Starting phenix.real_space_refine on Sat Feb 7 17:04:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z6s_39803/02_2026/8z6s_39803.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z6s_39803/02_2026/8z6s_39803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z6s_39803/02_2026/8z6s_39803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z6s_39803/02_2026/8z6s_39803.map" model { file = "/net/cci-nas-00/data/ceres_data/8z6s_39803/02_2026/8z6s_39803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z6s_39803/02_2026/8z6s_39803.cif" } resolution = 2.84 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= 0.040 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 165 5.16 5 C 22344 2.51 5 N 5814 2.21 5 O 6691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.04s 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: 35014 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1443 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 13, 'TRANS': 180} Chain breaks: 3 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: 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: "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: "C" Number of atoms: 8662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1106, 8662 Classifications: {'peptide': 1106} Link IDs: {'PTRANS': 59, 'TRANS': 1046} Chain breaks: 4 Chain: "B" Number of atoms: 8650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8650 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 60, 'TRANS': 1042} Chain breaks: 5 Chain: "A" Number of atoms: 8769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8769 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 60, 'TRANS': 1058} Chain breaks: 3 Time building chain proxies: 8.61, per 1000 atoms: 0.25 Number of scatterers: 35014 At special positions: 0 Unit cell: (154.712, 175.216, 246.98, 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 165 16.00 O 6691 8.00 N 5814 7.00 C 22344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 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 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=2.03 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=2.02 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 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 747 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B 844 " - pdb=" SG CYS B 855 " 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 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 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: 2.94 Conformation dependent library (CDL) restraints added in 1.6 seconds 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8396 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 78 sheets defined 21.1% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'D' and resid 95 through 99 removed outlier: 3.676A pdb=" N GLU D 99 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 148 removed outlier: 3.637A pdb=" N LEU D 146 " --> pdb=" O SER D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 208 Processing helix chain 'E' and resid 69 through 72 removed outlier: 3.937A 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: 3.972A pdb=" N THR E 99 " --> pdb=" O ALA E 96 " (cutoff:3.500A) 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 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: 4.062A 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: 4.010A pdb=" N THR G 99 " --> pdb=" O ALA G 96 " (cutoff:3.500A) 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: 3.615A pdb=" N GLU H 99 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 148 removed outlier: 3.610A pdb=" N LEU H 146 " --> pdb=" O SER H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 208 Processing helix chain 'I' and resid 69 through 72 removed outlier: 3.983A 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: 3.901A pdb=" N THR I 99 " --> pdb=" O ALA I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 173 No H-bonds generated for 'chain 'I' and resid 171 through 173' Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 97 through 100 removed outlier: 3.643A pdb=" N ASN C 100 " --> pdb=" O GLU C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.953A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.709A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.977A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 741 through 747 Processing helix chain 'C' and resid 750 through 758 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: 3.565A pdb=" N VAL C 830 " --> pdb=" O LEU C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 859 removed outlier: 3.898A pdb=" N ALA C 856 " --> pdb=" O ASP C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 889 Processing helix chain 'C' and resid 890 through 895 removed outlier: 3.645A pdb=" N ALA C 894 " --> pdb=" O TRP C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 913 Processing helix chain 'C' and resid 916 through 945 removed outlier: 4.178A pdb=" N LEU C 920 " --> pdb=" O THR C 916 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS C 925 " --> pdb=" O TYR C 921 " (cutoff:3.500A) removed outlier: 6.459A 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 removed outlier: 3.642A pdb=" N VAL C 955 " --> pdb=" O LYS C 951 " (cutoff:3.500A) 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 987 removed outlier: 3.517A pdb=" N ILE C 984 " --> pdb=" O VAL C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1037 removed outlier: 4.503A pdb=" N VAL C 995 " --> pdb=" O PRO C 991 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN C 996 " --> pdb=" O GLU C 992 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG C 999 " --> pdb=" O VAL C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1122 No H-bonds generated for 'chain 'C' and resid 1120 through 1122' Processing helix chain 'C' and resid 1144 through 1163 removed outlier: 4.055A pdb=" N GLU C1148 " --> pdb=" O PRO C1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.716A pdb=" N ASN B 100 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 101 " --> pdb=" O LYS B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.607A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.888A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.779A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY B 639 " --> pdb=" O VAL B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 639' Processing helix chain 'B' and resid 741 through 747 Processing helix chain 'B' and resid 750 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 removed outlier: 3.528A pdb=" N ASP B 779 " --> pdb=" O ALA B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 830 Processing helix chain 'B' and resid 852 through 859 removed outlier: 3.881A pdb=" N ALA B 856 " --> pdb=" O ASP B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 889 Processing helix chain 'B' and resid 890 through 895 removed outlier: 3.657A 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: 4.182A pdb=" N LEU B 920 " --> pdb=" O THR B 916 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS B 925 " --> pdb=" O TYR B 921 " (cutoff:3.500A) removed outlier: 6.452A 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 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: 4.725A pdb=" N VAL B 995 " --> pdb=" O PRO B 991 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLN B 996 " --> pdb=" O GLU B 992 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 999 " --> pdb=" O VAL B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1163 removed outlier: 4.329A pdb=" N GLU B1148 " --> pdb=" O PRO B1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 100 removed outlier: 3.587A pdb=" N ASN A 100 " --> pdb=" O GLU A 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 100' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.787A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.763A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.826A pdb=" N GLY A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 747 Processing helix chain 'A' and resid 750 through 758 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 Processing helix chain 'A' and resid 853 through 859 Processing helix chain 'A' and resid 870 through 889 Processing helix chain 'A' and resid 890 through 895 removed outlier: 3.714A pdb=" N ALA A 894 " --> pdb=" O TRP A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 913 Processing helix chain 'A' and resid 916 through 945 removed outlier: 4.143A pdb=" N LEU A 920 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 926 " --> pdb=" O GLU A 922 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A 939 " --> pdb=" O ILE A 935 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP A 940 " --> pdb=" O GLY A 936 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR A 945 " --> pdb=" O SER A 941 " (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: 3.562A pdb=" N ILE A 984 " --> pdb=" O VAL A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1037 removed outlier: 4.624A pdb=" N VAL A 995 " --> pdb=" O PRO A 991 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN A 996 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 999 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1164 removed outlier: 4.301A pdb=" N GLU A1148 " --> pdb=" O PRO A1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 9 through 11 removed outlier: 3.557A pdb=" N TYR D 102 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL D 39 " --> pdb=" O TYR D 55 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR D 55 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP D 41 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET D 53 " --> pdb=" O TRP D 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 9 through 11 removed outlier: 3.557A pdb=" N TYR D 102 " --> pdb=" O THR D 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 19 through 23 removed outlier: 4.026A pdb=" N VAL D 19 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 88 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER D 79 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 137 through 139 removed outlier: 6.340A pdb=" N TYR D 193 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 196 " --> pdb=" O THR D 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 166 through 170 Processing sheet with id=AA6, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.649A pdb=" N ILE E 39 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE E 55 