Starting phenix.real_space_refine on Tue Mar 19 21:18:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx1_32167/03_2024/7vx1_32167.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx1_32167/03_2024/7vx1_32167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx1_32167/03_2024/7vx1_32167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx1_32167/03_2024/7vx1_32167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx1_32167/03_2024/7vx1_32167.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vx1_32167/03_2024/7vx1_32167.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 117 5.16 5 C 16197 2.51 5 N 4230 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25362 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 5 Chain: "B" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 5 Chain: "C" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 5 Time building chain proxies: 12.98, per 1000 atoms: 0.51 Number of scatterers: 25362 At special positions: 0 Unit cell: (162.857, 150.834, 217.507, 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 117 16.00 O 4818 8.00 N 4230 7.00 C 16197 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - 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 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 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - 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 361 " - pdb=" SG CYS B 391 " distance=2.63 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " 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 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - 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 379 " - pdb=" SG CYS C 432 " 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 9.12 Conformation dependent library (CDL) restraints added in 4.5 seconds 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6060 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 49 sheets defined 23.7% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.716A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.579A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.690A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.683A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 removed outlier: 4.259A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.930A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.307A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.607A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 5.559A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.957A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.692A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.213A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 3.589A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.563A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.843A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.731A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.104A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.568A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.783A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.959A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.304A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.570A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 5.598A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.845A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.514A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.026A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 4.180A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.579A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.959A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.503A pdb=" N TYR C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.951A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.675A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 removed outlier: 3.780A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 882 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.058A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.592A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.754A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.961A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.627A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.440A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.321A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C1154 " --> pdb=" O GLU C1150 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR C1155 " --> pdb=" O GLU C1151 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE C1156 " --> pdb=" O LEU C1152 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR C1160 " --> pdb=" O PHE C1156 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.129A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.106A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.645A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.686A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.513A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.095A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.780A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.969A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.045A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.629A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.425A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC1, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.916A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.987A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.804A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 141 through 142 removed outlier: 4.397A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.587A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 327 removed outlier: 4.055A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.687A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.941A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.642A pdb=" N VAL B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.555A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.650A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.231A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.694A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.746A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.708A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 359 removed outlier: 3.708A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.949A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.547A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 727 removed outlier: 3.655A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 807 through 808 removed outlier: 4.520A pdb=" N ARG C 815 " --> pdb=" O ASP C 808 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 944 hydrogen bonds defined for protein. 