Starting phenix.real_space_refine on Thu Apr 11 15:14:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x27_32960/04_2024/7x27_32960_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x27_32960/04_2024/7x27_32960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x27_32960/04_2024/7x27_32960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x27_32960/04_2024/7x27_32960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x27_32960/04_2024/7x27_32960_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x27_32960/04_2024/7x27_32960_neut.pdb" } resolution = 2.49 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 14427 2.51 5 N 3816 2.21 5 O 4407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 32": "OE1" <-> "OE2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 247": "OE1" <-> "OE2" Residue "G GLU 357": "OE1" <-> "OE2" Residue "G GLU 376": "OE1" <-> "OE2" Residue "G ARG 700": "NH1" <-> "NH2" Residue "G GLU 793": "OE1" <-> "OE2" Residue "G GLU 818": "OE1" <-> "OE2" Residue "G GLU 875": "OE1" <-> "OE2" Residue "G GLU 891": "OE1" <-> "OE2" Residue "G GLU 992": "OE1" <-> "OE2" Residue "G GLU 1017": "OE1" <-> "OE2" Residue "G GLU 1039": "OE1" <-> "OE2" Residue "G GLU 1062": "OE1" <-> "OE2" Residue "G ARG 1179": "NH1" <-> "NH2" Residue "G GLU 1183": "OE1" <-> "OE2" Residue "I GLU 32": "OE1" <-> "OE2" Residue "I TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 247": "OE1" <-> "OE2" Residue "I TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 666": "OE1" <-> "OE2" Residue "I GLU 680": "OE1" <-> "OE2" Residue "I ARG 700": "NH1" <-> "NH2" Residue "I GLU 725": "OE1" <-> "OE2" Residue "I GLU 793": "OE1" <-> "OE2" Residue "I GLU 818": "OE1" <-> "OE2" Residue "I GLU 875": "OE1" <-> "OE2" Residue "I GLU 891": "OE1" <-> "OE2" Residue "I GLU 1039": "OE1" <-> "OE2" Residue "I GLU 1062": "OE1" <-> "OE2" Residue "I ARG 1179": "NH1" <-> "NH2" Residue "I GLU 1183": "OE1" <-> "OE2" Residue "J GLU 32": "OE1" <-> "OE2" Residue "J PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 357": "OE1" <-> "OE2" Residue "J GLU 376": "OE1" <-> "OE2" Residue "J GLU 666": "OE1" <-> "OE2" Residue "J GLU 680": "OE1" <-> "OE2" Residue "J ARG 700": "NH1" <-> "NH2" Residue "J GLU 725": "OE1" <-> "OE2" Residue "J GLU 793": "OE1" <-> "OE2" Residue "J GLU 818": "OE1" <-> "OE2" Residue "J GLU 875": "OE1" <-> "OE2" Residue "J GLU 891": "OE1" <-> "OE2" Residue "J GLU 1039": "OE1" <-> "OE2" Residue "J GLU 1090": "OE1" <-> "OE2" Residue "J GLU 1105": "OE1" <-> "OE2" Residue "J ARG 1179": "NH1" <-> "NH2" Residue "J GLU 1183": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22770 Number of models: 1 Model: "" Number of chains: 3 Chain: "G" Number of atoms: 7590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7590 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 45, 'TRANS': 937} Chain breaks: 3 Chain: "I" Number of atoms: 7590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7590 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 45, 'TRANS': 937} Chain breaks: 3 Chain: "J" Number of atoms: 7590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7590 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 45, 'TRANS': 937} Chain breaks: 3 Time building chain proxies: 12.19, per 1000 atoms: 0.54 Number of scatterers: 22770 At special positions: 0 Unit cell: (153.715, 143.972, 163.457, 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 120 16.00 O 4407 8.00 N 3816 7.00 C 14427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS G 30 " - pdb=" SG CYS G 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 176 " - pdb=" SG CYS G 214 " distance=2.04 Simple disulfide: pdb=" SG CYS G 185 " - pdb=" SG CYS G 237 " distance=2.04 Simple disulfide: pdb=" SG CYS G 339 " - pdb=" SG CYS G 349 " distance=2.03 Simple disulfide: pdb=" SG CYS G 603 " - pdb=" SG CYS G 654 " distance=2.03 Simple disulfide: pdb=" SG CYS G 620 " - pdb=" SG CYS G 650 " distance=2.03 Simple disulfide: pdb=" SG CYS G 727 " - pdb=" SG CYS G 736 " distance=2.03 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.03 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.03 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.03 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.03 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.03 Simple disulfide: pdb=" SG CYS I 30 " - pdb=" SG CYS I 195 " distance=2.03 Simple disulfide: pdb=" SG CYS I 176 " - pdb=" SG CYS I 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 185 " - pdb=" SG CYS I 237 " distance=2.04 Simple disulfide: pdb=" SG CYS I 339 " - pdb=" SG CYS I 349 " distance=2.03 Simple disulfide: pdb=" SG CYS I 603 " - pdb=" SG CYS I 654 " distance=2.03 Simple disulfide: pdb=" SG CYS I 620 " - pdb=" SG CYS I 650 " distance=2.04 Simple disulfide: pdb=" SG CYS I 727 " - pdb=" SG CYS I 736 " distance=2.03 Simple disulfide: pdb=" SG CYS I 806 " - pdb=" SG CYS I 828 " distance=2.03 Simple disulfide: pdb=" SG CYS I 811 " - pdb=" SG CYS I 817 " distance=2.03 Simple disulfide: pdb=" SG CYS I 912 " - pdb=" SG CYS I 925 " distance=2.03 Simple disulfide: pdb=" SG CYS I1106 " - pdb=" SG CYS I1117 " distance=2.03 Simple disulfide: pdb=" SG CYS I1156 " - pdb=" SG CYS I1164 " distance=2.03 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.03 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.03 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.03 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.03 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=2.03 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=2.03 Simple disulfide: pdb=" SG CYS J 806 " - pdb=" SG CYS J 828 " distance=2.03 Simple disulfide: pdb=" SG CYS J 811 " - pdb=" SG CYS J 817 " distance=2.03 Simple disulfide: pdb=" SG CYS J 912 " - pdb=" SG CYS J 925 " distance=2.03 Simple disulfide: pdb=" SG CYS J1106 " - pdb=" SG CYS J1117 " distance=2.03 Simple disulfide: pdb=" SG CYS J1156 " - pdb=" SG CYS J1164 " 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: 8.81 Conformation dependent library (CDL) restraints added in 4.6 seconds 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5460 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 45 sheets defined 25.4% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'G' and resid 36 through 41 removed outlier: 4.095A pdb=" N PHE G 40 " --> pdb=" O GLN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'G' and resid 103 through 108 removed outlier: 4.687A pdb=" N SER G 106 " --> pdb=" O ALA G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 232 removed outlier: 4.007A pdb=" N TYR G 231 " --> pdb=" O SER G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 351 Processing helix chain 'G' and resid 805 through 812 Processing helix chain 'G' and resid 814 through 823 removed outlier: 3.616A pdb=" N GLN G 819 " --> pdb=" O GLN G 815 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU G 820 " --> pdb=" O LYS G 816 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU G 823 " --> pdb=" O GLN G 819 " (cutoff:3.500A) Processing helix chain 'G' and resid 826 through 854 removed outlier: 3.600A pdb=" N LYS G 830 " --> pdb=" O GLN G 826 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 907 through 915 removed outlier: 3.711A pdb=" N CYS G 912 " --> pdb=" O GLY G 908 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET G 913 " --> pdb=" O TYR G 909 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN G 914 " --> pdb=" O ASP G 910 " (cutoff:3.500A) Processing helix chain 'G' and resid 926 through 931 Processing helix chain 'G' and resid 940 through 953 Processing helix chain 'G' and resid 971 through 982 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1007 Processing helix chain 'G' and resid 1008 through 1012 removed outlier: 4.473A pdb=" N PHE G1012 " --> pdb=" O GLN G1009 " (cutoff:3.500A) Processing helix chain 'G' and resid 1016 through 1039 removed outlier: 3.601A pdb=" N LEU G1036 " --> pdb=" O ALA G1032 " (cutoff:3.500A) Processing helix chain 'G' and resid 1050 through 1056 removed outlier: 3.722A pdb=" N GLN G1056 " --> pdb=" O GLY G1052 " (cutoff:3.500A) Processing helix chain 'G' and resid 1059 through 1107 removed outlier: 3.991A pdb=" N ALA G1065 " --> pdb=" O PRO G1061 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G1094 " --> pdb=" O GLU G1090 " (cutoff:3.500A) Processing helix chain 'G' and resid 1219 through 1223 Processing helix chain 'I' and resid 36 through 41 removed outlier: 4.101A pdb=" N PHE I 40 " --> pdb=" O GLN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 53 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 222 through 232 removed outlier: 4.065A pdb=" N TYR I 231 " --> pdb=" O