855 ( 102) hydrogen bonds : bond 0.03796 ( 1238) hydrogen bonds : angle 5.48040 ( 3474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 186 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8357 (m-40) cc_final: 0.8035 (t0) REVERT: A 558 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8875 (mmmt) REVERT: A 983 ASP cc_start: 0.9323 (m-30) cc_final: 0.8816 (t0) REVERT: A 992 GLU cc_start: 0.8803 (mp0) cc_final: 0.8475 (mp0) REVERT: E 41 TRP cc_start: 0.6832 (m100) cc_final: 0.5674 (m100) REVERT: E 66 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.5849 (mmt180) REVERT: E 224 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6999 (pttp) REVERT: F 56 ASP cc_start: 0.8278 (m-30) cc_final: 0.7406 (p0) REVERT: G 41 TRP cc_start: 0.7634 (m100) cc_final: 0.7318 (m100) REVERT: G 53 MET cc_start: 0.6850 (mtm) cc_final: 0.6401 (mtm) REVERT: G 106 ARG cc_start: 0.8384 (ttp80) cc_final: 0.7363 (ttp80) REVERT: G 117 TYR cc_start: 0.8487 (m-80) cc_final: 0.8191 (m-80) REVERT: H 117 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7592 (p) REVERT: H 123 MET cc_start: 0.8708 (tmm) cc_final: 0.7983 (ppp) REVERT: H 215 GLN cc_start: 0.7568 (pt0) cc_final: 0.7319 (pp30) REVERT: I 23 CYS cc_start: 0.8694 (p) cc_final: 0.7963 (t) REVERT: I 53 MET cc_start: 0.7925 (mpp) cc_final: 0.7184 (mpp) REVERT: I 144 LYS cc_start: 0.0737 (mttt) cc_final: -0.0141 (mtmt) REVERT: B 126 ASN cc_start: 0.8868 (m-40) cc_final: 0.8287 (t0) REVERT: B 173 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: B 498 ARG cc_start: 0.8990 (ttm-80) cc_final: 0.8747 (mmm-85) REVERT: B 553 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8743 (p) REVERT: B 744 MET cc_start: 0.9467 (ttp) cc_final: 0.9078 (tpp) REVERT: B 983 ASP cc_start: 0.9204 (OUTLIER) cc_final: 0.8544 (t0) REVERT: B 1021 GLU cc_start: 0.9375 (tt0) cc_final: 0.9041 (tm-30) REVERT: C 54 ASP cc_start: 0.8901 (t0) cc_final: 0.8617 (t0) REVERT: C 126 ASN cc_start: 0.8657 (m-40) cc_final: 0.8217 (t0) REVERT: C 153 MET cc_start: 0.6504 (mpt) cc_final: 0.6150 (mpp) REVERT: C 177 MET cc_start: 0.7182 (mmt) cc_final: 0.6925 (mmt) REVERT: C 414 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: C 780 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.8517 (tmmm) REVERT: C 784 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.9051 (mt-10) REVERT: C 992 GLU cc_start: 0.8775 (mp0) cc_final: 0.8398 (mp0) outliers start: 84 outliers final: 45 residues processed: 257 average time/residue: 0.6606 time to fit residues: 206.0731 Evaluate side-chains 234 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 179 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 193 TYR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 161 PHE Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 161 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 780 LYS Chi-restraints excluded: chain C residue 784 GLU Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 229 optimal weight: 9.9990 chunk 133 optimal weight: 30.0000 chunk 74 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 387 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 358 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 chunk 361 optimal weight: 0.7980 chunk 353 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 90 HIS B 138 ASN B 207 HIS B 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.087717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.052202 restraints weight = 112926.733| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 4.03 r_work: 0.2796 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34401 Z= 0.189 Angle : 0.626 12.019 46834 Z= 0.316 Chirality : 0.045 0.277 5288 Planarity : 0.004 0.065 5974 Dihedral : 4.238 38.985 4604 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.92 % Allowed : 14.24 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.23 (0.13), residues: 4201 helix: 2.04 (0.20), residues: 726 sheet: 0.01 (0.15), residues: 1174 loop : -0.98 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 106 TYR 0.034 0.001 TYR H 55 PHE 0.022 0.001 PHE A 400 TRP 0.034 0.001 TRP G 52 HIS 0.012 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00434 (34350) covalent geometry : angle 0.62163 (46732) SS BOND : bond 0.00276 ( 51) SS BOND : angle 1.78238 ( 102) hydrogen bonds : bond 0.03799 ( 