2631 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: 10.63 Time building geometry restraints manager: 10.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8189 1.34 - 1.46: 6314 1.46 - 1.58: 11306 1.58 - 1.70: 0 1.70 - 1.82: 147 Bond restraints: 25956 Sorted by residual: bond pdb=" C THR A 478 " pdb=" N PRO A 479 " ideal model delta sigma weight residual 1.334 1.424 -0.090 2.34e-02 1.83e+03 1.49e+01 bond pdb=" C CYS C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 1.334 1.405 -0.071 2.34e-02 1.83e+03 9.33e+00 bond pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.64e+00 bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.371 -0.038 2.34e-02 1.83e+03 2.57e+00 bond pdb=" CA THR C 531 " pdb=" C THR C 531 " ideal model delta sigma weight residual 1.522 1.543 -0.021 1.33e-02 5.65e+03 2.49e+00 ... (remaining 25951 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.14: 757 107.14 - 113.85: 14260 113.85 - 120.57: 9986 120.57 - 127.28: 10062 127.28 - 133.99: 239 Bond angle restraints: 35304 Sorted by residual: angle pdb=" CA CYS C 361 " pdb=" C CYS C 361 " pdb=" N VAL C 362 " ideal model delta sigma weight residual 119.52 115.80 3.72 7.90e-01 1.60e+00 2.21e+01 angle pdb=" C CYS C 361 " pdb=" CA CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sigma weight residual 116.54 111.29 5.25 1.15e+00 7.56e-01 2.08e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 121.54 129.59 -8.05 1.91e+00 2.74e-01 1.78e+01 angle pdb=" N VAL B 362 " pdb=" CA VAL B 362 " pdb=" C VAL B 362 " ideal model delta sigma weight residual 108.11 113.16 -5.05 1.40e+00 5.10e-01 1.30e+01 angle pdb=" C SER C 359 " pdb=" N ASN C 360 " pdb=" CA ASN C 360 " ideal model delta sigma weight residual 122.74 127.84 -5.10 1.44e+00 4.82e-01 1.26e+01 ... (remaining 35299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 15082 16.40 - 32.81: 247 32.81 - 49.21: 96 49.21 - 65.62: 15 65.62 - 82.02: 4 Dihedral angle restraints: 15444 sinusoidal: 6021 harmonic: 9423 Sorted by residual: dihedral pdb=" CA CYS C 361 " pdb=" C CYS C 361 " pdb=" N VAL C 362 " pdb=" CA VAL C 362 " ideal model delta harmonic sigma weight residual 180.00 153.29 26.71 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " ideal model delta harmonic sigma weight residual 122.80 133.73 -10.93 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" CA LYS C 529 " pdb=" C LYS C 529 " pdb=" N SER C 530 " pdb=" CA SER C 530 " ideal model delta harmonic sigma weight residual 180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 15441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3577 0.072 - 0.143: 398 0.143 - 0.215: 3 0.215 - 0.286: 1 0.286 - 0.358: 2 Chirality restraints: 3981 Sorted by residual: chirality pdb=" CA ASN B 360 " pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CB ASN B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA ASN C 360 " pdb=" N ASN C 360 " pdb=" C ASN C 360 " pdb=" CB ASN C 360 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ASN C 532 " pdb=" N ASN C 532 " pdb=" C ASN C 532 " pdb=" CB ASN C 532 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 3978 not shown) Planarity restraints: 4581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 359 " -0.009 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C SER C 359 " 0.034 2.00e-02 2.50e+03 pdb=" O SER C 359 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN C 360 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 241 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" C LEU A 241 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU A 241 " -0.010 2.00e-02 2.50e+03 pdb=" N HIS A 245 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.022 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 479 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.020 5.00e-02 4.00e+02 ... (remaining 4578 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 49 2.38 - 3.01: 13496 3.01 - 3.64: 35752 3.64 - 4.27: 56522 4.27 - 4.90: 94359 Nonbonded interactions: 200178 Sorted by model distance: nonbonded pdb=" ND2 ASN B 360 " pdb=" OG1 THR B 523 " model vdw 1.753 2.520 nonbonded pdb=" OG1 THR C 333 " pdb=" ND2 ASN C 360 " model vdw 2.018 2.520 nonbonded pdb=" CB LEU B 335 " pdb=" O ALA B 363 " model vdw 2.083 3.440 nonbonded pdb=" O VAL B 327 " pdb=" OG1 THR B 531 " model vdw 2.198 2.440 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.202 2.440 ... (remaining 200173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.200 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 66.510 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.110 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5756 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 0.090 25956 Z= 0.124 Angle : 0.485 8.048 35304 Z= 0.292 Chirality : 0.042 0.358 3981 Planarity : 0.003 0.035 4581 Dihedral : 7.462 82.019 9279 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.28 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.12), residues: 3201 helix: -2.79 (0.13), residues: 653 sheet: -0.50 (0.17), residues: 660 loop : -1.19 (0.12), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.005 0.000 HIS A 245 PHE 0.014 0.001 PHE A 32 TYR 0.013 0.001 TYR B 501 ARG 0.002 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 579 time to evaluate : 2.434 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: A 106 PHE cc_start: 0.4920 (m-10) cc_final: 0.4665 (m-10) REVERT: A 285 ILE cc_start: 0.5833 (mt) cc_final: 0.5376 (mt) REVERT: A 309 GLU cc_start: 0.6442 (mt-10) cc_final: 0.5721 (mt-10) REVERT: A 417 ASN cc_start: 0.6370 (m-40) cc_final: 0.6001 (t0) REVERT: A 612 TYR cc_start: 0.6251 (m-10) cc_final: 0.5619 (m-80) REVERT: A 701 VAL cc_start: 0.8436 (t) cc_final: 0.8025 (p) REVERT: A 704 SER cc_start: 0.8352 (t) cc_final: 0.8065 (p) REVERT: A 733 LYS cc_start: 0.7802 (mtpt) cc_final: 0.7045 (ttmt) REVERT: A 736 VAL cc_start: 0.7480 (t) cc_final: 0.7263 (t) REVERT: A 884 SER cc_start: 0.7048 (m) cc_final: 0.6696 (t) REVERT: A 933 LYS cc_start: 0.7700 (mttt) cc_final: 0.7407 (mttt) REVERT: A 955 ASN cc_start: 0.7608 (m-40) cc_final: 0.7368 (m-40) REVERT: A 1028 LYS cc_start: 0.7509 (mttt) cc_final: 0.7238 (ttmm) REVERT: A 1113 GLN cc_start: 0.7123 (mt0) cc_final: 0.6916 (mt0) REVERT: B 61 ASN cc_start: 0.7614 (m-40) cc_final: 