SER I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 351 Processing helix chain 'I' and resid 805 through 812 Processing helix chain 'I' and resid 814 through 823 removed outlier: 3.792A pdb=" N GLU I 823 " --> pdb=" O GLN I 819 " (cutoff:3.500A) Processing helix chain 'I' and resid 826 through 854 removed outlier: 3.564A pdb=" N LYS I 830 " --> pdb=" O GLN I 826 " (cutoff:3.500A) Processing helix chain 'I' and resid 888 through 898 Processing helix chain 'I' and resid 907 through 915 removed outlier: 3.604A pdb=" N CYS I 912 " --> pdb=" O GLY I 908 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN I 914 " --> pdb=" O ASP I 910 " (cutoff:3.500A) Processing helix chain 'I' and resid 926 through 931 Processing helix chain 'I' and resid 940 through 954 removed outlier: 3.626A pdb=" N SER I 954 " --> pdb=" O SER I 950 " (cutoff:3.500A) Processing helix chain 'I' and resid 971 through 982 Processing helix chain 'I' and resid 986 through 993 Processing helix chain 'I' and resid 993 through 1007 Processing helix chain 'I' and resid 1008 through 1012 removed outlier: 4.414A pdb=" N PHE I1012 " --> pdb=" O GLN I1009 " (cutoff:3.500A) Processing helix chain 'I' and resid 1016 through 1039 removed outlier: 3.597A pdb=" N LEU I1036 " --> pdb=" O ALA I1032 " (cutoff:3.500A) Processing helix chain 'I' and resid 1050 through 1056 removed outlier: 3.820A pdb=" N GLN I1056 " --> pdb=" O GLY I1052 " (cutoff:3.500A) Processing helix chain 'I' and resid 1059 through 1107 removed outlier: 3.982A pdb=" N ALA I1065 " --> pdb=" O PRO I1061 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU I1094 " --> pdb=" O GLU I1090 " (cutoff:3.500A) Processing helix chain 'I' and resid 1219 through 1223 Processing helix chain 'J' and resid 36 through 41 removed outlier: 4.067A pdb=" N PHE J 40 " --> pdb=" O GLN J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 222 through 232 removed outlier: 4.028A pdb=" N TYR J 231 " --> pdb=" O SER J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 805 through 812 Processing helix chain 'J' and resid 814 through 823 removed outlier: 3.822A pdb=" N GLU J 823 " --> pdb=" O GLN J 819 " (cutoff:3.500A) Processing helix chain 'J' and resid 826 through 854 removed outlier: 3.654A pdb=" N LYS J 830 " --> pdb=" O GLN J 826 " (cutoff:3.500A) Processing helix chain 'J' and resid 888 through 898 Processing helix chain 'J' and resid 907 through 915 removed outlier: 3.936A pdb=" N GLN J 914 " --> pdb=" O ASP J 910 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 931 Processing helix chain 'J' and resid 940 through 953 Processing helix chain 'J' and resid 971 through 982 Processing helix chain 'J' and resid 986 through 993 Processing helix chain 'J' and resid 993 through 1007 Processing helix chain 'J' and resid 1008 through 1012 removed outlier: 4.467A pdb=" N PHE J1012 " --> pdb=" O GLN J1009 " (cutoff:3.500A) Processing helix chain 'J' and resid 1016 through 1039 removed outlier: 3.630A pdb=" N LEU J1036 " --> pdb=" O ALA J1032 " (cutoff:3.500A) Processing helix chain 'J' and resid 1050 through 1056 removed outlier: 3.670A pdb=" N GLN J1056 " --> pdb=" O GLY J1052 " (cutoff:3.500A) Processing helix chain 'J' and resid 1059 through 1107 removed outlier: 3.938A pdb=" N ALA J1065 " --> pdb=" O PRO J1061 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU J1094 " --> pdb=" O GLU J1090 " (cutoff:3.500A) Processing helix chain 'J' and resid 1219 through 1223 Processing sheet with id=AA1, first strand: chain 'G' and resid 33 through 35 removed outlier: 6.432A pdb=" N HIS G 91 " --> pdb=" O GLN G 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 67 through 75 removed outlier: 4.301A pdb=" N ARG G 335 " --> pdb=" O ASP G 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 83 through 85 removed outlier: 3.532A pdb=" N TYR G 314 " --> pdb=" O ARG G 119 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL G 263 " --> pdb=" O THR G 283 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR G 283 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU G 265 " --> pdb=" O PHE G 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 88 through 89 removed outlier: 7.322A pdb=" N SER G 88 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR G 206 " --> pdb=" O SER G 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 