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TRP E 41 " --> pdb=" O MET E 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.772A pdb=" N TYR E 117 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 135 through 138 removed outlier: 3.668A pdb=" N ASP E 159 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TYR E 191 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N SER E 192 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA E 183 " --> pdb=" O SER E 192 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER E 194 " --> pdb=" O PHE E 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 166 through 169 removed outlier: 3.594A pdb=" N THR E 166 " --> pdb=" O ASN E 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 9 through 14 removed outlier: 6.545A pdb=" N GLN F 43 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 9 through 14 Processing sheet with id=AB4, first strand: chain 'F' and resid 18 through 23 removed outlier: 3.508A pdb=" N SER F 79 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 135 through 139 removed outlier: 6.228A pdb=" N TYR F 193 " --> pdb=" O ASP F 159 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER F 196 " --> pdb=" O THR F 183 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU F 181 " --> pdb=" O TYR F 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 166 through 170 Processing sheet with id=AB7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.701A pdb=" N GLU G 11 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL G 124 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE G 39 " --> pdb=" O ILE G 55 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE G 55 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TRP G 41 " --> pdb=" O MET G 53 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.701A pdb=" N GLU G 11 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL G 124 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR G 117 " --> pdb=" O ARG G 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 135 through 138 removed outlier: 3.632A pdb=" N ASP G 159 " --> pdb=" O TYR G 191 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR G 191 " --> pdb=" O ASP G 159 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER G 194 " --> pdb=" O PRO G 182 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL G 196 " --> pdb=" O THR G 180 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N THR G 180 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR G 198 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL G 178 " --> pdb=" O THR G 198 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 166 through 169 removed outlier: 3.588A pdb=" N THR G 166 " --> pdb=" O ASN G 214 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 13 Processing sheet with id=AC4, first strand: chain 'H' and resid 19 through 24 removed outlier: 4.109A pdb=" N VAL H 19 " --> pdb=" O ILE H 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 50 through 55 removed outlier: 5.077A pdb=" N LEU H 52 " --> pdb=" O GLN H 43 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLN H 43 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER H 106 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL H 117 " --> pdb=" O SER H 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 135 through 139 removed outlier: 3.610A pdb=" N ASP H 159 " --> pdb=" O TYR H 193 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR H 193 " --> pdb=" O ASP H 159 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER H 196 " --> pdb=" O THR H 183 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU H 181 " --> pdb=" O TYR H 198 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 166 through 170 Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.654A pdb=" N GLU I 11 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE I 39 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE I 55 " --> pdb=" O ILE I 39 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TRP I 41 " --> pdb=" O MET I 53 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET I 53 " --> pdb=" O TRP I 41 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.654A pdb=" N GLU I 11 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR I 117 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 135 through 138 removed outlier: 3.643A pdb=" N ASP I 159 " --> pdb=" O TYR I 191 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 135 through 138 removed outlier: 3.643A pdb=" N ASP I 159 " --> pdb=" O TYR I 191 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 166 through 169 Processing sheet with id=AD5, first strand: chain 'C' and resid 24 through 32 removed outlier: 3.614A pdb=" N SER C 61 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ASN C 62 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY C 261 " --> pdb=" O HIS C 70 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 49 through 56 removed outlier: 4.076A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 85 through 86 removed outlier: 7.512A pdb=" N ASP C 143 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 85 through 86 removed outlier: 7.210A pdb=" N ARG C 237 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLN C 239 " --> pdb=" O TRP C 105 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU C 241 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 128 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C 168 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.182A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.752A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE C 565 " --> pdb=" O PHE A 44 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.668A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA C 435 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.668A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.906A pdb=" N GLU C 654 " --> pdb=" O ALA C 698 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR C 700 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 705 through 708 removed outlier: 6.728A pdb=" N ALA C 705 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LYS A 794 " --> pdb=" O ALA C 705 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASN C 707 " --> pdb=" O LYS A 794 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 732 removed outlier: 6.727A pdb=" N SER C 715 " --> pdb=" O THR C1080 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C1080 " --> pdb=" O SER C 715 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA C 717 " --> pdb=" O ASN C1078 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASN C1078 " --> pdb=" O ALA C 717 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1076 " --> pdb=" O PRO C 719 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C1072 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY C1063 " --> pdb=" O SER C1059 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N SER C1059 " --> pdb=" O GLY C1063 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C1065 " --> pdb=" O PRO C1057 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU C1067 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER C1055 " --> pdb=" O LEU C1067 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C1069 " --> pdb=" O LEU C1053 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 715 through 732 removed outlier: 6.727A pdb=" N SER C 715 " --> pdb=" O THR C1080 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C1080 " --> pdb=" O SER C 715 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA C 717 " --> pdb=" O ASN C1078 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASN C1078 " --> pdb=" O ALA C 717 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1076 " --> pdb=" O PRO C 719 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C1072 " --> pdb=" O THR C 723 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 737 through 740 removed outlier: 4.032A pdb=" N LYS C 737 " --> pdb=" O LEU C 865 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 792 through 794 removed outlier: 5.460A pdb=" N ILE C 792 " --> pdb=" O ASN B 707 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 1124 through 1129 removed outlier: 5.594A pdb=" N VAL C1126 " --> pdb=" O PHE C1093 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE C1093 " --> pdb=" O VAL C1126 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLY C1128 " --> pdb=" O ALA C1091 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 24 through 32 removed outlier: 3.521A pdb=" N SER B 61 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASN B 62 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR B 269 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 49 through 56 removed outlier: 4.048A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 85 through 86 removed outlier: 4.178A pdb=" N PHE B 168 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AF7, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.184A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.581A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.529A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.662A 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 473 through 474 removed outlier: 3.553A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.827A pdb=" N GLU B 654 " --> pdb=" O ALA B 698 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR B 700 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 715 through 732 removed outlier: 7.108A pdb=" N GLN B1075 " --> pdb=" O THR B 720 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE B 722 " --> pdb=" O PRO B1073 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE B 724 " --> pdb=" O TYR B1071 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N TYR B1071 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B 726 " --> pdb=" O VAL B1069 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B1069 " --> pdb=" O VAL B 726 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B 728 " --> pdb=" O LEU B1067 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B1067 " --> pdb=" O THR B 728 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE B 730 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL B1065 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLY B1063 " --> pdb=" O PRO B 732 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLY B1063 " --> pdb=" O SER B1059 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER B1059 " --> pdb=" O GLY B1063 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B1065 " --> pdb=" O PRO B1057 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU B1067 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER B1055 " --> pdb=" O LEU B1067 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL B1069 " --> pdb=" O LEU B1053 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 739 through 740 Processing sheet with id=AG7, first strand: chain 'B' and resid 792 through 794 Processing sheet with id=AG8, first strand: chain 'B' and resid 1124 through 1129 removed outlier: 4.698A 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 'A' and resid 24 through 32 removed outlier: 7.979A pdb=" N ASN A 62 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR A 269 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 91 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 194 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL A 37 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 49 through 56 removed outlier: 4.015A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.647A pdb=" N LEU A 85 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A 144 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 145 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET A 153 " --> pdb=" O TYR A 145 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.647A pdb=" N LEU A 85 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA A 243 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE A 102 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 168 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLU A 133 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N CYS A 166 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N GLN A 135 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N ASN A 164 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.174A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.695A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.854A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.812A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AI1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.668A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.915A pdb=" N GLU A 654 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N THR A 700 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'A' and resid 715 through 732 removed outlier: 7.096A pdb=" N GLN A1075 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE A 722 " --> pdb=" O PRO A1073 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE A 724 " --> pdb=" O TYR A1071 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N TYR A1071 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A 726 " --> pdb=" O VAL A1069 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A1069 " --> pdb=" O VAL A 726 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A 728 " --> pdb=" O LEU A1067 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU A1067 " --> pdb=" O THR A 728 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE A 730 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A1065 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY A1063 " --> pdb=" O PRO A 732 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLY A1063 " --> pdb=" O SER A1059 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER A1059 " --> pdb=" O GLY A1063 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A1065 " --> pdb=" O PRO A1057 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU A1067 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A1055 " --> pdb=" O LEU A1067 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL A1069 " --> pdb=" O LEU A1053 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'A' and resid 715 through 732 removed outlier: 7.096A pdb=" N GLN A1075 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE A 722 " --> pdb=" O PRO A1073 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE A 724 " --> pdb=" O TYR A1071 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N TYR A1071 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A 726 " --> pdb=" O VAL A1069 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A1069 " --> pdb=" O VAL A 726 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A 728 " --> pdb=" O LEU A1067 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU A1067 " --> pdb=" O THR A 728 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE A 730 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A1065 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY A1063 " --> pdb=" O PRO A 732 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'A' and resid 739 through 740 Processing sheet with id=AI6, first strand: chain 'A' and resid 1124 through 1129 removed outlier: 4.877A pdb=" N ALA A1091 " --> pdb=" O SER A1127 " (cutoff:3.500A) 1417 hydrogen bonds defined for protein. 3819 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: 10.33 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10667 1.34 - 1.46: 6563 1.46 - 1.58: 18417 1.58 - 1.70: 0 1.70 - 1.82: 213 Bond restraints: 35860 Sorted by residual: bond pdb=" CA SER C 695 " pdb=" C SER C 695 " ideal model delta sigma weight residual 1.522 1.497 0.025 1.20e-02 6.94e+03 4.44e+00 bond pdb=" C ILE C 697 " pdb=" O ILE C 697 " ideal model delta sigma weight residual 1.237 1.215 0.022 1.13e-02 7.83e+03 3.77e+00 bond pdb=" C TYR F 161 " pdb=" N PRO F 162 " ideal model delta sigma weight residual 1.332 1.358 -0.026 1.34e-02 5.57e+03 3.66e+00 bond pdb=" C ILE C 696 " pdb=" O ILE C 696 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.09e-02 8.42e+03 3.58e+00 bond pdb=" CA ILE C 697 " pdb=" CB ILE C 697 " ideal model delta sigma weight residual 1.542 1.519 0.023 1.26e-02 6.30e+03 3.35e+00 ... (remaining 35855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 47800 1.62 - 3.23: 889 3.23 - 4.85: 87 4.85 - 6.46: 12 6.46 - 8.08: 7 Bond angle restraints: 48795 Sorted by residual: angle pdb=" C GLU B 619 " pdb=" N VAL B 620 " pdb=" CA VAL B 620 " ideal model delta sigma weight residual 120.24 123.10 -2.86 6.30e-01 2.52e+00 2.06e+01 angle pdb=" N ALA B 626 " pdb=" CA ALA B 626 " pdb=" C ALA B 626 " ideal model delta sigma weight residual 113.55 108.39 5.16 1.26e+00 6.30e-01 1.67e+01 angle pdb=" N ILE G 84 " pdb=" CA ILE G 84 " pdb=" C ILE G 84 " ideal model delta sigma weight residual 113.20 109.58 3.62 9.60e-01 1.09e+00 1.42e+01 angle pdb=" N GLN C 675 " pdb=" CA GLN C 675 " pdb=" C GLN C 675 " ideal model delta sigma weight residual 109.52 115.21 -5.69 1.55e+00 4.16e-01 1.35e+01 angle pdb=" N ILE I 84 " pdb=" CA ILE I 84 " pdb=" C ILE I 84 " ideal model delta sigma weight residual 113.20 109.70 3.50 9.60e-01 1.09e+00 1.33e+01 ... (remaining 48790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 20661 17.54 - 35.08: 572 35.08 - 52.62: 87 52.62 - 70.16: 16 70.16 - 87.70: 8 Dihedral angle restraints: 21344 sinusoidal: 8260 harmonic: 13084 Sorted by residual: dihedral pdb=" CA ASP F 56 " pdb=" C ASP F 56 " pdb=" N VAL F 57 " pdb=" CA VAL F 57 " ideal model delta harmonic sigma weight residual 180.00 -157.68 -22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ASP D 56 " pdb=" C ASP D 56 " pdb=" N VAL D 57 " pdb=" CA VAL D 57 " ideal model delta harmonic sigma weight residual 180.00 -157.77 -22.23 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ASP H 56 " pdb=" C ASP H 56 " pdb=" N VAL H 57 " pdb=" CA VAL H 57 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 21341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4476 0.047 - 0.094: 668 0.094 - 0.141: 339 0.141 - 0.187: 5 0.187 - 0.234: 1 Chirality restraints: 5489 Sorted by residual: chirality pdb=" CA VAL D 136 " pdb=" N VAL D 136 " pdb=" C VAL D 136 " pdb=" CB VAL D 136 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA TYR B 145 " pdb=" N TYR B 145 " pdb=" C TYR B 145 " pdb=" CB TYR B 145 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA GLN C 675 " pdb=" N GLN C 675 " pdb=" C GLN C 675 " pdb=" CB GLN C 675 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 5486 not shown) Planarity restraints: 6271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 330 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 173 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO B 174 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 174 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 174 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 173 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO C 174 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 174 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 174 " 0.023 5.00e-02 4.00e+02 ... (remaining 6268 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3311 2.75 - 3.29: 33844 3.29 - 3.82: 58639 3.82 - 4.36: 67368 4.36 - 4.90: 120199 Nonbonded interactions: 283361 Sorted by model distance: nonbonded pdb=" O GLY A 104 " pdb=" OG1 THR A 240 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASP H 56 " pdb=" OH TYR H 107 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR D 5 " pdb=" OG1 THR D 24 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR F 5 " pdb=" OG1 THR F 24 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR C 645 " pdb=" O GLY C 648 " model vdw 2.243 3.040 ... (remaining 283356 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 72 or resid 81 through 146 or resid 152 through \ 179 or resid 186 through 247 or resid 258 through 621 or resid 640 through 1166 \ )) selection = (chain 'B' and (resid 18 through 621 or resid 640 through 675 or resid 695 throu \ gh 1166)) selection = (chain 'C' and (resid 18 through 72 or resid 81 through 146 or resid 152 through \ 179 or resid 186 through 247 or resid 258 through 675 or resid 695 through 1166 \ )) } ncs_group { reference = (chain 'D' and (resid 2 through 130 or resid 133 through 219)) selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 37.060 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 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:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 0.026 35911 Z= 0.126 Angle : 0.538 8.075 48897 Z= 0.323 Chirality : 0.041 0.234 5489 Planarity : 0.003 0.047 6271 Dihedral : 7.993 87.695 12795 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.07 % Favored : 96.88 % Rotamer: Outliers : 2.23 % Allowed : 4.48 % Favored : 93.30 % 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: -1.32 (0.12), residues: 4430 helix: 0.58 (0.18), residues: 769 sheet: -0.25 (0.14), residues: 1223 loop : -1.75 (0.11), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 769 TYR 0.010 0.001 TYR B 145 PHE 0.017 0.001 PHE C 141 TRP 0.010 0.001 TRP C 152 HIS 0.001 0.000 HIS C1052 Details of bonding type rmsd covalent geometry : bond 0.00192 (35860) covalent geometry : angle 0.53850 (48795) SS BOND : bond 0.00148 ( 51) SS BOND : angle 0.41222 ( 102) hydrogen bonds : bond 0.22853 ( 1348) hydrogen bonds : angle 8.78674 ( 3819) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 413 time to evaluate : 1.460 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: D 85 ASN cc_start: 0.9411 (p0) cc_final: 0.8927 (t0) REVERT: D 91 ILE cc_start: 0.7852 (mt) cc_final: 0.7509 (tp) REVERT: D 98 ASP cc_start: 0.6554 (m-30) cc_final: 0.6284 (m-30) REVERT: D 126 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8476 (p) REVERT: D 169 TRP cc_start: 0.0049 (OUTLIER) cc_final: -0.0631 (m-90) REVERT: E 30 PHE cc_start: 0.8782 (t80) cc_final: 0.7379 (t80) REVERT: E 36 TYR cc_start: 0.8911 (m-10) cc_final: 0.8695 (m-80) REVERT: E 53 MET cc_start: 0.8864 (mtm) cc_final: 0.8468 (mtm) REVERT: E 106 ARG cc_start: 0.8053 (ptm-80) cc_final: 0.6884 (tmm-80) REVERT: E 114 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7872 (tm) REVERT: E 117 TYR cc_start: 0.9256 (m-80) cc_final: 0.8480 (m-80) REVERT: E 191 TYR cc_start: 0.9489 (m-80) cc_final: 0.9115 (m-80) REVERT: F 56 ASP cc_start: 0.7806 (m-30) cc_final: 0.7430 (m-30) REVERT: F 91 ILE cc_start: 0.9271 (mt) cc_final: 0.9044 (tp) REVERT: F 107 TYR cc_start: 0.8631 (p90) cc_final: 0.8271 (p90) REVERT: F 157 ILE cc_start: 0.5675 (mt) cc_final: 0.5470 (mp) REVERT: F 169 TRP cc_start: 0.5572 (OUTLIER) cc_final: 0.4459 (m-90) REVERT: G 21 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8968 (pp) REVERT: G 51 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7427 (mp0) REVERT: G 53 MET cc_start: 0.8656 (mtm) cc_final: 0.8353 (mpp) REVERT: G 75 GLN cc_start: 0.9105 (mp10) cc_final: 0.8039 (mp10) REVERT: G 117 TYR cc_start: 0.8637 (m-80) cc_final: 0.8247 (m-80) REVERT: H 169 TRP cc_start: 0.1921 (OUTLIER) cc_final: -0.0141 (m-90) REVERT: I 38 TRP cc_start: 0.7544 (m100) cc_final: 0.5853 (m100) REVERT: I 71 PHE cc_start: 0.8971 (m-80) cc_final: 0.8366 (m-10) REVERT: I 88 TYR cc_start: 0.9346 (m-80) cc_final: 0.8767 (m-80) REVERT: C 177 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.5878 (pmm) REVERT: C 336 CYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7298 (p) REVERT: C 571 ASP cc_start: 0.8019 (t0) cc_final: 0.7703 (t0) REVERT: C 675 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7703 (tm-30) REVERT: C 676 THR cc_start: 0.9411 (OUTLIER) cc_final: 0.9002 (m) REVERT: C 697 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.8958 (pp) REVERT: C 777 GLU cc_start: 0.8232 (tt0) cc_final: 0.7919 (tt0) REVERT: C 781 ASN cc_start: 0.7309 (m-40) cc_final: 0.6988 (m110) REVERT: B 138 ASN cc_start: 0.8245 (m-40) cc_final: 0.7626 (p0) REVERT: B 269 TYR cc_start: 0.8145 (m-80) cc_final: 0.7916 (m-80) REVERT: B 341 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8209 (p) REVERT: B 658 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8113 (p0) REVERT: B 1006 GLN cc_start: 0.8299 (tp40) cc_final: 0.7610 (tp-100) REVERT: A 129 ILE cc_start: 0.8938 (mp) cc_final: 0.8674 (mp) REVERT: A 145 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7473 (p90) REVERT: A 314 GLN cc_start: 0.6846 (tm-30) cc_final: 0.6621 (tm-30) REVERT: A 498 ARG cc_start: 0.8729 (mtt-85) cc_final: 0.8510 (mpt90) REVERT: A 697 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8437 (pp) REVERT: A 951 LYS cc_start: 0.8963 (mttm) cc_final: 0.8411 (mttp) outliers start: 87 outliers final: 14 residues processed: 492 average time/residue: 0.6847 time to fit residues: 407.0587 Evaluate side-chains 268 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 169 TRP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain F residue 169 TRP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 1165 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 9.9990 chunk 424 optimal weight: 7.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN D 215 GLN E 107 GLN E 179 HIS F 44 GLN F 95 GLN ** G 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN H 95 GLN I 179 HIS C 21 ASN ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 474 GLN C 580 GLN C 644 GLN C 788 GLN C1015 GLN C1075 GLN ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 196 ASN B 339 HIS B 370 ASN B 474 GLN B 519 HIS B 613 GLN B 658 ASN B 876 GLN B1015 GLN B1075 GLN A 50 HIS A 88 ASN A 148 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 474 GLN A 519 HIS A 580 GLN A 607 GLN A 613 GLN A 876 GLN ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN A1129 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.105448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.063056 restraints weight = 123076.996| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 4.10 r_work: 0.2961 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 35911 Z= 0.272 Angle : 0.666 10.285 48897 Z= 0.338 Chirality : 0.047 0.202 5489 Planarity : 0.004 0.066 6271 Dihedral : 4.581 59.132 4867 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.69 % Allowed : 9.11 % Favored : 88.20 % 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: -0.60 (0.12), residues: 4430 helix: 1.15 (0.19), residues: 791 sheet: 0.03 (0.14), residues: 1248 loop : -1.18 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 8 TYR 0.038 0.002 TYR C 841 PHE 0.025 0.002 PHE A 56 TRP 0.027 0.002 TRP A 105 HIS 0.012 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00613 (35860) covalent geometry : angle 0.66506 (48795) SS BOND : bond 0.00282 ( 51) SS BOND : angle 1.01992 ( 102) hydrogen bonds : bond 0.04247 ( 1348) hydrogen bonds : angle 6.23623 ( 3819) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 240 time to evaluate : 1.725 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: D 51 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8146 (tmmt) REVERT: D 85 ASN cc_start: 0.9448 (p0) cc_final: 0.8800 (t0) REVERT: D 91 ILE cc_start: 0.7789 (mt) cc_final: 0.7435 (tp) REVERT: D 98 ASP cc_start: 0.6773 (m-30) cc_final: 0.6398 (m-30) REVERT: E 2 MET cc_start: 0.7001 (mtm) cc_final: 0.6763 (mmm) REVERT: E 36 TYR cc_start: 0.8888 (m-10) cc_final: 0.8634 (m-80) REVERT: E 106 ARG cc_start: 0.8007 (ptm-80) cc_final: 0.7685 (ttp80) REVERT: E 117 TYR cc_start: 0.9407 (m-80) cc_final: 0.8667 (m-80) REVERT: F 43 GLN cc_start: 0.7658 (tt0) cc_final: 0.7419 (tm130) REVERT: F 44 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7869 (tp40) REVERT: F 48 LYS cc_start: 0.9065 (mtpp) cc_final: 0.8795 (mtmm) REVERT: F 56 ASP cc_start: 0.8241 (m-30) cc_final: 0.8007 (m-30) REVERT: F 67 ARG cc_start: 0.8357 (ptm160) cc_final: 0.7851 (ttm-80) REVERT: F 75 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.7783 (ppp80) REVERT: F 91 ILE cc_start: 0.9476 (mt) cc_final: 0.8612 (tt) REVERT: F 95 GLN cc_start: 0.9033 (mt0) cc_final: 0.8805 (mp10) REVERT: F 98 ASP cc_start: 0.7658 (m-30) cc_final: 0.4691 (m-30) REVERT: F 101 ASP cc_start: 0.8856 (t0) cc_final: 0.8248 (p0) REVERT: F 169 TRP cc_start: 0.5974 (OUTLIER) cc_final: 0.4959 (m-90) REVERT: G 45 MET cc_start: 0.8129 (tmm) cc_final: 0.7907 (ppp) REVERT: G 51 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7750 (pt0) REVERT: G 53 MET cc_start: 0.9175 (mtm) cc_final: 0.8688 (mtm) REVERT: G 75 GLN cc_start: 0.8816 (mp10) cc_final: 0.8257 (mp10) REVERT: G 81 ASP cc_start: 0.7638 (t0) cc_final: 0.7391 (t0) REVERT: G 114 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8308 (tm) REVERT: G 161 PHE cc_start: 0.8365 (m-80) cc_final: 0.7734 (m-10) REVERT: H 41 TRP cc_start: 0.3905 (m100) cc_final: 0.3423 (m100) REVERT: H 123 MET cc_start: 0.8636 (mmm) cc_final: 0.8171 (mmt) REVERT: H 169 TRP cc_start: 0.6607 (OUTLIER) cc_final: 0.5978 (m-90) REVERT: I 2 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7937 (tmt) REVERT: I 21 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7130 (pp) REVERT: I 38 TRP cc_start: 0.7075 (m100) cc_final: 0.5090 (m100) REVERT: I 45 MET cc_start: 0.9064 (mmt) cc_final: 0.8765 (mmm) REVERT: I 88 TYR cc_start: 0.9587 (m-80) cc_final: 0.9379 (m-80) REVERT: I 112 TRP cc_start: 0.7481 (p-90) cc_final: 0.6767 (p-90) REVERT: C 336 CYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7798 (p) REVERT: C 571 ASP cc_start: 0.8766 (t0) cc_final: 0.8467 (t0) REVERT: C 646 ARG cc_start: 0.9308 (OUTLIER) cc_final: 0.8661 (ttp80) REVERT: C 675 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8161 (pp30) REVERT: C 676 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.9109 (m) REVERT: C 697 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8892 (pp) REVERT: C 904 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8764 (mtt) REVERT: B 138 ASN cc_start: 0.8469 (m-40) cc_final: 0.7705 (p0) REVERT: B 269 TYR cc_start: 0.8806 (m-80) cc_final: 0.8573 (m-80) REVERT: B 341 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8544 (p) REVERT: B 378 LYS cc_start: 0.9093 (ttmm) cc_final: 0.8696 (ptmm) REVERT: B 658 ASN cc_start: 0.8978 (OUTLIER) cc_final: 0.8468 (p0) REVERT: B 983 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8189 (t0) REVERT: A 487 ASN cc_start: 0.8313 (p0) cc_final: 0.7962 (p0) REVERT: A 701 MET cc_start: 0.9175 (ptp) cc_final: 0.8907 (ptm) REVERT: A 853 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8556 (tp) REVERT: A 983 ASP cc_start: 0.9102 (m-30) cc_final: 0.8848 (m-30) outliers start: 105 outliers final: 31 residues processed: 321 average time/residue: 0.6318 time to fit residues: 248.3446 Evaluate side-chains 250 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 169 TRP Chi-restraints excluded: chain F residue 193 TYR Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 853 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 198 optimal weight: 0.7980 chunk 417 optimal weight: 20.0000 chunk 202 optimal weight: 1.9990 chunk 414 optimal weight: 0.9990 chunk 86 optimal weight: 30.0000 chunk 255 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 328 optimal weight: 1.9990 chunk 162 optimal weight: 30.0000 chunk 192 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN E 90 HIS F 44 GLN G 90 HIS G 107 GLN G 179 HIS C 409 GLN ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 613 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 905 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.106339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.064068 