0.6647 (p0) REVERT: B 206 LYS cc_start: 0.7613 (tptt) cc_final: 0.6940 (tptp) REVERT: B 300 LYS cc_start: 0.6417 (mttt) cc_final: 0.6004 (mttm) REVERT: B 730 SER cc_start: 0.8200 (p) cc_final: 0.7917 (m) REVERT: B 776 LYS cc_start: 0.8212 (mttt) cc_final: 0.7871 (ttmt) REVERT: B 822 LEU cc_start: 0.7642 (mt) cc_final: 0.7431 (mm) REVERT: B 864 LEU cc_start: 0.7775 (tp) cc_final: 0.7522 (tp) REVERT: B 884 SER cc_start: 0.6549 (m) cc_final: 0.6216 (t) REVERT: B 887 THR cc_start: 0.7153 (p) cc_final: 0.6346 (t) REVERT: B 933 LYS cc_start: 0.7787 (mttt) cc_final: 0.7465 (ttmm) REVERT: B 953 ASN cc_start: 0.7604 (m-40) cc_final: 0.7285 (m-40) REVERT: B 1084 ASP cc_start: 0.4873 (p0) cc_final: 0.4442 (p0) REVERT: B 1105 THR cc_start: 0.7791 (t) cc_final: 0.7473 (p) REVERT: C 44 ARG cc_start: 0.7577 (mtt90) cc_final: 0.7375 (mtt90) REVERT: C 50 SER cc_start: 0.8172 (t) cc_final: 0.7956 (p) REVERT: C 117 LEU cc_start: 0.5425 (tp) cc_final: 0.4709 (mp) REVERT: C 129 LYS cc_start: 0.6257 (mttt) cc_final: 0.5570 (tppt) REVERT: C 206 LYS cc_start: 0.5776 (tptt) cc_final: 0.5224 (tttp) REVERT: C 588 THR cc_start: 0.7349 (m) cc_final: 0.7058 (t) REVERT: C 604 THR cc_start: 0.7391 (m) cc_final: 0.7154 (p) REVERT: C 704 SER cc_start: 0.8404 (t) cc_final: 0.7827 (p) REVERT: C 726 ILE cc_start: 0.7644 (mp) cc_final: 0.7331 (mt) REVERT: C 773 GLU cc_start: 0.6059 (mm-30) cc_final: 0.5855 (mm-30) REVERT: C 922 LEU cc_start: 0.6548 (mt) cc_final: 0.6264 (mt) REVERT: C 926 GLN cc_start: 0.6441 (mm-40) cc_final: 0.5884 (tp40) REVERT: C 936 ASP cc_start: 0.7609 (m-30) cc_final: 0.7220 (m-30) REVERT: C 963 VAL cc_start: 0.7489 (t) cc_final: 0.6806 (p) REVERT: C 976 VAL cc_start: 0.7322 (t) cc_final: 0.7039 (p) REVERT: C 1029 MET cc_start: 0.7343 (tpp) cc_final: 0.6996 (tpp) REVERT: C 1048 HIS cc_start: 0.7313 (t70) cc_final: 0.6812 (t70) outliers start: 0 outliers final: 0 residues processed: 579 average time/residue: 0.3887 time to fit residues: 345.6111 Evaluate side-chains 431 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 1.9990 chunk 243 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 chunk 187 optimal weight: 3.9990 chunk 291 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 563 GLN A 657 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN A 787 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 239 GLN B 360 ASN B 394 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1088 HIS B1101 HIS B1106 GLN C 417 ASN C 641 ASN C 644 GLN C 762 GLN C 824 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 965 GLN C1002 GLN C1005 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.137 25956 Z= 0.388 Angle : 0.709 11.054 35304 Z= 0.378 Chirality : 0.050 0.215 3981 Planarity : 0.005 0.067 4581 Dihedral : 4.825 23.109 3468 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.80 % Allowed : 5.05 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3201 helix: -0.22 (0.18), residues: 699 sheet: -0.26 (0.17), residues: 705 loop : -1.31 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 64 HIS 0.010 0.002 HIS C1064 PHE 0.041 0.003 PHE A1121 TYR 0.034 0.002 TYR C 789 ARG 0.008 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 471 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.7237 (mttt) cc_final: 0.6914 (mttp) REVERT: A 304 LYS cc_start: 0.7952 (mmmm) cc_final: 0.7582 (mmtm) REVERT: A 309 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6633 (mt-10) REVERT: A 417 ASN cc_start: 0.6679 (m-40) cc_final: 0.6308 (t0) REVERT: A 535 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8750 (mtmt) REVERT: A 701 VAL cc_start: 0.8636 (t) cc_final: 0.8365 (p) REVERT: A 702 GLU cc_start: 0.7243 (tt0) cc_final: 0.6941 (tm-30) REVERT: A 704 SER cc_start: 0.8452 (t) cc_final: 0.8074 (p) REVERT: A 746 SER cc_start: 0.5820 (t) cc_final: 0.5555 (t) REVERT: A 819 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7139 (mt-10) REVERT: A 954 GLN cc_start: 0.7563 (mm-40) cc_final: 0.7352 (mm-40) REVERT: A 967 SER cc_start: 0.7319 (p) cc_final: 0.7046 (t) REVERT: A 969 ASN cc_start: 0.8319 (m-40) cc_final: 0.7995 (m-40) REVERT: A 995 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.7197 (ttm-80) REVERT: A 1028 LYS cc_start: 0.7899 (mttt) cc_final: 0.7396 (ttmm) REVERT: A 1072 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6273 (mt-10) REVERT: A 1139 ASP cc_start: 0.7730 (t0) cc_final: 0.7517 (t0) REVERT: B 206 LYS cc_start: 0.7824 (tptt) cc_final: 0.7512 (tptp) REVERT: B 302 THR cc_start: 0.7820 (m) cc_final: 0.7570 (t) REVERT: B 539 VAL cc_start: 0.8329 (m) cc_final: 0.8077 (t) REVERT: B 752 LEU cc_start: 0.7949 (mt) cc_final: 0.7736 (tt) REVERT: B 765 ARG cc_start: 0.7210 (mtt180) cc_final: 0.6931 (mtt180) REVERT: B 775 ASP cc_start: 0.6909 (m-30) cc_final: 0.6618 (m-30) REVERT: B 776 LYS cc_start: 0.8311 (mttt) cc_final: 0.7985 (ttmt) REVERT: B 864 LEU cc_start: 0.7878 (tp) cc_final: 0.7658 (tp) REVERT: B 933 LYS cc_start: 0.7984 (mttt) cc_final: 0.7668 (ttmm) REVERT: B 934 ILE cc_start: 0.7857 (mm) cc_final: 0.7545 (mm) REVERT: B 950 ASP cc_start: 0.6464 (m-30) cc_final: 0.6243 (m-30) REVERT: B 1028 LYS cc_start: 0.7479 (mtmm) cc_final: 0.6932 (mtmm) REVERT: B 1068 VAL cc_start: 0.6075 (t) cc_final: 0.5216 (p) REVERT: B 1105 THR cc_start: 0.7896 (t) cc_final: 0.7676 (p) REVERT: C 31 SER cc_start: 0.6433 (OUTLIER) cc_final: 0.5323 (p) REVERT: C 129 LYS cc_start: 0.6794 (mttt) cc_final: 0.6550 (tmtt) REVERT: C 568 ASP cc_start: 0.6184 (p0) cc_final: 0.5905 (p0) REVERT: C 572 THR cc_start: 0.6560 (p) cc_final: 0.5600 (m) REVERT: C 588 THR cc_start: 0.7652 (m) cc_final: 0.7365 (t) REVERT: C 644 GLN cc_start: 0.6206 (OUTLIER) cc_final: 0.5656 (mt0) REVERT: C 655 HIS cc_start: 0.6880 (t-90) cc_final: 0.6475 (t70) REVERT: C 661 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6523 (mm-30) REVERT: C 698 SER cc_start: 0.8655 (t) cc_final: 0.8322 (t) REVERT: C 761 THR cc_start: 0.8484 (m) cc_final: 0.8219 (t) REVERT: C 773 GLU cc_start: 0.6492 (mm-30) cc_final: 0.6152 (mm-30) REVERT: C 912 THR cc_start: 0.6385 (m) cc_final: 0.5469 (p) REVERT: C 936 ASP cc_start: 0.7359 (m-30) cc_final: 0.7109 (m-30) REVERT: C 963 VAL cc_start: 0.7840 (t) cc_final: 0.7320 (p) REVERT: C 994 ASP cc_start: 0.6671 (m-30) cc_final: 0.6231 (m-30) REVERT: C 1029 MET cc_start: 0.7736 (tpp) cc_final: 0.7425 (tpp) REVERT: C 1031 GLU cc_start: 0.6409 (mt-10) cc_final: 0.6158 (mt-10) REVERT: C 1048 HIS cc_start: 0.7199 (t70) cc_final: 0.6813 (t70) outliers start: 51 outliers final: 29 residues processed: 499 average time/residue: 0.3829 time to fit residues: 