110 through 111 Processing sheet with id=AA6, first strand: chain 'G' and resid 127 through 129 removed outlier: 3.879A pdb=" N ALA G 309 " --> pdb=" O THR G 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 153 through 155 Processing sheet with id=AA8, first strand: chain 'G' and resid 689 through 690 removed outlier: 5.499A pdb=" N VAL G 360 " --> pdb=" O TYR G 663 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR G 663 " --> pdb=" O VAL G 360 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER G 362 " --> pdb=" O VAL G 661 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL G 661 " --> pdb=" O SER G 362 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N SER G 364 " --> pdb=" O VAL G 659 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL G 659 " --> pdb=" O SER G 364 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS G 713 " --> pdb=" O PHE G 674 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 373 through 376 removed outlier: 4.615A pdb=" N VAL G 639 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL G 631 " --> pdb=" O VAL G 639 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 717 through 724 removed outlier: 6.739A pdb=" N VAL G 718 " --> pdb=" O LEU G 759 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N SER G 761 " --> pdb=" O VAL G 718 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N SER G 720 " --> pdb=" O SER G 761 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU G 735 " --> pdb=" O LEU G 731 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 768 through 769 removed outlier: 5.799A pdb=" N ILE G 768 " --> pdb=" O SER I 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 1121 through 1130 removed outlier: 6.072A pdb=" N HIS G1122 " --> pdb=" O TYR G1141 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR G1141 " --> pdb=" O HIS G1122 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL G1124 " --> pdb=" O VAL G1139 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY G1188 " --> pdb=" O ALA G1193 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ALA G1193 " --> pdb=" O GLY G1188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 1121 through 1130 removed outlier: 6.072A pdb=" N HIS G1122 " --> pdb=" O TYR G1141 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR G1141 " --> pdb=" O HIS G1122 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL G1124 " --> pdb=" O VAL G1139 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS G1146 " --> pdb=" O PRO G 783 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU G1148 " --> pdb=" O SER G 781 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER G 781 " --> pdb=" O GLU G1148 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL G1150 " --> pdb=" O LYS G 779 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS G 779 " --> pdb=" O VAL G1150 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA G1152 " --> pdb=" O TYR G 777 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N TYR G 777 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS G 779 " --> pdb=" O ALA I 969 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AB6, first strand: chain 'G' and resid 857 through 858 Processing sheet with id=AB7, first strand: chain 'G' and resid 967 through 969 removed outlier: 4.304A pdb=" N LYS J 779 " --> pdb=" O ALA G 969 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR J 777 " --> pdb=" O ALA J1152 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA J1152 " --> pdb=" O TYR J 777 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS J 779 " --> pdb=" O VAL J1150 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL J1150 " --> pdb=" O LYS J 779 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER J 781 " --> pdb=" O GLU J1148 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU J1148 " --> pdb=" O SER J 781 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N HIS J1146 " --> pdb=" O PRO J 783 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL J1124 " --> pdb=" O VAL J1139 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TYR J1141 " --> pdb=" O HIS J1122 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N HIS J1122 " --> pdb=" O TYR J1141 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 967 through 969 removed outlier: 4.304A pdb=" N LYS J 779 " --> pdb=" O