restraints weight = 122179.173| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 4.22 r_work: 0.2991 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35911 Z= 0.129 Angle : 0.555 12.021 48897 Z= 0.277 Chirality : 0.044 0.182 5489 Planarity : 0.004 0.060 6271 Dihedral : 4.169 58.285 4842 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.33 % Allowed : 10.24 % Favored : 87.44 % 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 (0.12), residues: 4430 helix: 1.62 (0.19), residues: 782 sheet: 0.18 (0.14), residues: 1256 loop : -1.01 (0.12), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 646 TYR 0.026 0.001 TYR C 841 PHE 0.020 0.001 PHE A 56 TRP 0.029 0.001 TRP A 105 HIS 0.009 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00286 (35860) covalent geometry : angle 0.55325 (48795) SS BOND : bond 0.00205 ( 51) SS BOND : angle 1.03761 ( 102) hydrogen bonds : bond 0.03712 ( 1348) hydrogen bonds : angle 5.76690 ( 3819) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 221 time to evaluate : 1.443 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: D 51 LYS cc_start: 0.8710 (tmtm) cc_final: 0.8124 (tmmt) REVERT: D 85 ASN cc_start: 0.9417 (p0) cc_final: 0.8737 (t0) REVERT: D 91 ILE cc_start: 0.7837 (mt) cc_final: 0.7469 (tp) REVERT: D 98 ASP cc_start: 0.6761 (m-30) cc_final: 0.6393 (m-30) REVERT: E 2 MET cc_start: 0.6751 (mtm) cc_final: 0.6444 (mmm) REVERT: E 36 TYR cc_start: 0.8732 (m-10) cc_final: 0.8495 (m-80) REVERT: E 37 TYR cc_start: 0.8452 (m-80) cc_final: 0.8218 (m-80) REVERT: E 39 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8976 (pp) REVERT: E 106 ARG cc_start: 0.8143 (ptm-80) cc_final: 0.7515 (ttp80) REVERT: E 114 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7295 (tm) REVERT: E 117 TYR cc_start: 0.9423 (m-80) cc_final: 0.8682 (m-80) REVERT: F 43 GLN cc_start: 0.7836 (tt0) cc_final: 0.7607 (tm130) REVERT: F 48 LYS cc_start: 0.9323 (mtpp) cc_final: 0.9053 (mptt) REVERT: F 67 ARG cc_start: 0.8392 (ptm160) cc_final: 0.7876 (ttm-80) REVERT: F 91 ILE cc_start: 0.9455 (mt) cc_final: 0.8520 (tt) REVERT: F 98 ASP cc_start: 0.7742 (m-30) cc_final: 0.7463 (m-30) REVERT: F 169 TRP cc_start: 0.6001 (OUTLIER) cc_final: 0.5305 (m-90) REVERT: F 180 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7821 (p) REVERT: G 3 GLN cc_start: 0.9060 (tp40) cc_final: 0.8516 (pp30) REVERT: G 45 MET cc_start: 0.8340 (tmm) cc_final: 0.8025 (ppp) REVERT: G 51 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7609 (pt0) REVERT: G 53 MET cc_start: 0.9110 (mtm) cc_final: 0.8549 (mtm) REVERT: G 75 GLN cc_start: 0.8946 (mp10) cc_final: 0.8284 (mp10) REVERT: G 114 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8195 (tm) REVERT: G 117 TYR cc_start: 0.8671 (m-80) cc_final: 0.8273 (m-10) REVERT: G 161 PHE cc_start: 0.8338 (m-80) cc_final: 0.7724 (m-80) REVERT: H 123 MET cc_start: 0.8701 (mmm) cc_final: 0.8066 (mpt) REVERT: H 169 TRP cc_start: 0.6980 (OUTLIER) cc_final: 0.6450 (m-90) REVERT: I 2 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8430 (tmm) REVERT: I 38 TRP cc_start: 0.7170 (m100) cc_final: 0.5664 (m100) REVERT: I 45 MET cc_start: 0.9027 (mmt) cc_final: 0.8674 (mmp) REVERT: I 53 MET cc_start: 0.8261 (mpp) cc_final: 0.7908 (mmt) REVERT: I 71 PHE cc_start: 0.9502 (m-80) cc_final: 0.9290 (m-80) REVERT: I 88 TYR cc_start: 0.9592 (m-80) cc_final: 0.9376 (m-80) REVERT: I 112 TRP cc_start: 0.7506 (p-90) cc_final: 0.7017 (p-90) REVERT: C 242 LEU cc_start: 0.8971 (mm) cc_final: 0.8666 (tm) REVERT: C 336 CYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7731 (p) REVERT: C 571 ASP cc_start: 0.8697 (t0) cc_final: 0.8392 (t0) REVERT: C 646 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8594 (ttp80) REVERT: C 697 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8967 (pp) REVERT: C 904 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8701 (mtt) REVERT: B 138 ASN cc_start: 0.8568 (m-40) cc_final: 0.7747 (p0) REVERT: B 269 TYR cc_start: 0.8809 (m-80) cc_final: 0.8543 (m-80) REVERT: B 341 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8438 (p) REVERT: B 378 LYS cc_start: 0.9077 (ttmm) cc_final: 0.8730 (ptmm) REVERT: B 983 ASP cc_start: 0.8920 (t70) cc_final: 0.8183 (t0) REVERT: B 1006 GLN cc_start: 0.9149 (tp40) cc_final: 0.8585 (tp-100) REVERT: A 701 MET cc_start: 0.9217 (ptp) cc_final: 0.8957 (ptm) REVERT: A 777 GLU cc_start: 0.9066 (tt0) cc_final: 0.8830 (tt0) outliers start: 91 outliers final: 33 residues processed: 291 average time/residue: 0.6478 time to fit residues: 230.6646 Evaluate side-chains 250 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 169 TRP Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 193 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 1153 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 61 optimal weight: 20.0000 chunk 393 optimal weight: 7.9990 chunk 114 optimal weight: 50.0000 chunk 76 optimal weight: 50.0000 chunk 192 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 286 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 405 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN E 90 HIS F 6 GLN G 90 HIS G 179 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN C 409 GLN ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 613 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.104599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.061157 restraints weight = 122936.475| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 4.10 r_work: 0.2910 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35911 Z= 0.213 Angle : 0.580 9.444 48897 Z= 0.292 Chirality : 0.045 0.265 5489 Planarity : 0.004 0.061 6271 Dihedral : 4.227 56.212 4836 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.43 % Allowed : 10.52 % Favored : 87.05 % 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: -0.14 (0.13), residues: 4430 helix: 1.62 (0.19), residues: 790 sheet: 0.30 (0.15), residues: 1230 loop : -0.88 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 8 TYR 0.029 0.001 TYR D 161 PHE 0.019 0.001 PHE F 76 TRP 0.019 0.001 TRP A 105 HIS 0.008 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00479 (35860) covalent geometry : angle 0.57928 (48795) SS BOND : bond 0.00242 ( 51) SS BOND : angle 0.96360 ( 102) hydrogen bonds : bond 0.03745 ( 1348) hydrogen bonds : angle 5.60976 ( 3819) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 210 time to evaluate : 1.523 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: D 51 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8088 (tmmt) REVERT: D 85 ASN cc_start: 0.9419 (p0) cc_final: 0.8707 (t0) REVERT: D 91 ILE cc_start: 0.7892 (mt) cc_final: 0.7520 (tp) REVERT: D 98 ASP cc_start: 0.6803 (m-30) cc_final: 0.6419 (m-30) REVERT: D 161 TYR cc_start: 0.8928 (t80) cc_final: 0.8680 (m-80) REVERT: E 2 MET cc_start: 0.7074 (mtm) cc_final: 0.6715 (mmm) REVERT: E 36 TYR cc_start: 0.8910 (m-80) cc_final: 0.8623 (m-80) REVERT: E 37 TYR cc_start: 0.8549 (m-80) cc_final: 0.8321 (m-10) REVERT: E 106 ARG cc_start: 0.8150 (ptm-80) cc_final: 0.6814 (tmm-80) REVERT: E 114 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7449 (tm) REVERT: E 117 TYR cc_start: 0.9402 (m-80) cc_final: 0.8589 (m-80) REVERT: F 26 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8152 (pp) REVERT: F 48 LYS cc_start: 0.9294 (mtpp) cc_final: 0.9046 (mptt) REVERT: F 67 ARG cc_start: 0.8385 (ptm160) cc_final: 0.7928 (ttm-80) REVERT: F 74 ASP cc_start: 0.9526 (p0) cc_final: 0.9218 (t0) REVERT: F 91 ILE cc_start: 0.9304 (mt) cc_final: 0.9007 (mt) REVERT: F 169 TRP cc_start: 0.5951 (OUTLIER) cc_final: 0.5246 (m-90) REVERT: F 180 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7716 (p) REVERT: G 2 MET cc_start: 0.8450 (mtp) cc_final: 0.8103 (ptm) REVERT: G 45 MET cc_start: 0.8583 (tmm) cc_final: 0.8341 (tmm) REVERT: G 51 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7589 (pt0) REVERT: G 53 MET cc_start: 0.9114 (mtm) cc_final: 0.8536 (mtm) REVERT: G 75 GLN cc_start: 0.9020 (mp10) cc_final: 0.8382 (mp10) REVERT: G 161 PHE cc_start: 0.8352 (m-80) cc_final: 0.7595 (m-80) REVERT: H 23 CYS cc_start: 0.0911 (t) cc_final: 0.0079 (t) REVERT: H 105 CYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6131 (t) REVERT: H 123 MET cc_start: 0.8670 (mmm) cc_final: 0.7990 (mpt) REVERT: H 169 TRP cc_start: 0.6073 (OUTLIER) cc_final: 0.5150 (m-90) REVERT: I 2 MET cc_start: 0.8510 (tmt) cc_final: 0.8208 (tmm) REVERT: I 21 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7379 (pp) REVERT: I 38 TRP cc_start: 0.7179 (m100) cc_final: 0.5340 (m100) REVERT: I 45 MET cc_start: 0.9071 (mmt) cc_final: 0.8729 (mmm) REVERT: I 88 TYR cc_start: 0.9574 (m-80) cc_final: 0.9352 (m-80) REVERT: I 112 TRP cc_start: 0.7483 (p-90) cc_final: 0.7010 (p-90) REVERT: I 114 LEU cc_start: 0.5102 (OUTLIER) cc_final: 0.4846 (tp) REVERT: C 126 ASN cc_start: 0.8666 (t0) cc_final: 0.8247 (t0) REVERT: C 242 LEU cc_start: 0.9040 (mm) cc_final: 0.8712 (tm) REVERT: C 336 CYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7771 (p) REVERT: C 571 ASP cc_start: 0.8692 (t0) cc_final: 0.8372 (t0) REVERT: C 646 ARG cc_start: 0.9303 (OUTLIER) cc_final: 0.8594 (ttp80) REVERT: C 697 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.9046 (pp) REVERT: B 55 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9145 (mm) REVERT: B 179 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7355 (pt) REVERT: B 269 TYR cc_start: 0.8867 (m-80) cc_final: 0.8419 (m-80) REVERT: B 983 ASP cc_start: 0.8996 (OUTLIER) cc_final: 0.8319 (OUTLIER) REVERT: A 105 TRP cc_start: 0.8484 (m-90) cc_final: 0.8185 (m-90) REVERT: A 701 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8974 (ptm) REVERT: A 777 GLU cc_start: 0.9132 (tt0) cc_final: 0.8899 (tt0) outliers start: 95 outliers final: 34 residues processed: 291 average time/residue: 0.6346 time to fit residues: 226.7323 Evaluate side-chains 238 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 169 TRP Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 193 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 961 GLN Chi-restraints excluded: chain A residue 1153 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 1 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 chunk 331 optimal weight: 4.9990 chunk 269 optimal weight: 0.6980 chunk 86 optimal weight: 50.0000 chunk 103 optimal weight: 50.0000 chunk 84 optimal weight: 20.0000 chunk 388 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 325 optimal weight: 0.5980 chunk 216 optimal weight: 2.