295.6251 Evaluate side-chains 442 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 410 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 4.9990 chunk 90 optimal weight: 0.0070 chunk 242 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 292 optimal weight: 0.8980 chunk 315 optimal weight: 0.8980 chunk 260 optimal weight: 7.9990 chunk 289 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN B 536 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 914 ASN B1134 ASN C 239 GLN C 321 GLN C 641 ASN C 644 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1005 GLN C1011 GLN C1108 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25956 Z= 0.187 Angle : 0.528 9.406 35304 Z= 0.275 Chirality : 0.044 0.205 3981 Planarity : 0.004 0.063 4581 Dihedral : 4.280 21.648 3468 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.73 % Allowed : 8.02 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 3201 helix: 0.62 (0.19), residues: 711 sheet: -0.14 (0.18), residues: 693 loop : -1.15 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.004 0.001 HIS B 245 PHE 0.027 0.001 PHE C 643 TYR 0.015 0.001 TYR C1138 ARG 0.013 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 432 time to evaluate : 3.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 LYS cc_start: 0.7852 (mmmm) cc_final: 0.7590 (mmmm) REVERT: A 306 PHE cc_start: 0.5381 (p90) cc_final: 0.5142 (p90) REVERT: A 313 TYR cc_start: 0.7407 (m-80) cc_final: 0.7081 (m-80) REVERT: A 417 ASN cc_start: 0.6717 (m-40) cc_final: 0.6367 (t0) REVERT: A 534 VAL cc_start: 0.8197 (t) cc_final: 0.7931 (m) REVERT: A 567 ARG cc_start: 0.7331 (mpp80) cc_final: 0.7088 (mtm-85) REVERT: A 568 ASP cc_start: 0.6992 (p0) cc_final: 0.6719 (p0) REVERT: A 701 VAL cc_start: 0.8586 (t) cc_final: 0.8290 (p) REVERT: A 702 GLU cc_start: 0.7180 (tt0) cc_final: 0.6890 (tm-30) REVERT: A 704 SER cc_start: 0.8520 (t) cc_final: 0.8074 (p) REVERT: A 965 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7476 (mm-40) REVERT: A 969 ASN cc_start: 0.8272 (m-40) cc_final: 0.8045 (m-40) REVERT: A 1028 LYS cc_start: 0.7857 (mttt) cc_final: 0.7411 (ttmm) REVERT: A 1029 MET cc_start: 0.7663 (tpp) cc_final: 0.7367 (tpp) REVERT: A 1111 GLU cc_start: 0.6806 (mp0) cc_final: 0.6422 (mp0) REVERT: A 1139 ASP cc_start: 0.7701 (t0) cc_final: 0.7470 (t0) REVERT: B 195 LYS cc_start: 0.6626 (pttt) cc_final: 0.5827 (pttt) REVERT: B 201 PHE cc_start: 0.6650 (m-10) cc_final: 0.6410 (m-10) REVERT: B 302 THR cc_start: 0.7728 (m) cc_final: 0.7485 (t) REVERT: B 724 THR cc_start: 0.7960 (m) cc_final: 0.7597 (p) REVERT: B 727 LEU cc_start: 0.8307 (mt) cc_final: 0.8059 (mt) REVERT: B 752 LEU cc_start: 0.7971 (mt) cc_final: 0.7707 (tt) REVERT: B 933 LYS cc_start: 0.7838 (mttt) cc_final: 0.7550 (ttmm) REVERT: B 934 ILE cc_start: 0.7822 (mm) cc_final: 0.7526 (mm) REVERT: B 950 ASP cc_start: 0.6330 (m-30) cc_final: 0.6005 (m-30) REVERT: B 1105 THR cc_start: 0.7879 (t) cc_final: 0.7643 (p) REVERT: C 31 SER cc_start: 0.5955 (OUTLIER) cc_final: 0.5170 (p) REVERT: C 129 LYS cc_start: 0.6665 (mttt) cc_final: 0.6430 (tmtt) REVERT: C 567 ARG cc_start: 0.7212 (mtp85) cc_final: 0.6986 (mtm-85) REVERT: C 588 THR cc_start: 0.7408 (m) cc_final: 0.7120 (t) REVERT: C 655 HIS cc_start: 0.6790 (t-90) cc_final: 0.6429 (t70) REVERT: C 661 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6552 (mm-30) REVERT: C 773 GLU cc_start: 0.6183 (mm-30) cc_final: 0.5880 (mm-30) REVERT: C 776 LYS cc_start: 0.7846 (tttt) cc_final: 0.7638 (tttt) REVERT: C 854 LYS cc_start: 0.6594 (mtpt) cc_final: 0.6230 (mtpt) REVERT: C 902 MET cc_start: 0.7271 (tpp) cc_final: 0.6965 (mmt) REVERT: C 912 THR cc_start: 0.6266 (m) cc_final: 0.5402 (p) REVERT: C 963 VAL cc_start: 0.7804 (t) cc_final: 0.7116 (p) REVERT: C 964 LYS cc_start: 0.7454 (mttt) cc_final: 0.7169 (mttt) REVERT: C 994 ASP cc_start: 0.6585 (m-30) cc_final: 0.6161 (m-30) REVERT: C 1029 MET cc_start: 0.7657 (tpp) cc_final: 0.7166 (tpp) REVERT: C 1031 GLU cc_start: 0.6371 (mt-10) cc_final: 0.6110 (mt-10) REVERT: C 1048 HIS cc_start: 0.7337 (t70) cc_final: 0.6933 (t70) outliers start: 49 outliers final: 24 residues processed: 457 average time/residue: 0.3775 time to fit residues: 267.9294 Evaluate side-chains 421 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 396 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1011 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 0.6980 chunk 219 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 293 optimal weight: 0.6980 chunk 310 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 277 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 657 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 928 ASN A1088 HIS B 360 ASN B 536 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 641 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1011 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 25956 Z= 0.286 Angle : 0.579 10.118 35304 Z= 0.305 Chirality : 0.045 0.167 3981 Planarity : 0.005 0.084 4581 Dihedral : 4.544 25.250 3468 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.37 % Allowed : 9.07 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3201 helix: 0.67 (0.19), residues: 707 sheet: -0.17 (0.18), residues: 711 loop : -1.16 (0.13), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.006 0.001 HIS A 49 PHE 0.024 0.002 PHE A1121 TYR 0.020 0.002 TYR C 789 ARG 0.011 0.001 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 422 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.6560 (pm20) cc_final: 0.5645 (pm20) REVERT: A 301 CYS cc_start: 0.6169 (m) cc_final: 0.5919 (m) REVERT: A 304 LYS cc_start: 0.7882 (mmmm) cc_final: 0.7665 (mmmm) REVERT: A 417 ASN cc_start: 0.6804 (m-40) cc_final: 0.6431 (t0) REVERT: A 534 VAL cc_start: 0.8188 (t) cc_final: 0.7908 (m) REVERT: A 567 ARG cc_start: 0.7435 (mpp80) cc_final: 0.7207 (mtp85) REVERT: A 663 ASP cc_start: 0.7022 (m-30) cc_final: 0.6781 (m-30) REVERT: A 671 CYS cc_start: 0.4455 (OUTLIER) cc_final: 0.1998 (p) REVERT: A 701 VAL cc_start: 0.8636 (t) cc_final: 0.8340 (p) REVERT: A 702 GLU cc_start: 0.7248 (tt0) cc_final: 0.7011 (tm-30) REVERT: A 704 SER cc_start: 0.8616 (t) cc_final: 0.8155 (p) REVERT: A 737 ASP cc_start: 0.7316 (t0) cc_final: 0.6554 (t0) REVERT: A 965 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7625 (mm-40) REVERT: A 969 ASN cc_start: 0.8368 (m-40) cc_final: 0.8165 (m-40) REVERT: A 1005 GLN cc_start: 0.7716 (tp-100) cc_final: 0.7453 (tp-100) REVERT: A 1028 LYS cc_start: 0.7843 (mttt) cc_final: 0.7433 (ttmm) REVERT: A 1111 GLU cc_start: 0.6983 (mp0) cc_final: 0.6578 (mp0) REVERT: A 1139 ASP cc_start: 0.7756 (t0) cc_final: 0.7545 (t0) REVERT: B 195 LYS cc_start: 0.6915 (pttt) cc_final: 0.5906 (ttpt) REVERT: B 201 PHE cc_start: 0.6886 (m-10) cc_final: 0.6476 (m-10) REVERT: B 302 THR cc_start: 0.7752 (m) cc_final: 0.7516 (t) REVERT: B 328 ARG cc_start: 0.6811 (ttm-80) cc_final: 0.6388 (ttm-80) REVERT: B 536 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8086 (t0) REVERT: B 592 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6221 (p90) REVERT: B 692 ILE cc_start: 0.6808 (mt) cc_final: 0.6454 (mt) REVERT: B 748 GLU cc_start: 0.6724 (mp0) cc_final: 0.6353 (mp0) REVERT: B 752 LEU cc_start: 0.8074 (mt) cc_final: 0.7730 (tt) REVERT: B 856 ASN cc_start: 0.5426 (OUTLIER) cc_final: 0.5102 (p0) REVERT: B 861 LEU cc_start: 0.8981 (mm) cc_final: 0.8771 (mt) REVERT: B 933 LYS cc_start: 0.7900 (mttt) cc_final: 0.7575 (ttmm) REVERT: B 934 ILE cc_start: 0.7874 (mm) cc_final: 0.7487 (mm) REVERT: B 947 LYS cc_start: 0.5858 (OUTLIER) cc_final: 0.5455 (mtmt) REVERT: B 950 ASP cc_start: 0.6374 (m-30) cc_final: 0.6027 (m-30) REVERT: B 985 ASP cc_start: 0.7147 (t0) cc_final: 0.6915 (t70) REVERT: B 1068 VAL cc_start: 0.6533 (t) cc_final: 0.5643 (p) REVERT: B 1084 ASP cc_start: 0.5960 (OUTLIER) cc_final: 0.5677 (t0) REVERT: C 31 SER cc_start: 0.6093 (OUTLIER) cc_final: 0.5801 (m) REVERT: C 588 THR cc_start: 0.7019 (m) cc_final: 0.6789 (t) REVERT: C 655 HIS cc_start: 0.6846 (t-90) cc_final: 0.6582 (t70) REVERT: C 661 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6605 (mm-30) REVERT: C 741 TYR cc_start: 0.7520 (t80) cc_final: 0.7150 (t80) REVERT: C 773 GLU cc_start: 0.6278 (mm-30) cc_final: 0.6003 (mm-30) REVERT: C 854 LYS cc_start: 0.6664 (mtpt) cc_final: 0.6332 (mtpt) REVERT: C 918 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6566 (tt0) REVERT: C 963 VAL cc_start: 0.7853 (t) cc_final: 0.7318 (p) REVERT: C 964 LYS cc_start: 0.7655 (mttt) cc_final: 0.7385 (mttt) REVERT: C 994 ASP cc_start: 0.6616 (m-30) cc_final: 0.6222 (m-30) REVERT: C 1029 MET cc_start: 0.7619 (tpp) cc_final: 0.7007 (tpp) REVERT: C 1048 HIS cc_start: 0.7364 (t70) cc_final: 0.6759 (t70) outliers start: 67 outliers final: 49 residues processed: 457 average time/residue: 0.3604 time to fit residues: 257.0036 Evaluate side-chains 469 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 412 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 0.0060 chunk 176 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 231 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 214 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 158 optimal weight: 1.9990 chunk 278 optimal weight: 0.2980 chunk 78 optimal weight: 0.0270 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 895 GLN C1011 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 25956 Z= 0.139 Angle : 0.503 9.638 35304 Z= 0.258 Chirality : 0.043 0.179 3981 Planarity : 0.004 0.052 4581 Dihedral : 4.114 19.853 3468 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.73 % Allowed : 10.28 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3201 helix: 1.13 (0.20), residues: 707 sheet: -0.00 (0.18), residues: 677 loop : -1.06 (0.13), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.004 0.001 HIS B 245 PHE 0.012 0.001 PHE C 888 TYR 0.016 0.001 TYR C 266 ARG 0.006 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 403 time to evaluate : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.6418 (pm20) cc_final: 0.5415 (pm20) REVERT: A 301 CYS cc_start: 0.6021 (m) cc_final: 0.5770 (m) REVERT: A 417 ASN cc_start: 0.6829 (m-40) cc_final: 0.6422 (t0) REVERT: A 701 VAL cc_start: 0.8491 (t) cc_final: 0.8186 (p) REVERT: A 702 GLU cc_start: 0.7123 (tt0) cc_final: 0.6917 (tm-30) REVERT: A 704 SER cc_start: 0.8542 (t) cc_final: 0.8075 (p) REVERT: A 740 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6677 (mtm) REVERT: A 965 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7567 (mm-40) REVERT: A 969 ASN cc_start: 0.8191 (m-40) cc_final: 0.7877 (t0) REVERT: A 1028 LYS cc_start: 0.7869 (mttt) cc_final: 0.7551 (ttmt) REVERT: A 1029 MET cc_start: 0.7682 (tpp) cc_final: 0.7420 (tpp) REVERT: A 1111 GLU cc_start: 0.6903 (mp0) cc_final: 0.6606 (mp0) REVERT: A 1118 ASP cc_start: 0.7473 (t0) cc_final: 0.6931 (p0) REVERT: A 1139 ASP cc_start: 0.7740 (t0) cc_final: 0.7438 (t0) REVERT: B 195 LYS cc_start: 0.6828 (pttt) cc_final: 0.5780 (ttpt) REVERT: B 201 PHE cc_start: 0.6819 (m-10) cc_final: 0.6489 (m-10) REVERT: B 302 THR cc_start: 0.7703 (m) cc_final: 0.7445 (t) REVERT: B 692 ILE cc_start: 0.6726 (mt) cc_final: 0.6241 (mt) REVERT: B 748 GLU cc_start: 0.6511 (mp0) cc_final: 0.6226 (mp0) REVERT: B 752 LEU cc_start: 0.8013 (mt) cc_final: 0.7668 (tt) REVERT: B 861 LEU cc_start: 0.8888 (mm) cc_final: 0.8684 (mt) REVERT: B 933 LYS cc_start: 0.7830 (mttt) cc_final: 0.7529 (ttmm) REVERT: B 934 ILE cc_start: 0.7767 (mm) cc_final: 0.7368 (mm) REVERT: B 947 LYS cc_start: 0.5839 (OUTLIER) cc_final: 0.5421 (mtmt) REVERT: B 985 ASP cc_start: 0.7133 (t0) cc_final: 0.6829 (t70) REVERT: B 1029 MET cc_start: 0.6455 (OUTLIER) cc_final: 0.6047 (tpt) REVERT: B 1084 ASP cc_start: 0.5719 (OUTLIER) cc_final: 0.5420 (m-30) REVERT: C 31 SER cc_start: 0.5896 (OUTLIER) cc_final: 0.5601 (m) REVERT: C 285 ILE cc_start: 0.7669 (mt) cc_final: 0.7460 (mt) REVERT: C 655 HIS cc_start: 0.6756 (t-90) cc_final: 0.6521 (t70) REVERT: C 661 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6595 (mm-30) REVERT: C 698 SER cc_start: 0.8772 (t) cc_final: 0.8552 (t) REVERT: C 773 GLU cc_start: 0.6169 (mm-30) cc_final: 0.5833 (mm-30) REVERT: C 854 LYS cc_start: 0.6564 (mtpt) cc_final: 0.6228 (mtpt) REVERT: C 963 VAL cc_start: 0.7722 (t) cc_final: 0.7050 (p) REVERT: C 964 LYS cc_start: 0.7418 (mttt) cc_final: 0.7155 (mttt) REVERT: C 974 SER cc_start: 0.8608 (m) cc_final: 0.8077 (p) REVERT: C 994 ASP cc_start: 0.6424 (m-30) cc_final: 0.6079 (m-30) REVERT: C 1029 MET cc_start: 0.7570 (tpp) cc_final: 0.6971 (tpp) REVERT: C 1048 HIS cc_start: 0.7227 (t70) cc_final: 0.6702 (t70) outliers start: 49 outliers final: 31 residues processed: 423 average time/residue: 0.3604 time to fit residues: 241.5658 Evaluate side-chains 421 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 385 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 0.8980 chunk 279 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 182 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 310 optimal weight: 0.9980 chunk 257 optimal weight: 30.0000 chunk 143 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B 957 GLN B1134 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25956 