ALA G 969 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR J 777 " --> pdb=" O ALA J1152 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA J1152 " --> pdb=" O TYR J 777 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS J 779 " --> pdb=" O VAL J1150 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL J1150 " --> pdb=" O LYS J 779 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER J 781 " --> pdb=" O GLU J1148 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU J1148 " --> pdb=" O SER J 781 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N HIS J1146 " --> pdb=" O PRO J 783 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL J1150 " --> pdb=" O LYS J1174 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE J1172 " --> pdb=" O ALA J1152 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLY J1188 " --> pdb=" O ALA J1193 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ALA J1193 " --> pdb=" O GLY J1188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 1202 through 1205 removed outlier: 4.150A pdb=" N CYS G1164 " --> pdb=" O VAL G1205 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 33 through 35 removed outlier: 6.413A pdb=" N HIS I 91 " --> pdb=" O GLN I 98 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 67 through 75 removed outlier: 4.233A pdb=" N ARG I 335 " --> pdb=" O ASP I 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 83 through 85 removed outlier: 6.312A pdb=" N VAL I 263 " --> pdb=" O THR I 283 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR I 283 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU I 265 " --> pdb=" O PHE I 281 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 110 through 111 Processing sheet with id=AC5, first strand: chain 'I' and resid 127 through 129 removed outlier: 3.718A pdb=" N ALA I 309 " --> pdb=" O THR I 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 153 through 155 Processing sheet with id=AC7, first strand: chain 'I' and resid 206 through 208 removed outlier: 6.400A pdb=" N THR I 206 " --> pdb=" O SER I 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'I' and resid 689 through 690 removed outlier: 4.544A pdb=" N VAL I 659 " --> pdb=" O VAL I 363 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER I 365 " --> pdb=" O VAL I 657 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL I 657 " --> pdb=" O SER I 365 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N CYS I 713 " --> pdb=" O PHE I 674 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 372 through 376 removed outlier: 6.765A pdb=" N GLY I 372 " --> pdb=" O GLU I 605 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N SER I 607 " --> pdb=" O GLY I 372 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL I 374 " --> pdb=" O SER I 607 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL I 639 " --> pdb=" O LEU I 651 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL I 631 " --> pdb=" O VAL I 639 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 717 through 724 removed outlier: 6.707A pdb=" N VAL I 718 " --> pdb=" O LEU I 759 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N SER I 761 " --> pdb=" O VAL I 718 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N SER I 720 " --> pdb=" O SER I 761 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU I 735 " --> pdb=" O LEU I 731 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 768 through 769 removed outlier: 5.811A pdb=" N ILE I 768 " --> pdb=" O SER J 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 1121 through 1130 removed outlier: 6.063A pdb=" N HIS I1122 " --> pdb=" O TYR I1141 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYR I1141 " --> pdb=" O HIS I1122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL I1124 " --> pdb=" O VAL I1139 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL I1150 " --> pdb=" O LYS I1174 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE I1172 " --> pdb=" O ALA I1152 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1121 through 1130 removed outlier: 6.063A pdb=" N HIS I1122 " --> pdb=" O TYR I1141 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYR I1141 " --> pdb=" O HIS I1122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL I1124 " --> pdb=" O VAL I1139 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N