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN D 37 ASN D 45 HIS D 129 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 HIS G 179 HIS I 170 ASN C 409 GLN ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN A 959 ASN A 961 GLN A1009 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.104505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.060857 restraints weight = 123137.188| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 4.34 r_work: 0.2903 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35911 Z= 0.188 Angle : 0.566 9.948 48897 Z= 0.284 Chirality : 0.044 0.185 5489 Planarity : 0.004 0.062 6271 Dihedral : 4.216 54.960 4835 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.64 % Allowed : 10.93 % Favored : 86.44 % 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: -0.06 (0.13), residues: 4430 helix: 1.73 (0.19), residues: 784 sheet: 0.30 (0.15), residues: 1214 loop : -0.81 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 646 TYR 0.021 0.001 TYR C 841 PHE 0.027 0.001 PHE I 71 TRP 0.023 0.001 TRP H 41 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00425 (35860) covalent geometry : angle 0.56482 (48795) SS BOND : bond 0.00207 ( 51) SS BOND : angle 0.85792 ( 102) hydrogen bonds : bond 0.03547 ( 1348) hydrogen bonds : angle 5.46180 ( 3819) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 193 time to evaluate : 1.413 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: D 17 GLN cc_start: 0.7171 (pt0) cc_final: 0.6414 (pp30) REVERT: D 51 LYS cc_start: 0.8778 (tmtm) cc_final: 0.8434 (tmmm) REVERT: D 85 ASN cc_start: 0.9423 (p0) cc_final: 0.8600 (t0) REVERT: D 91 ILE cc_start: 0.7859 (mt) cc_final: 0.7407 (tp) REVERT: D 98 ASP cc_start: 0.6791 (m-30) cc_final: 0.6386 (m-30) REVERT: E 36 TYR cc_start: 0.9003 (m-80) cc_final: 0.8734 (m-80) REVERT: E 45 MET cc_start: 0.9008 (tmm) cc_final: 0.8559 (ppp) REVERT: E 106 ARG cc_start: 0.8287 (ptm-80) cc_final: 0.7942 (ttp80) REVERT: E 117 TYR cc_start: 0.9421 (m-80) cc_final: 0.8625 (m-80) REVERT: F 26 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8048 (pp) REVERT: F 48 LYS cc_start: 0.9412 (mtpp) cc_final: 0.9166 (mptt) REVERT: F 67 ARG cc_start: 0.8312 (ptm160) cc_final: 0.7754 (ttm-80) REVERT: F 74 ASP cc_start: 0.9480 (p0) cc_final: 0.9107 (t0) REVERT: F 91 ILE cc_start: 0.9345 (mt) cc_final: 0.9109 (mt) REVERT: F 169 TRP cc_start: 0.6099 (OUTLIER) cc_final: 0.5688 (m-90) REVERT: F 180 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.8026 (p) REVERT: G 21 ILE cc_start: 0.9104 (mp) cc_final: 0.8787 (mm) REVERT: G 51 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7577 (pt0) REVERT: G 53 MET cc_start: 0.9094 (mtm) cc_final: 0.8544 (mtm) REVERT: G 161 PHE cc_start: 0.8406 (m-80) cc_final: 0.7700 (m-80) REVERT: H 53 MET cc_start: 0.7794 (mtm) cc_final: 0.7355 (pmt) REVERT: H 123 MET cc_start: 0.8792 (mmm) cc_final: 0.8261 (mpt) REVERT: H 169 TRP cc_start: 0.7018 (OUTLIER) cc_final: 0.6438 (m-90) REVERT: I 2 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8532 (tmm) REVERT: I 21 ILE cc_start: 0.7325 (OUTLIER) cc_final: 0.7021 (pp) REVERT: I 38 TRP cc_start: 0.7677 (m100) cc_final: 0.5826 (m100) REVERT: I 45 MET cc_start: 0.9041 (mmt) cc_final: 0.8788 (mmm) REVERT: I 88 TYR cc_start: 0.9596 (m-80) cc_final: 0.9389 (m-80) REVERT: I 112 TRP cc_start: 0.7518 (p-90) cc_final: 0.7056 (p-90) REVERT: C 126 ASN cc_start: 0.8692 (t0) cc_final: 0.8211 (t0) REVERT: C 242 LEU cc_start: 0.9094 (mm) cc_final: 0.8761 (tm) REVERT: C 314 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8393 (tm-30) REVERT: C 336 CYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7757 (p) REVERT: C 571 ASP cc_start: 0.8756 (t0) cc_final: 0.8453 (t0) REVERT: C 646 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8577 (ttp80) REVERT: C 697 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.9005 (pp) REVERT: B 55 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9179 (mm) REVERT: B 179 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7182 (pt) REVERT: B 983 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8369 (OUTLIER) REVERT: A 105 TRP cc_start: 0.8515 (m-90) cc_final: 0.8260 (m-90) REVERT: A 701 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.9002 (ptm) REVERT: A 777 GLU cc_start: 0.9109 (tt0) cc_final: 0.8859 (tt0) REVERT: A 983 ASP cc_start: 0.9124 (m-30) cc_final: 0.8903 (m-30) outliers start: 103 outliers final: 44 residues processed: 280 average time/residue: 0.6233 time to fit residues: 215.8890 Evaluate side-chains 240 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 169 TRP Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 193 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 961 GLN Chi-restraints excluded: chain A residue 1153 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 280 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 109 optimal weight: 50.0000 chunk 82 optimal weight: 8.9990 chunk 258 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 266 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 411 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN D 45 HIS D 129 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 939 GLN ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN A 148 ASN A1009 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.104117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.060391 restraints weight = 122585.799| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 4.24 r_work: 0.2889 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 35911 Z= 0.217 Angle : 0.583 10.322 48897 Z= 0.292 Chirality : 0.045 0.180 5489 Planarity : 0.004 0.055 6271 Dihedral : 4.307 53.682 4835 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.18 % Allowed : 11.77 % Favored : 86.05 % 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: -0.05 (0.13), residues: 4430 helix: 1.73 (0.19), residues: 783 sheet: 0.31 (0.15), residues: 1217 loop : -0.80 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 75 TYR 0.019 0.001 TYR C 841 PHE 0.017 0.001 PHE B 175 TRP 0.031 0.001 TRP H 41 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00490 (35860) covalent geometry : angle 0.58257 (48795) SS BOND : bond 0.00225 ( 51) SS BOND : angle 0.85918 ( 102) hydrogen bonds : bond 0.03620 ( 1348) hydrogen bonds : angle 5.44151 ( 3819) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 190 time to evaluate : 1.439 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: D 17 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6504 (pp30) REVERT: D 51 LYS cc_start: 0.8776 (tmtm) cc_final: 0.8357 (tmmt) REVERT: D 91 ILE cc_start: 0.7930 (mt) cc_final: 0.7476 (tt) REVERT: D 98 ASP cc_start: 0.6690 (m-30) cc_final: 0.6296 (m-30) REVERT: E 2 MET cc_start: 0.7553 (mmm) cc_final: 0.7294 (mmm) REVERT: E 36 TYR cc_start: 0.8971 (m-80) cc_final: 0.8668 (m-80) REVERT: E 106 ARG cc_start: 0.8334 (ptm-80) cc_final: 0.7920 (ttp80) REVERT: E 117 TYR cc_start: 0.9476 (m-80) cc_final: 0.8664 (m-80) REVERT: F 26 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8249 (pp) REVERT: F 48 LYS cc_start: 0.9309 (mtpp) cc_final: 0.9067 (mptt) REVERT: F 54 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7882 (mp) REVERT: F 67 ARG cc_start: 0.8344 (ptm160) cc_final: 0.7677 (ttm-80) REVERT: F 74 ASP cc_start: 0.9495 (p0) cc_final: 0.9145 (t0) REVERT: F 91 ILE cc_start: 0.9331 (mt) cc_final: 0.9084 (mt) REVERT: F 169 TRP cc_start: 0.6096 (OUTLIER) cc_final: 0.5556 (m-90) REVERT: F 180 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7908 (p) REVERT: G 21 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8861 (mm) REVERT: G 45 MET cc_start: 0.8476 (tmm) cc_final: 0.8118 (ppp) REVERT: G 53 MET cc_start: 0.9060 (mtm) cc_final: 0.8604 (mtm) REVERT: G 161 PHE cc_start: 0.8413 (m-80) cc_final: 0.7695 (m-10) REVERT: H 53 MET cc_start: 0.7767 (mtm) cc_final: 0.7234 (pmt) REVERT: H 123 MET cc_start: 0.8797 (mmm) cc_final: 0.8467 (mmt) REVERT: H 169 TRP cc_start: 0.7021 (OUTLIER) cc_final: 0.6405 (m-90) REVERT: I 2 MET cc_start: 0.8727 (tmt) cc_final: 0.8476 (tmm) REVERT: I 21 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7004 (pp) REVERT: I 38 TRP cc_start: 0.7735 (m100) cc_final: 0.5859 (m100) REVERT: I 45 MET cc_start: 0.9080 (mmt) cc_final: 0.8753 (mmp) REVERT: I 88 TYR cc_start: 0.9583 (m-80) cc_final: 0.9377 (m-80) REVERT: I 112 TRP cc_start: 0.7508 (p-90) cc_final: 0.7104 (p-90) REVERT: I 118 TRP cc_start: 0.7415 (m-90) cc_final: 0.7213 (m-90) REVERT: C 126 ASN cc_start: 0.8757 (t0) cc_final: 0.8297 (t0) REVERT: C 314 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8347 (tm-30) REVERT: C 336 CYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7746 (p) REVERT: C 571 ASP cc_start: 0.8756 (t0) cc_final: 0.8459 (t0) REVERT: C 646 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8568 (ttp80) REVERT: C 697 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.9005 (pp) REVERT: C 832 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9125 (tt) REVERT: B 55 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9199 (mm) REVERT: B 179 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7180 (pt) REVERT: B 378 LYS cc_start: 0.8929 (ttmm) cc_final: 0.8581 (ptmm) REVERT: B 983 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8437 (OUTLIER) REVERT: A 338 PHE cc_start: 0.8499 (m-80) cc_final: 0.8073 (t80) REVERT: A 701 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.9013 (ptm) REVERT: A 777 GLU cc_start: 0.9081 (tt0) cc_final: 0.8823 (tt0) outliers start: 85 outliers final: 45 residues processed: 262 average time/residue: 0.6269 time to fit residues: 202.8488 Evaluate side-chains 238 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 169 TRP Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 193 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 518 LEU 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 862 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 742 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 103 optimal weight: 4.9990 chunk 291 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 357 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 330 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN D 129 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN A 959 ASN A 961 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.104466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.060923 restraints weight = 123239.624| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.29 r_work: 0.2899 