Z= 0.207 Angle : 0.525 9.198 35304 Z= 0.273 Chirality : 0.044 0.192 3981 Planarity : 0.004 0.100 4581 Dihedral : 4.201 19.152 3468 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.91 % Allowed : 10.63 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3201 helix: 1.17 (0.20), residues: 712 sheet: 0.01 (0.18), residues: 675 loop : -1.08 (0.13), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.005 0.001 HIS A1058 PHE 0.020 0.001 PHE C 643 TYR 0.016 0.001 TYR A1067 ARG 0.005 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 397 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 CYS cc_start: 0.6132 (m) cc_final: 0.5883 (m) REVERT: A 701 VAL cc_start: 0.8556 (t) cc_final: 0.8226 (p) REVERT: A 702 GLU cc_start: 0.7205 (tt0) cc_final: 0.6972 (tm-30) REVERT: A 704 SER cc_start: 0.8597 (t) cc_final: 0.8151 (p) REVERT: A 776 LYS cc_start: 0.8761 (tptp) cc_final: 0.8505 (tptp) REVERT: A 965 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7609 (mm-40) REVERT: A 969 ASN cc_start: 0.8224 (m-40) cc_final: 0.7927 (m-40) REVERT: A 973 ILE cc_start: 0.8000 (mp) cc_final: 0.7602 (mp) REVERT: A 1005 GLN cc_start: 0.7767 (tp-100) cc_final: 0.7500 (tp-100) REVERT: A 1028 LYS cc_start: 0.7865 (mttt) cc_final: 0.7497 (ttmm) REVERT: A 1029 MET cc_start: 0.7744 (tpp) cc_final: 0.7461 (tpp) REVERT: A 1111 GLU cc_start: 0.6933 (mp0) cc_final: 0.6644 (mp0) REVERT: A 1118 ASP cc_start: 0.7522 (t0) cc_final: 0.6965 (p0) REVERT: A 1139 ASP cc_start: 0.7728 (t0) cc_final: 0.7472 (t0) REVERT: B 195 LYS cc_start: 0.6905 (pttt) cc_final: 0.5986 (ttpt) REVERT: B 302 THR cc_start: 0.7712 (m) cc_final: 0.7469 (t) REVERT: B 592 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6210 (p90) REVERT: B 692 ILE cc_start: 0.6816 (mt) cc_final: 0.6327 (mt) REVERT: B 748 GLU cc_start: 0.6575 (mp0) cc_final: 0.6325 (mp0) REVERT: B 752 LEU cc_start: 0.8032 (mt) cc_final: 0.7684 (tt) REVERT: B 815 ARG cc_start: 0.7131 (tpp80) cc_final: 0.6471 (mmt90) REVERT: B 861 LEU cc_start: 0.8922 (mm) cc_final: 0.8718 (mt) REVERT: B 933 LYS cc_start: 0.7849 (mttt) cc_final: 0.7542 (ttmm) REVERT: B 934 ILE cc_start: 0.7815 (mm) cc_final: 0.7425 (mm) REVERT: B 985 ASP cc_start: 0.7202 (t0) cc_final: 0.6910 (t70) REVERT: B 1084 ASP cc_start: 0.5900 (OUTLIER) cc_final: 0.5358 (m-30) REVERT: C 31 SER cc_start: 0.5861 (OUTLIER) cc_final: 0.5651 (m) REVERT: C 655 HIS cc_start: 0.6843 (t-90) cc_final: 0.6598 (t70) REVERT: C 661 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6631 (mm-30) REVERT: C 698 SER cc_start: 0.8859 (t) cc_final: 0.8604 (t) REVERT: C 773 GLU cc_start: 0.6281 (mm-30) cc_final: 0.5948 (mm-30) REVERT: C 854 LYS cc_start: 0.6601 (mtpt) cc_final: 0.6311 (mtpt) REVERT: C 963 VAL cc_start: 0.7842 (t) cc_final: 0.7307 (p) REVERT: C 964 LYS cc_start: 0.7552 (mttt) cc_final: 0.7300 (mttt) REVERT: C 994 ASP cc_start: 0.6562 (m-30) cc_final: 0.6214 (m-30) REVERT: C 1029 MET cc_start: 0.7526 (tpp) cc_final: 0.6992 (tpp) outliers start: 54 outliers final: 39 residues processed: 422 average time/residue: 0.3639 time to fit residues: 241.4450 Evaluate side-chains 423 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 381 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 3.9990 chunk 35 optimal weight: 0.0020 chunk 176 optimal weight: 0.6980 chunk 226 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 261 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 309 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 188 optimal weight: 0.8980 chunk 142 optimal weight: 0.4980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B 957 GLN C 317 ASN C 641 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25956 Z= 0.157 Angle : 0.502 10.447 35304 Z= 0.259 Chirality : 0.043 0.159 3981 Planarity : 0.004 0.085 4581 Dihedral : 4.053 19.602 3468 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.66 % Allowed : 11.05 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3201 helix: 1.31 (0.20), residues: 709 sheet: 0.04 (0.19), residues: 679 loop : -1.04 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.009 0.001 HIS C1048 PHE 0.018 0.001 PHE C 565 TYR 0.015 0.001 TYR C1067 ARG 0.004 0.000 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 389 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 ASN cc_start: 0.7123 (m-40) cc_final: 0.6400 (t0) REVERT: A 701 VAL cc_start: 0.8485 (t) cc_final: 0.8131 (p) REVERT: A 704 SER cc_start: 0.8575 (t) cc_final: 0.8129 (p) REVERT: A 737 ASP cc_start: 0.7451 (p0) cc_final: 0.7164 (p0) REVERT: A 776 LYS cc_start: 0.8730 (tptp) cc_final: 0.8405 (tptp) REVERT: A 965 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7596 (mm-40) REVERT: A 969 ASN cc_start: 0.8171 (m-40) cc_final: 0.7896 (t0) REVERT: A 973 ILE cc_start: 0.7983 (mp) cc_final: 0.7550 (mp) REVERT: A 1005 GLN cc_start: 0.7776 (tp-100) cc_final: 0.7509 (tp-100) REVERT: A 1028 LYS cc_start: 0.7924 (mttt) cc_final: 0.7560 (ttmt) REVERT: A 1029 MET cc_start: 0.7708 (tpp) cc_final: 0.7400 (tpp) REVERT: A 1111 GLU cc_start: 0.6918 (mp0) cc_final: 0.6627 (mp0) REVERT: A 1118 ASP cc_start: 0.7517 (t0) cc_final: 0.6952 (p0) REVERT: A 1139 ASP cc_start: 0.7736 (t0) cc_final: 0.7456 (t0) REVERT: B 195 LYS cc_start: 0.6900 (pttt) cc_final: 0.5953 (ttpt) REVERT: B 302 THR cc_start: 0.7676 (m) cc_final: 0.7437 (t) REVERT: B 692 ILE cc_start: 0.6751 (mt) cc_final: 0.6252 (mt) REVERT: B 748 GLU cc_start: 0.6530 (mp0) cc_final: 0.6272 (mp0) REVERT: B 752 LEU cc_start: 0.8022 (mt) cc_final: 0.7642 (tt) REVERT: B 815 ARG cc_start: 0.7088 (tpp80) cc_final: 0.6312 (mmt90) REVERT: B 906 PHE cc_start: 0.5696 (OUTLIER) cc_final: 0.5445 (m-10) REVERT: B 933 LYS cc_start: 0.7838 (mttt) cc_final: 0.7529 (ttmm) REVERT: B 934 ILE cc_start: 0.7761 (mm) cc_final: 0.7377 (mm) REVERT: B 985 ASP cc_start: 0.7248 (t0) cc_final: 0.7026 (t70) REVERT: B 1029 MET cc_start: 0.6538 (OUTLIER) cc_final: 0.6113 (tpt) REVERT: B 1084 ASP cc_start: 0.5925 (OUTLIER) cc_final: 0.5325 (m-30) REVERT: C 31 SER cc_start: 0.6011 (OUTLIER) cc_final: 0.5807 (m) REVERT: C 535 LYS cc_start: 0.7533 (mmtm) cc_final: 0.7145 (ttpt) REVERT: C 615 VAL cc_start: 0.7333 (p) cc_final: 0.7121 (p) REVERT: C 655 HIS cc_start: 0.6811 (t-90) cc_final: 0.6559 (t70) REVERT: C 661 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6627 (mm-30) REVERT: C 773 GLU cc_start: 0.6242 (mm-30) cc_final: 0.6034 (mm-30) REVERT: C 776 LYS cc_start: 0.7989 (tmtt) cc_final: 0.7674 (tmtt) REVERT: C 854 LYS cc_start: 0.6487 (mtpt) cc_final: 0.6177 (mtpt) REVERT: C 868 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7768 (tp30) REVERT: C 963 VAL cc_start: 0.7811 (t) cc_final: 0.7238 (p) REVERT: C 964 LYS cc_start: 0.7479 (mttt) cc_final: 0.7235 (mttt) REVERT: C 974 SER cc_start: 0.8590 (m) cc_final: 0.8051 (p) REVERT: C 1029 MET cc_start: 0.7514 (tpp) cc_final: 0.6932 (tpp) outliers start: 47 outliers final: 34 residues processed: 413 average time/residue: 0.3702 time to fit residues: 240.9357 Evaluate side-chains 421 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 383 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 152 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 243 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A 928 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25956 Z= 0.214 Angle : 0.528 10.847 35304 Z= 0.274 Chirality : 0.044 0.206 3981 Planarity : 0.004 0.082 4581 Dihedral : 4.217 37.100 3468 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.94 % Allowed : 10.88 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3201 helix: 1.27 (0.20), residues: 709 sheet: 0.04 (0.19), residues: 693 loop : -1.06 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.006 0.001 HIS C1048 PHE 0.017 0.001 PHE A 220 TYR 0.018 0.001 TYR A1067 ARG 0.007 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 406 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 ARG cc_start: 0.7004 (ttm-80) cc_final: 0.6136 (mtp-110) REVERT: A 701 VAL cc_start: 0.8539 (t) cc_final: 0.8201 (p) REVERT: A 704 SER cc_start: 0.8601 (t) cc_final: 0.8170 (p) REVERT: A 737 ASP cc_start: 0.7312 (p0) cc_final: 0.7109 (p0) REVERT: A 740 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6328 (mtm) REVERT: A 776 LYS cc_start: 0.8763 (tptp) cc_final: 0.8418 (tptp) REVERT: A 965 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7653 (mm-40) REVERT: A 969 ASN cc_start: 0.8249 (m-40) cc_final: 0.7922 (t0) REVERT: A 973 ILE cc_start: 0.8038 (mp) cc_final: 0.7595 (mp) REVERT: A 1005 GLN cc_start: 0.7794 (tp-100) cc_final: 0.7337 (tp-100) REVERT: A 1028 LYS cc_start: 0.7860 (mttt) cc_final: 0.7521 (ttmm) REVERT: A 1029 MET cc_start: 0.7757 (tpp) cc_final: 0.7436 (tpp) REVERT: A 1111 GLU cc_start: 0.6946 (mp0) cc_final: 0.6652 (mp0) REVERT: A 1118 ASP cc_start: 0.7541 (t0) cc_final: 0.7333 (t0) REVERT: A 1139 ASP cc_start: 0.7762 (t0) cc_final: 0.7510 (t0) REVERT: B 195 LYS cc_start: 0.6977 (pttt) cc_final: 0.6046 (ttpt) REVERT: B 302 THR cc_start: 0.7698 (m) cc_final: 0.7447 (t) REVERT: B 592 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.6285 (p90) REVERT: B 692 ILE cc_start: 0.6799 (mt) cc_final: 0.6302 (mt) REVERT: B 748 GLU cc_start: 0.6415 (mp0) cc_final: 0.6212 (mp0) REVERT: B 752 LEU cc_start: 0.8012 (mt) cc_final: 0.7616 (tt) REVERT: B 815 ARG cc_start: 0.7091 (tpp80) cc_final: 0.6366 (mmt90) REVERT: B 906 PHE cc_start: 0.5652 (OUTLIER) cc_final: 0.5400 (m-10) REVERT: B 933 LYS cc_start: 0.7844 (mttt) cc_final: 0.7535 (ttmm) REVERT: B 934 ILE cc_start: 0.7788 (mm) cc_final: 0.7408 (mm) REVERT: B 985 ASP cc_start: 0.7282 (t0) cc_final: 0.7081 (t70) REVERT: B 1072 GLU cc_start: 0.7058 (pm20) cc_final: 0.6300 (mp0) REVERT: B 1084 ASP cc_start: 0.6110 (OUTLIER) cc_final: 0.5393 (m-30) REVERT: C 58 PHE cc_start: 0.6744 (OUTLIER) cc_final: 0.6260 (t80) REVERT: C 129 LYS cc_start: 0.6811 (mttt) cc_final: 0.6541 (mmtp) REVERT: C 214 ARG cc_start: 0.7780 (mmm160) cc_final: 0.7459 (mmm-85) REVERT: C 273 ARG cc_start: 0.7094 (tpp-160) cc_final: 0.6828 (ttm110) REVERT: C 615 VAL cc_start: 0.7482 (p) cc_final: 0.7276 (p) REVERT: C 655 HIS cc_start: 0.6854 (t-90) cc_final: 0.6614 (t70) REVERT: C 661 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6721 (mm-30) REVERT: C 773 GLU cc_start: 0.6391 (mm-30) cc_final: 0.6177 (mm-30) REVERT: C 776 LYS cc_start: 0.7995 (tmtt) cc_final: 0.7675 (tmtt) REVERT: C 854 LYS cc_start: 0.6532 (mtpt) cc_final: 0.6245 (mtpt) REVERT: C 963 VAL cc_start: 0.7848 (t) cc_final: 0.7305 (p) REVERT: C 964 LYS cc_start: 0.7610 (mttt) cc_final: 0.7345 (mttt) REVERT: C 974 SER cc_start: 0.8577 (m) cc_final: 0.8058 (p) REVERT: C 1029 MET cc_start: 0.7586 (tpp) cc_final: 0.6988 (tpp) REVERT: C 1038 LYS cc_start: 0.7116 (mtmm) cc_final: 0.6534 (mttm) REVERT: C 1073 LYS cc_start: 0.7500 (mtmm) cc_final: 0.7147 (mtpp) outliers start: 55 outliers final: 43 residues processed: 430 average time/residue: 0.3757 time to fit residues: 254.0440 Evaluate side-chains 429 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 381 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 288 optimal weight: 0.4980 chunk 173 optimal weight: 0.6980 chunk 125 optimal weight: 0.2980 chunk 226 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 272 optimal weight: 0.8980 chunk 287 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 25956 Z= 0.156 Angle : 0.505 11.806 35304 Z= 0.259 Chirality : 0.043 0.201 3981 Planarity : 0.004 0.073 4581 Dihedral : 4.022 21.177 3468 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.66 % Allowed : 11.72 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3201 helix: 1.41 (0.20), residues: 710 sheet: 0.03 (0.19), residues: 683 loop : -1.01 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.007 0.001 HIS C1048 PHE 0.018 0.001 PHE A 220 TYR 0.029 0.001 TYR A 204 ARG 0.006 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 381 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 701 VAL cc_start: 0.8477 (t) cc_final: 0.8128 (p) REVERT: A 704 SER cc_start: 0.8523 (t) cc_final: 0.8053 (p) REVERT: A 776 LYS cc_start: 0.8707 (tptp) cc_final: 0.8370 (tptp) REVERT: A 965 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7568 (mm-40) REVERT: A 969 ASN cc_start: 0.8190 (m-40) cc_final: 0.7888 (t0) REVERT: A 973 ILE cc_start: 0.8034 (mp) cc_final: 0.7589 (mp) REVERT: A 1005 GLN cc_start: 0.7792 (tp-100) cc_final: 0.7506 (tp-100) REVERT: A 1028 LYS cc_start: 0.7822 (mttt) cc_final: 0.7455 (ttmm) REVERT: A 1029 MET cc_start: 0.7722 (tpp) cc_final: 0.7418 (tpp) REVERT: A 1111 GLU cc_start: 0.6924 (mp0) cc_final: 0.6645 (mp0) REVERT: A 1118 ASP cc_start: 0.7520 (t0) cc_final: 0.7303 (t0) REVERT: A 1139 ASP cc_start: 0.7718 (t0) cc_final: 0.7501 (t0) REVERT: B 195 LYS cc_start: 0.6971 (pttt) cc_final: 0.6023 (ttpt) REVERT: B 302 THR cc_start: 0.7664 (m) cc_final: 0.7423 (t) REVERT: B 328 ARG cc_start: 0.6447 (ttm-80) cc_final: 0.5810 (ttm-80) REVERT: B 592 PHE cc_start: 0.6885 (OUTLIER) cc_final: 0.6289 (p90) REVERT: B 692 ILE cc_start: 0.6780 (mt) cc_final: 0.6287 (mt) REVERT: B 752 LEU cc_start: 0.8012 (mt) cc_final: 0.7620 (tt) REVERT: B 933 LYS cc_start: 0.7836 (mttt) cc_final: 0.7531 (ttmm) REVERT: B 934 ILE cc_start: 