1238) hydrogen bonds : angle 5.47885 ( 3474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 185 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8355 (m-40) cc_final: 0.8048 (t0) REVERT: A 516 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7541 (pm20) REVERT: A 558 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8882 (mmmt) REVERT: A 992 GLU cc_start: 0.8807 (mp0) cc_final: 0.8473 (mp0) REVERT: E 2 MET cc_start: 0.5238 (ppp) cc_final: 0.3360 (mtp) REVERT: E 41 TRP cc_start: 0.6770 (m100) cc_final: 0.5718 (m100) REVERT: E 66 ARG cc_start: 0.6646 (OUTLIER) cc_final: 0.5845 (mmt180) REVERT: E 224 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.7049 (pttp) REVERT: F 56 ASP cc_start: 0.8292 (m-30) cc_final: 0.7430 (p0) REVERT: G 23 CYS cc_start: 0.8098 (t) cc_final: 0.6751 (m) REVERT: G 41 TRP cc_start: 0.7639 (m100) cc_final: 0.6891 (m100) REVERT: G 53 MET cc_start: 0.6829 (mtm) cc_final: 0.6385 (mtm) REVERT: G 106 ARG cc_start: 0.8399 (ttp80) cc_final: 0.7478 (ttp80) REVERT: G 117 TYR cc_start: 0.8484 (m-80) cc_final: 0.8260 (m-80) REVERT: H 123 MET cc_start: 0.8724 (tmm) cc_final: 0.8008 (ppp) REVERT: H 215 GLN cc_start: 0.7744 (pt0) cc_final: 0.7479 (pp30) REVERT: I 23 CYS cc_start: 0.8726 (p) cc_final: 0.7997 (t) REVERT: I 53 MET cc_start: 0.7868 (mpp) cc_final: 0.7116 (mpp) REVERT: I 144 LYS cc_start: 0.0667 (mttt) cc_final: -0.0262 (mtmt) REVERT: B 126 ASN cc_start: 0.8934 (m-40) cc_final: 0.8363 (t0) REVERT: B 173 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: B 553 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8728 (p) REVERT: B 744 MET cc_start: 0.9357 (ttp) cc_final: 0.8923 (tpp) REVERT: B 983 ASP cc_start: 0.9214 (OUTLIER) cc_final: 0.8580 (t0) REVERT: B 1021 GLU cc_start: 0.9380 (tt0) cc_final: 0.9052 (tm-30) REVERT: C 54 ASP cc_start: 0.8921 (t0) cc_final: 0.8633 (t0) REVERT: C 126 ASN cc_start: 0.8695 (m-40) cc_final: 0.8219 (t0) REVERT: C 153 MET cc_start: 0.6501 (mpt) cc_final: 0.6161 (mpp) REVERT: C 177 MET cc_start: 0.7145 (mmt) cc_final: 0.6889 (mmt) REVERT: C 414 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7901 (tt0) REVERT: C 780 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.8524 (tmmm) REVERT: C 784 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.9033 (mt-10) REVERT: C 992 GLU cc_start: 0.8812 (mp0) cc_final: 0.8454 (mp0) outliers start: 72 outliers final: 46 residues processed: 247 average time/residue: 0.6366 time to fit residues: 190.8337 Evaluate side-chains 235 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 161 PHE Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain I residue 161 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 938 ILE Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 780 LYS Chi-restraints excluded: chain C residue 784 GLU Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 347 optimal weight: 3.9990 chunk 211 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 277 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 chunk 319 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 230 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 44 GLN B 207 HIS ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.086337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050861 restraints weight = 114218.882| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.95 r_work: 0.2761 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 34401 Z= 0.298 Angle : 0.690 14.041 46834 Z= 0.347 Chirality : 0.047 0.300 5288 Planarity : 0.004 0.065 5974 Dihedral : 4.470 40.095 4604 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.84 % Allowed : 14.72 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.32 (0.13), residues: 4201 helix: 2.00 (0.20), residues: 723 sheet: -0.04 (0.15), residues: 1173 loop : -1.04 (0.13), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 75 TYR 0.021 0.001 TYR A 501 PHE 0.026 0.002 PHE A 400 TRP 0.036 0.002 TRP G 52 HIS 0.025 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00677 (34350) covalent geometry : angle 0.68457 (46732) SS BOND : bond 0.00379 ( 51) SS BOND : angle 1.94323 ( 102) hydrogen bonds : bond 0.04152 ( 1238) hydrogen bonds : angle 5.59807 ( 3474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 180 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8528 (m-40) cc_final: 