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35911 Z= 0.167 Angle : 0.567 11.539 48897 Z= 0.282 Chirality : 0.044 0.177 5489 Planarity : 0.004 0.055 6271 Dihedral : 4.270 53.313 4835 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.33 % Allowed : 12.28 % Favored : 85.39 % 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: 0.01 (0.13), residues: 4430 helix: 1.79 (0.19), residues: 790 sheet: 0.35 (0.15), residues: 1203 loop : -0.77 (0.12), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 8 TYR 0.021 0.001 TYR I 103 PHE 0.015 0.001 PHE B 175 TRP 0.038 0.001 TRP H 41 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00378 (35860) covalent geometry : angle 0.56635 (48795) SS BOND : bond 0.00186 ( 51) SS BOND : angle 0.81315 ( 102) hydrogen bonds : bond 0.03418 ( 1348) hydrogen bonds : angle 5.31741 ( 3819) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 183 time to evaluate : 1.435 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: D 17 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6601 (pp30) REVERT: D 51 LYS cc_start: 0.8870 (tmtm) cc_final: 0.8438 (tmmt) REVERT: D 98 ASP cc_start: 0.6667 (m-30) cc_final: 0.6446 (m-30) REVERT: E 2 MET cc_start: 0.7548 (mmm) cc_final: 0.7302 (mmm) REVERT: E 36 TYR cc_start: 0.9013 (m-80) cc_final: 0.8723 (m-80) REVERT: E 45 MET cc_start: 0.9029 (tmm) cc_final: 0.8514 (ppp) REVERT: E 117 TYR cc_start: 0.9476 (m-80) cc_final: 0.8678 (m-80) REVERT: F 48 LYS cc_start: 0.9359 (mtpp) cc_final: 0.9105 (mptt) REVERT: F 54 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7912 (mp) REVERT: F 56 ASP cc_start: 0.7903 (t70) cc_final: 0.7486 (t70) REVERT: F 67 ARG cc_start: 0.8340 (ptm160) cc_final: 0.7701 (ttm-80) REVERT: F 74 ASP cc_start: 0.9488 (p0) cc_final: 0.9074 (t0) REVERT: F 75 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7037 (tmm-80) REVERT: F 91 ILE cc_start: 0.9264 (mt) cc_final: 0.9039 (tt) REVERT: F 101 ASP cc_start: 0.8906 (t0) cc_final: 0.8652 (t0) REVERT: F 169 TRP cc_start: 0.6092 (OUTLIER) cc_final: 0.5553 (m-90) REVERT: F 180 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7943 (p) REVERT: G 2 MET cc_start: 0.8513 (mtp) cc_final: 0.7927 (ptm) REVERT: G 3 GLN cc_start: 0.9131 (tp40) cc_final: 0.8885 (pp30) REVERT: G 45 MET cc_start: 0.8546 (tmm) cc_final: 0.8260 (ppp) REVERT: G 51 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7842 (mm-30) REVERT: G 53 MET cc_start: 0.9007 (mtm) cc_final: 0.8618 (mtm) REVERT: G 101 MET cc_start: 0.8172 (tpp) cc_final: 0.7960 (tpp) REVERT: G 161 PHE cc_start: 0.8434 (m-80) cc_final: 0.7695 (m-10) REVERT: H 53 MET cc_start: 0.7799 (mtm) cc_final: 0.7266 (pmt) REVERT: H 123 MET cc_start: 0.8853 (mmm) cc_final: 0.8537 (mmt) REVERT: I 2 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8336 (tmm) REVERT: I 21 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7226 (pp) REVERT: I 38 TRP cc_start: 0.7660 (m100) cc_final: 0.5679 (m100) REVERT: I 45 MET cc_start: 0.9071 (mmt) cc_final: 0.8719 (mmp) REVERT: I 88 TYR cc_start: 0.9578 (m-80) cc_final: 0.9359 (m-80) REVERT: I 115 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7533 (mm) REVERT: C 126 ASN cc_start: 0.8758 (t0) cc_final: 0.8320 (t0) REVERT: C 129 ILE cc_start: 0.8509 (mt) cc_final: 0.8305 (mp) REVERT: C 314 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8340 (tm-30) REVERT: C 336 CYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7762 (p) REVERT: C 571 ASP cc_start: 0.8775 (t0) cc_final: 0.8447 (t0) REVERT: C 646 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.8574 (ttp80) REVERT: C 697 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.9016 (pp) REVERT: C 832 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9215 (tt) REVERT: B 179 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7115 (pt) REVERT: B 378 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8526 (ptmm) REVERT: B 983 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8436 (OUTLIER) REVERT: A 701 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.9018 (ptm) REVERT: A 983 ASP cc_start: 0.9135 (m-30) cc_final: 0.8923 (m-30) outliers start: 91 outliers final: 46 residues processed: 256 average time/residue: 0.5807 time to fit residues: 185.0201 Evaluate side-chains 237 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 177 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 169 TRP Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 193 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 518 LEU 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 862 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 742 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 137 optimal weight: 3.9990 chunk 271 optimal weight: 6.9990 chunk 359 optimal weight: 30.0000 chunk 411 optimal weight: 0.0170 chunk 12 optimal weight: 40.0000 chunk 189 optimal weight: 4.9990 chunk 392 optimal weight: 2.9990 chunk 51 optimal weight: 50.0000 chunk 138 optimal weight: 4.9990 chunk 237 optimal weight: 9.9990 chunk 420 optimal weight: 1.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN D 129 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 644 GLN C 917 GLN ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN A 658 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.104245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.061187 restraints weight = 123292.109| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 4.04 r_work: 0.2897 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35911 Z= 0.179 Angle : 0.580 11.522 48897 Z= 0.288 Chirality : 0.044 0.168 5489 Planarity : 0.004 0.056 6271 Dihedral : 4.225 52.758 4833 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.05 % Allowed : 12.69 % Favored : 85.26 % 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: 0.03 (0.13), residues: 4430 helix: 1.83 (0.19), residues: 784 sheet: 0.37 (0.15), residues: 1200 loop : -0.76 (0.12), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 106 TYR 0.016 0.001 TYR C 841 PHE 0.022 0.001 PHE B1152 TRP 0.042 0.001 TRP H 41 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00407 (35860) covalent geometry : angle 0.57943 (48795) SS BOND : bond 0.00220 ( 51) SS BOND : angle 0.82392 ( 102) hydrogen bonds : bond 0.03423 ( 1348) hydrogen bonds : angle 5.28874 ( 3819) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 179 time to evaluate : 1.441 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: D 17 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6601 (pp30) REVERT: D 51 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8429 (tmmt) REVERT: D 98 ASP cc_start: 0.6990 (m-30) cc_final: 0.6755 (m-30) REVERT: E 36 TYR cc_start: 0.9012 (m-80) cc_final: 0.8734 (m-80) REVERT: E 45 MET cc_start: 0.9032 (tmm) cc_final: 0.8573 (ppp) REVERT: E 106 ARG cc_start: 0.9083 (ttp80) cc_final: 0.8322 (tmm-80) REVERT: E 117 TYR cc_start: 0.9436 (m-80) cc_final: 0.8682 (m-80) REVERT: F 54 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7917 (mp) REVERT: F 56 ASP cc_start: 0.7979 (t70) cc_final: 0.7741 (t70) REVERT: F 67 ARG cc_start: 0.8406 (ptm160) cc_final: 0.7784 (ttp-170) REVERT: F 74 ASP cc_start: 0.9502 (p0) cc_final: 0.9173 (t0) REVERT: F 101 ASP cc_start: 0.8814 (t0) cc_final: 0.8578 (t0) REVERT: F 169 TRP cc_start: 0.5860 (OUTLIER) cc_final: 0.5093 (m-90) REVERT: F 180 VAL cc_start: 0.7986 (OUTLIER) cc_final: 0.7619 (p) REVERT: G 2 MET cc_start: 0.8526 (mtp) cc_final: 0.7966 (ptm) REVERT: G 3 GLN cc_start: 0.9160 (tp40) cc_final: 0.8942 (pp30) REVERT: G 45 MET cc_start: 0.8568 (tmm) cc_final: 0.8342 (ppp) REVERT: G 51 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7913 (mm-30) REVERT: G 53 MET cc_start: 0.8987 (mtm) cc_final: 0.8581 (mtm) REVERT: G 161 PHE cc_start: 0.8488 (m-80) cc_final: 0.7614 (m-10) REVERT: H 53 MET cc_start: 0.8184 (mtm) cc_final: 0.7628 (pmt) REVERT: H 123 MET cc_start: 0.8815 (mmm) cc_final: 0.8403 (mmt) REVERT: I 2 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7726 (tmm) REVERT: I 21 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7453 (pp) REVERT: I 38 TRP cc_start: 0.7700 (m100) cc_final: 0.5284 (m100) REVERT: I 45 MET cc_start: 0.9073 (mmt) cc_final: 0.8686 (mmp) REVERT: I 88 TYR cc_start: 0.9548 (m-80) cc_final: 0.9253 (m-80) REVERT: C 126 ASN cc_start: 0.8737 (t0) cc_final: 0.8296 (t0) REVERT: C 129 ILE cc_start: 0.8579 (mt) cc_final: 0.8328 (mp) REVERT: C 336 CYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7707 (p) REVERT: C 571 ASP cc_start: 0.8825 (t0) cc_final: 0.8449 (t0) REVERT: C 646 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8586 (ttp80) REVERT: C 697 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9052 (pp) REVERT: B 143 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6668 (m-30) REVERT: B 179 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7079 (pt) REVERT: B 378 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8556 (ptmm) REVERT: B 983 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8451 (OUTLIER) REVERT: A 338 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8131 (t80) REVERT: A 701 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.9027 (ptm) REVERT: A 983 ASP cc_start: 0.9125 (m-30) cc_final: 0.8912 (m-30) outliers start: 80 outliers final: 49 residues processed: 243 average time/residue: 0.6218 time to fit residues: 187.4601 Evaluate side-chains 234 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 171 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 169 TRP Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 193 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 518 LEU 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 862 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 701 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 201 optimal weight: 0.8980 chunk 391 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 307 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 346 optimal weight: 30.0000 chunk 181 optimal weight: 0.8980 chunk 273 optimal weight: 2.9990 chunk 39 optimal weight: 30.