0.7748 (mm) cc_final: 0.7371 (mm) REVERT: B 985 ASP cc_start: 0.7330 (t0) cc_final: 0.7130 (t70) REVERT: B 1072 GLU cc_start: 0.7012 (pm20) cc_final: 0.6253 (mp0) REVERT: B 1084 ASP cc_start: 0.6144 (OUTLIER) cc_final: 0.5449 (t0) REVERT: C 58 PHE cc_start: 0.6740 (OUTLIER) cc_final: 0.6244 (t80) REVERT: C 129 LYS cc_start: 0.6814 (mttt) cc_final: 0.6398 (mttp) REVERT: C 214 ARG cc_start: 0.7732 (mmm160) cc_final: 0.7409 (mmm-85) REVERT: C 273 ARG cc_start: 0.7056 (tpp-160) cc_final: 0.6790 (ttm110) REVERT: C 615 VAL cc_start: 0.7133 (p) cc_final: 0.6912 (p) REVERT: C 655 HIS cc_start: 0.6798 (t-90) cc_final: 0.6561 (t70) REVERT: C 661 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6699 (mm-30) REVERT: C 776 LYS cc_start: 0.7978 (tmtt) cc_final: 0.7584 (tmtt) REVERT: C 854 LYS cc_start: 0.6488 (mtpt) cc_final: 0.6205 (mtpt) REVERT: C 963 VAL cc_start: 0.7796 (t) cc_final: 0.7258 (p) REVERT: C 964 LYS cc_start: 0.7473 (mttt) cc_final: 0.7238 (mttt) REVERT: C 974 SER cc_start: 0.8469 (m) cc_final: 0.8019 (p) REVERT: C 1029 MET cc_start: 0.7513 (tpp) cc_final: 0.6963 (tpp) outliers start: 47 outliers final: 39 residues processed: 403 average time/residue: 0.3697 time to fit residues: 234.7772 Evaluate side-chains 404 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 362 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 1.9990 chunk 304 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 319 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 254 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 196 optimal weight: 0.0000 chunk 156 optimal weight: 8.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B1134 ASN C 762 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 953 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25956 Z= 0.186 Angle : 0.519 12.250 35304 Z= 0.267 Chirality : 0.044 0.203 3981 Planarity : 0.004 0.068 4581 Dihedral : 4.111 30.767 3468 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 1.62 % Allowed : 11.62 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3201 helix: 1.39 (0.20), residues: 710 sheet: 0.07 (0.19), residues: 682 loop : -1.03 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.006 0.001 HIS C1048 PHE 0.031 0.001 PHE A 43 TYR 0.024 0.001 TYR A 204 ARG 0.006 0.000 ARG C 995 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 386 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.6892 (t80) cc_final: 0.6498 (t80) REVERT: A 417 ASN cc_start: 0.7308 (m110) cc_final: 0.6493 (t0) REVERT: A 577 ARG cc_start: 0.7016 (ttm-80) cc_final: 0.6284 (ttp80) REVERT: A 701 VAL cc_start: 0.8497 (t) cc_final: 0.8139 (p) REVERT: A 704 SER cc_start: 0.8535 (t) cc_final: 0.8078 (p) REVERT: A 775 ASP cc_start: 0.7898 (m-30) cc_final: 0.7021 (t0) REVERT: A 776 LYS cc_start: 0.8755 (tptp) cc_final: 0.8514 (tptp) REVERT: A 965 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7656 (mm-40) REVERT: A 969 ASN cc_start: 0.8177 (m-40) cc_final: 0.7921 (t0) REVERT: A 973 ILE cc_start: 0.8026 (mp) cc_final: 0.7576 (mp) REVERT: A 1005 GLN cc_start: 0.7805 (tp-100) cc_final: 0.7510 (tp-100) REVERT: A 1028 LYS cc_start: 0.7798 (mttt) cc_final: 0.7498 (ttmm) REVERT: A 1029 MET cc_start: 0.7740 (tpp) cc_final: 0.7461 (tpp) REVERT: A 1041 ASP cc_start: 0.7598 (t0) cc_final: 0.7363 (t0) REVERT: A 1111 GLU cc_start: 0.6937 (mp0) cc_final: 0.6644 (mp0) REVERT: A 1118 ASP cc_start: 0.7529 (t0) cc_final: 0.7084 (p0) REVERT: A 1139 ASP cc_start: 0.7768 (t0) cc_final: 0.7472 (t0) REVERT: B 195 LYS cc_start: 0.7006 (pttt) cc_final: 0.6081 (ttpt) REVERT: B 302 THR cc_start: 0.7692 (m) cc_final: 0.7457 (t) REVERT: B 328 ARG cc_start: 0.6376 (ttm-80) cc_final: 0.5665 (ttm-80) REVERT: B 592 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6295 (p90) REVERT: B 692 ILE cc_start: 0.6760 (mt) cc_final: 0.6261 (mt) REVERT: B 752 LEU cc_start: 0.8025 (mt) cc_final: 0.7648 (tt) REVERT: B 815 ARG cc_start: 0.6994 (tpp80) cc_final: 0.6280 (mmt90) REVERT: B 823 PHE cc_start: 0.6580 (m-80) cc_final: 0.6377 (m-80) REVERT: B 933 LYS cc_start: 0.7837 (mttt) cc_final: 0.7535 (ttmm) REVERT: B 934 ILE cc_start: 0.7762 (mm) cc_final: 0.7390 (mm) REVERT: B 1072 GLU cc_start: 0.7039 (pm20) cc_final: 0.6295 (mp0) REVERT: B 1084 ASP cc_start: 0.6422 (OUTLIER) cc_final: 0.5941 (t0) REVERT: C 58 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.6256 (t80) REVERT: C 129 LYS cc_start: 0.6826 (mttt) cc_final: 0.6409 (mttp) REVERT: C 214 ARG cc_start: 0.7733 (mmm160) cc_final: 0.7354 (mmm-85) REVERT: C 273 ARG cc_start: 0.7165 (tpp-160) cc_final: 0.6868 (ttm110) REVERT: C 655 HIS cc_start: 0.6814 (t-90) cc_final: 0.6563 (t70) REVERT: C 661 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6759 (mm-30) REVERT: C 854 LYS cc_start: 0.6521 (mtpt) cc_final: 0.6229 (mtpt) REVERT: C 964 LYS cc_start: 0.7559 (mttt) cc_final: 0.7253 (mttt) REVERT: C 974 SER cc_start: 0.8452 (m) cc_final: 0.8020 (p) REVERT: C 1029 MET cc_start: 0.7423 (tpp) cc_final: 0.6960 (tpp) REVERT: C 1129 VAL cc_start: 0.7215 (OUTLIER) cc_final: 0.6870 (m) outliers start: 46 outliers final: 38 residues processed: 407 average time/residue: 0.3659 time to fit residues: 233.3423 Evaluate side-chains 415 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 373 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 0.9990 chunk 271 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 234 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 255 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A 935 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B1134 ASN C 66 HIS ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.219020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.174168 restraints weight = 39522.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.174368 restraints weight = 24126.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.177585 restraints weight = 16258.915| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 25956 Z= 0.250 Angle : 0.562 12.227 35304 Z= 0.291 Chirality : 0.045 0.227 3981 Planarity : 0.004 0.071 4581 Dihedral : 4.324 25.890 3468 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 1.59 % Allowed : 11.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3201 helix: 1.19 (0.20), residues: 716 sheet: 0.00 (0.19), residues: 678 loop : -1.10 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.005 0.001 HIS C1048 PHE 0.032 0.002 PHE A 43 TYR 0.027 0.001 TYR C 917 ARG 0.006 0.000 ARG C 995 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6120.20 seconds wall clock time: 110 minutes 43.09 seconds (6643.09 seconds total)