0.8224 (t0) REVERT: A 516 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: A 558 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8899 (mmmt) REVERT: A 992 GLU cc_start: 0.8828 (mp0) cc_final: 0.8507 (mp0) REVERT: E 41 TRP cc_start: 0.6870 (m100) cc_final: 0.6087 (m100) REVERT: E 66 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.5840 (mmt180) REVERT: E 224 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6957 (pttp) REVERT: F 56 ASP cc_start: 0.8411 (m-30) cc_final: 0.7644 (p0) REVERT: G 23 CYS cc_start: 0.7908 (t) cc_final: 0.7228 (t) REVERT: G 41 TRP cc_start: 0.7595 (m100) cc_final: 0.7258 (m100) REVERT: G 45 MET cc_start: 0.7980 (tmm) cc_final: 0.7588 (tmm) REVERT: G 53 MET cc_start: 0.6913 (mtm) cc_final: 0.6517 (mtm) REVERT: G 106 ARG cc_start: 0.8419 (ttp80) cc_final: 0.7530 (ttp80) REVERT: G 117 TYR cc_start: 0.8520 (m-80) cc_final: 0.8281 (m-80) REVERT: H 38 TYR cc_start: 0.7251 (m-10) cc_final: 0.7032 (m-80) REVERT: H 80 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8225 (tptm) REVERT: H 117 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7753 (p) REVERT: H 123 MET cc_start: 0.8742 (tmm) cc_final: 0.8027 (ppp) REVERT: I 23 CYS cc_start: 0.8748 (p) cc_final: 0.8005 (t) REVERT: I 53 MET cc_start: 0.7908 (mpp) cc_final: 0.7263 (mpp) REVERT: I 144 LYS cc_start: 0.0832 (mttt) cc_final: -0.0201 (mtmt) REVERT: B 126 ASN cc_start: 0.9105 (m-40) cc_final: 0.8534 (t0) REVERT: B 173 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: B 553 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8644 (p) REVERT: B 744 MET cc_start: 0.9431 (ttp) cc_final: 0.9045 (tpp) REVERT: B 983 ASP cc_start: 0.9254 (OUTLIER) cc_final: 0.8668 (t0) REVERT: B 1021 GLU cc_start: 0.9407 (tt0) cc_final: 0.9070 (tm-30) REVERT: C 54 ASP cc_start: 0.8917 (t0) cc_final: 0.8609 (t0) REVERT: C 126 ASN cc_start: 0.8878 (m-40) cc_final: 0.8361 (t0) REVERT: C 153 MET cc_start: 0.6406 (mpt) cc_final: 0.6091 (mpp) REVERT: C 414 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: C 481 ASN cc_start: 0.9450 (m110) cc_final: 0.9217 (p0) REVERT: C 780 LYS cc_start: 0.9466 (OUTLIER) cc_final: 0.8586 (tmmm) REVERT: C 992 GLU cc_start: 0.8774 (mp0) cc_final: 0.8429 (mp0) outliers start: 69 outliers final: 45 residues processed: 242 average time/residue: 0.6113 time to fit residues: 178.7220 Evaluate side-chains 229 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 161 PHE Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain I residue 161 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 780 LYS Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 254 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 370 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 133 optimal weight: 30.0000 chunk 218 optimal weight: 40.0000 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 315 optimal weight: 1.9990 chunk 111 optimal weight: 30.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 ASN G 44 GLN ** H 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN B 207 HIS B 613 GLN B1009 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.087684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052253 restraints weight = 113242.568| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 4.04 r_work: 0.2803 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34401 Z= 0.151 Angle : 0.636 15.692 46834 Z= 0.318 Chirality : 0.045 0.248 5288 Planarity : 0.004 0.065 5974 Dihedral : 4.340 40.688 4604 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.89 % Allowed : 14.67 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.23 (0.13), residues: 4201 helix: 2.09 (0.20), residues: 726 sheet: 0.03 (0.15), residues: 1169 loop : -1.00 (0.13), residues: 2306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 106 TYR 0.036 0.001 TYR H 55 PHE 0.022 0.001 PHE A 400 TRP 0.038 0.001 TRP G 52 HIS 0.011 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00349 (34350) covalent geometry : angle 0.63241 (46732) SS BOND : bond 0.00242 ( 51) SS BOND : angle 1.56224 ( 102) hydrogen bonds : bond 0.03717 ( 1238) hydrogen bonds : angle 5.46546 ( 3474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 181 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8449 (m-40) cc_final: 0.8137 (t0) REVERT: A 153 MET cc_start: 0.7918 (pmm) cc_final: 0.6962 (pp-130) REVERT: A 558 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8891 (mmmt) REVERT: A 992 GLU cc_start: 0.8827 (mp0) cc_final: 0.8504 (mp0) REVERT: E 2 MET cc_start: 0.5327 (ppp) cc_final: 0.3086 (mtm) REVERT: E 41 TRP cc_start: 0.6630 (m100) cc_final: 0.5677 (m100) REVERT: E 66 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.5848 (mmt180) REVERT: E 224 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6904 (pttp) REVERT: F 56 ASP cc_start: 0.8356 (m-30) cc_final: 0.7576 (p0) REVERT: G 23 CYS cc_start: 0.8003 (t) cc_final: 0.7259 (t) REVERT: G 41 TRP cc_start: 0.7431 (m100) cc_final: 0.7044 (m100) REVERT: G 45 MET cc_start: 0.7937 (tmm) cc_final: 0.7155 (tmm) REVERT: G 53 MET cc_start: 0.6865 (mtm) cc_final: 0.6435 (mtm) REVERT: G 106 ARG cc_start: 0.8457 (ttp80) cc_final: 0.7547 (ttp80) REVERT: G 117 TYR cc_start: 0.8532 (m-80) cc_final: 0.8297 (m-80) REVERT: H 80 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8211 (tptm) REVERT: H 117 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7851 (p) REVERT: H 123 MET cc_start: 0.8721 (tmm) cc_final: 0.8007 (ppp) REVERT: I 23 CYS cc_start: 0.8578 (p) cc_final: 0.7840 (t) REVERT: I 53 MET cc_start: 0.7841 (mpp) cc_final: 0.7121 (mpp) REVERT: I 90 HIS cc_start: 0.9232 (t-90) cc_final: 0.9009 (m90) REVERT: I 144 LYS cc_start: 0.0791 (mttt) cc_final: -0.0436 (mtmt) REVERT: B 126 ASN cc_start: 0.9050 (m-40) cc_final: 0.8470 (t0) REVERT: B 173 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: B 553 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8732 (p) REVERT: B 661 GLU cc_start: 0.8912 (tp30) cc_final: 0.8609 (mm-30) REVERT: B 983 ASP cc_start: 0.9238 (OUTLIER) cc_final: 0.8625 (t0) REVERT: B 1021 GLU cc_start: 0.9381 (tt0) cc_final: 0.9049 (tm-30) REVERT: C 54 ASP cc_start: 0.8918 (t0) cc_final: 0.8631 (t0) REVERT: C 126 ASN cc_start: 0.8772 (m-40) cc_final: 0.8272 (t0) REVERT: C 153 MET cc_start: 0.6445 (mpt) cc_final: 0.6113 (mpp) REVERT: C 414 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: C 481 ASN cc_start: 0.9470 (m110) cc_final: 0.9236 (p0) REVERT: C 780 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.8537 (tmmm) REVERT: C 784 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8942 (mt-10) REVERT: C 992 GLU cc_start: 0.8846 (mp0) cc_final: 0.8493 (mp0) outliers start: 71 outliers final: 46 residues processed: 243 average time/residue: 0.6343 time to fit residues: 187.2735 Evaluate side-chains 230 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 173 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 161 PHE Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 161 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 938 ILE Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 780 LYS Chi-restraints excluded: chain C residue 784 GLU Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 208 optimal weight: 0.0170 chunk 34 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 134 optimal weight: 0.7980 chunk 391 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 959 ASN D 149 ASN G 44 GLN H 215 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN B 207 HIS B 613 GLN B1009 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.088299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.052897 restraints weight = 112228.371| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.98 r_work: 0.2826 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34401 Z= 0.129 Angle : 0.628 14.819 46834 Z= 0.313 Chirality : 0.045 0.253 5288 Planarity : 0.004 0.065 5974 Dihedral : 4.195 40.209 4602 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.63 % Allowed : 14.99 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.14 (0.13), residues: 4201 helix: 2.18 (0.20), residues: 722 sheet: 0.10 (0.15), residues: 1164 loop : -0.94 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 75 TYR 0.023 0.001 TYR D 193 PHE 0.021 0.001 PHE B 157 TRP 0.037 0.001 TRP G 52 HIS 0.024 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00298 (34350) covalent geometry : angle 0.62559 (46732) SS BOND : bond 0.00219 ( 51) SS BOND : angle 1.38863 ( 102) hydrogen bonds : bond 0.03526 ( 1238) hydrogen bonds : angle 5.34746 ( 3474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13724.24 seconds wall clock time: 234 minutes 20.34 seconds (14060.34 seconds total)