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN D 129 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN A 905 GLN A 961 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.104823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.061901 restraints weight = 122802.359| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.15 r_work: 0.2917 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35911 Z= 0.129 Angle : 0.576 12.429 48897 Z= 0.286 Chirality : 0.044 0.180 5489 Planarity : 0.004 0.057 6271 Dihedral : 4.194 52.928 4833 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.89 % Allowed : 12.97 % Favored : 85.13 % 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: 0.12 (0.13), residues: 4430 helix: 1.97 (0.19), residues: 778 sheet: 0.47 (0.15), residues: 1185 loop : -0.74 (0.12), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 8 TYR 0.019 0.001 TYR D 55 PHE 0.014 0.001 PHE B 175 TRP 0.041 0.001 TRP H 41 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00294 (35860) covalent geometry : angle 0.57563 (48795) SS BOND : bond 0.00165 ( 51) SS BOND : angle 0.83743 ( 102) hydrogen bonds : bond 0.03268 ( 1348) hydrogen bonds : angle 5.21997 ( 3819) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 173 time to evaluate : 1.405 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: D 17 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6626 (pp30) REVERT: D 51 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8391 (tmmt) REVERT: D 98 ASP cc_start: 0.6889 (m-30) cc_final: 0.6657 (m-30) REVERT: E 36 TYR cc_start: 0.8836 (m-80) cc_final: 0.8537 (m-80) REVERT: E 37 TYR cc_start: 0.8455 (m-10) cc_final: 0.8203 (m-80) REVERT: E 45 MET cc_start: 0.9054 (tmm) cc_final: 0.8609 (ppp) REVERT: E 106 ARG cc_start: 0.8988 (ttp80) cc_final: 0.8212 (tmm-80) REVERT: E 117 TYR cc_start: 0.9369 (m-80) cc_final: 0.8646 (m-80) REVERT: F 48 LYS cc_start: 0.9224 (mtpp) cc_final: 0.9014 (mptt) REVERT: F 67 ARG cc_start: 0.8271 (ptm160) cc_final: 0.7720 (ttp-170) REVERT: F 74 ASP cc_start: 0.9546 (p0) cc_final: 0.9202 (t0) REVERT: F 101 ASP cc_start: 0.8799 (t0) cc_final: 0.8568 (t0) REVERT: F 169 TRP cc_start: 0.5970 (OUTLIER) cc_final: 0.5188 (m-90) REVERT: F 180 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7767 (p) REVERT: G 2 MET cc_start: 0.8505 (mtp) cc_final: 0.7948 (ptm) REVERT: G 3 GLN cc_start: 0.9094 (tp40) cc_final: 0.8806 (pp30) REVERT: G 45 MET cc_start: 0.8661 (tmm) cc_final: 0.8344 (ppp) REVERT: G 51 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7841 (mm-30) REVERT: G 161 PHE cc_start: 0.8510 (m-80) cc_final: 0.8180 (m-10) REVERT: H 53 MET cc_start: 0.8036 (mtm) cc_final: 0.7011 (pmt) REVERT: H 123 MET cc_start: 0.8881 (mmm) cc_final: 0.8519 (mmt) REVERT: I 2 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8132 (tmm) REVERT: I 21 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7316 (pp) REVERT: I 38 TRP cc_start: 0.7762 (m100) cc_final: 0.5658 (m100) REVERT: I 45 MET cc_start: 0.9084 (mmt) cc_final: 0.8719 (mmp) REVERT: I 88 TYR cc_start: 0.9578 (m-80) cc_final: 0.9327 (m-80) REVERT: C 126 ASN cc_start: 0.8776 (t0) cc_final: 0.8371 (t0) REVERT: C 129 ILE cc_start: 0.8473 (mt) cc_final: 0.8262 (mp) REVERT: C 177 MET cc_start: 0.5754 (pmm) cc_final: 0.5259 (pmm) REVERT: C 336 CYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7856 (p) REVERT: C 571 ASP cc_start: 0.8768 (t0) cc_final: 0.8410 (t0) REVERT: C 646 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8569 (ttp80) REVERT: C 697 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.9044 (pp) REVERT: B 179 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7021 (pt) REVERT: B 378 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8519 (ptmm) REVERT: B 553 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8488 (p) REVERT: B 983 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8436 (OUTLIER) REVERT: A 338 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8147 (t80) REVERT: A 701 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.9027 (ptm) REVERT: A 983 ASP cc_start: 0.9140 (m-30) cc_final: 0.8926 (m-30) outliers start: 74 outliers final: 46 residues processed: 231 average time/residue: 0.6428 time to fit residues: 183.4295 Evaluate side-chains 223 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 164 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 169 TRP Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 193 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1153 LYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 518 LEU 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 862 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 742 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 200 optimal weight: 7.9990 chunk 90 optimal weight: 30.0000 chunk 104 optimal weight: 50.0000 chunk 272 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 chunk 49 optimal weight: 40.0000 chunk 111 optimal weight: 30.0000 chunk 100 optimal weight: 30.0000 chunk 327 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 345 optimal weight: 5.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C1092 HIS ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 808 GLN B 939 GLN ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.103124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.059104 restraints weight = 123849.770| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.35 r_work: 0.2861 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 35911 Z= 0.285 Angle : 0.649 13.291 48897 Z= 0.324 Chirality : 0.046 0.330 5489 Planarity : 0.004 0.055 6271 Dihedral : 4.425 51.144 4833 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.56 % Allowed : 13.43 % Favored : 85.01 % 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: 0.03 (0.13), residues: 4430 helix: 1.72 (0.19), residues: 789 sheet: 0.38 (0.15), residues: 1234 loop : -0.75 (0.13), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 158 TYR 0.018 0.002 TYR A 170 PHE 0.019 0.001 PHE C 175 TRP 0.035 0.002 TRP I 118 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00648 (35860) covalent geometry : angle 0.64760 (48795) SS BOND : bond 0.00293 ( 51) SS BOND : angle 1.02368 ( 102) hydrogen bonds : bond 0.03760 ( 1348) hydrogen bonds : angle 5.42287 ( 3819) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8860 Ramachandran restraints generated. 4430 Oldfield, 0 Emsley, 4430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 176 time to evaluate : 1.284 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: D 17 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6915 (pp30) REVERT: D 51 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8504 (tmmt) REVERT: D 98 ASP cc_start: 0.7031 (m-30) cc_final: 0.6808 (m-30) REVERT: E 45 MET cc_start: 0.9042 (tmm) cc_final: 0.8648 (ppp) REVERT: E 106 ARG cc_start: 0.9138 (ttp80) cc_final: 0.8580 (tmm-80) REVERT: E 117 TYR cc_start: 0.9407 (m-80) cc_final: 0.8648 (m-80) REVERT: F 56 ASP cc_start: 0.7540 (t70) cc_final: 0.7245 (t70) REVERT: F 67 ARG cc_start: 0.8618 (ptm160) cc_final: 0.8064 (ttp-170) REVERT: F 74 ASP cc_start: 0.9464 (p0) cc_final: 0.9103 (t0) REVERT: F 101 ASP cc_start: 0.8883 (t0) cc_final: 0.8607 (t0) REVERT: F 169 TRP cc_start: 0.6124 (OUTLIER) cc_final: 0.5586 (m-90) REVERT: F 180 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8091 (p) REVERT: G 2 MET cc_start: 0.8544 (mtp) cc_final: 0.8157 (ptm) REVERT: G 45 MET cc_start: 0.8626 (tmm) cc_final: 0.8380 (ppp) REVERT: G 51 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7902 (mm-30) REVERT: G 53 MET cc_start: 0.8992 (mtm) cc_final: 0.8320 (mtm) REVERT: G 161 PHE cc_start: 0.8547 (m-80) cc_final: 0.8196 (m-10) REVERT: H 123 MET cc_start: 0.8912 (mmm) cc_final: 0.8615 (mmt) REVERT: I 2 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8529 (tmm) REVERT: I 21 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.6987 (pp) REVERT: I 38 TRP cc_start: 0.7763 (m100) cc_final: 0.5584 (m100) REVERT: I 45 MET cc_start: 0.9048 (mmt) cc_final: 0.8692 (mmp) REVERT: C 177 MET cc_start: 0.5877 (pmm) cc_final: 0.5339 (pmm) REVERT: C 336 CYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7669 (p) REVERT: C 571 ASP cc_start: 0.8876 (t0) cc_final: 0.8525 (t0) REVERT: C 646 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.8598 (ttp80) REVERT: C 697 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.9005 (pp) REVERT: B 179 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7128 (pt) REVERT: B 378 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8443 (ptmm) REVERT: B 414 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8222 (tm-30) REVERT: B 983 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8458 (OUTLIER) REVERT: A 338 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8167 (t80) outliers start: 61 outliers final: 47 residues processed: 225 average time/residue: 0.5836 time to fit residues: 163.5992 Evaluate side-chains 227 residues out of total 3908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 169 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 169 TRP Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 193 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1153 LYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 518 LEU 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 862 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 742 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 103 optimal weight: 0.0570 chunk 102 optimal weight: 10.0000 chunk 216 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 264 optimal weight: 0.8980 chunk 299 optimal weight: 0.7980 chunk 190 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 317 optimal weight: 0.8980 chunk 286 optimal weight: 0.4980 chunk 257 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 606 ASN A 961 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.109978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.069461 restraints weight = 117694.504| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 4.27 r_work: 0.2925 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35911 Z= 0.114 Angle : 0.594 13.295 48897 Z= 0.295 Chirality : 0.044 0.187 5489 Planarity : 0.004 0.053 6271 Dihedral : 4.301 51.637 4833 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.59 % Allowed : 13.72 % Favored : 84.70 % 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: 4430 helix: 1.95 (0.19), residues: 778 sheet: 0.44 (0.15), residues: 1221 loop : -0.71 (0.13), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 106 TYR 0.026 0.001 TYR A 170 PHE 0.045 0.001 PHE A 168 TRP 0.033 0.001 TRP H 41 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00256 (35860) covalent geometry : angle 0.59341 (48795) SS BOND : bond 0.00163 ( 51) SS BOND : angle 0.86699 ( 102) hydrogen bonds : bond 0.03338 ( 1348) hydrogen bonds : angle 5.24507 ( 3819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19496.81 seconds wall clock time: 331 minutes 33.56 seconds (19893.56 seconds total)