HIS I1146 " --> pdb=" O PRO I 783 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU I1148 " --> pdb=" O SER I 781 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER I 781 " --> pdb=" O GLU I1148 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL I1150 " --> pdb=" O LYS I 779 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS I 779 " --> pdb=" O VAL I1150 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA I1152 " --> pdb=" O TYR I 777 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR I 777 " --> pdb=" O ALA I1152 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS I 779 " --> pdb=" O ALA J 969 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 802 through 804 Processing sheet with id=AD6, first strand: chain 'I' and resid 1202 through 1205 removed outlier: 4.150A pdb=" N CYS I1164 " --> pdb=" O VAL I1205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AD8, first strand: chain 'J' and resid 67 through 75 removed outlier: 4.297A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.528A pdb=" N TYR J 314 " --> pdb=" O ARG J 119 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL J 263 " --> pdb=" O THR J 283 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR J 283 " --> pdb=" O VAL J 263 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU J 265 " --> pdb=" O PHE J 281 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.291A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR J 206 " --> pdb=" O SER J 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 110 through 111 Processing sheet with id=AE3, first strand: chain 'J' and resid 127 through 129 removed outlier: 3.828A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 153 through 155 Processing sheet with id=AE5, first strand: chain 'J' and resid 689 through 690 removed outlier: 4.596A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N CYS J 713 " --> pdb=" O PHE J 674 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 372 through 376 removed outlier: 3.907A pdb=" N GLY J 372 " --> pdb=" O CYS J 603 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 717 through 724 removed outlier: 6.729A pdb=" N VAL J 718 " --> pdb=" O LEU J 759 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N SER J 761 " --> pdb=" O VAL J 718 " (cutoff:3.500A) removed outlier: 9.890A pdb=" N SER J 720 " --> pdb=" O SER J 761 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU J 735 " --> pdb=" O LEU J 731 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 802 through 804 Processing sheet with id=AE9, first strand: chain 'J' and resid 1202 through 1205 removed outlier: 4.167A pdb=" N CYS J1164 " --> pdb=" O VAL J1205 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2517 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: 11.08 Time building geometry restraints manager: 9.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7446 1.34 - 1.47: 5822 1.47 - 1.59: 9859 1.59 - 1.71: 0 1.71 - 1.84: 162 Bond restraints: 23289 Sorted by residual: bond pdb=" N GLN G 377 " pdb=" CA GLN G 377 " ideal model delta sigma weight residual 1.457 1.507 -0.050 1.29e-02 6.01e+03 1.49e+01 bond pdb=" N GLU G 376 " pdb=" CA GLU G 376 " ideal model delta sigma weight residual 1.455 1.502 -0.047 1.25e-02 6.40e+03 1.43e+01 bond pdb=" N ASN J 592 " pdb=" CA ASN J 592 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.18e+00 bond pdb=" N LYS G 595 " pdb=" CA LYS G 595 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.21e-02 6.83e+03 6.16e+00 bond pdb=" N ASP J 593 " pdb=" CA ASP J 593 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.79e+00 ... (remaining 23284 not shown) Histogram of bond angle deviations from ideal: 97.02 - 104.42: 355 104.42 - 111.81: 10742 111.81 - 119.21: 7590 119.21 - 126.61: 12754 126.61 - 134.00: 227 Bond angle restraints: 31668 Sorted by residual: angle pdb=" N ASN G 592 " pdb=" CA ASN G 592 " pdb=" C ASN G 592 " ideal model delta sigma weight residual 114.75 106.92 7.83 1.26e+00 6.30e-01 3.86e+01 angle pdb=" CA GLU G 376 " pdb=" C GLU G 376 " pdb=" O GLU G 376 " ideal model delta sigma weight residual 120.99 115.81 5.18 1.12e+00 7.97e-01 2.14e+01 angle pdb=" CB MET J 161 " pdb=" CG MET J 161 " pdb=" SD MET J 161 " ideal model delta sigma weight residual 112.70 125.69 -12.99 3.00e+00 1.11e-01 1.87e+01 angle pdb=" CB LYS J 698 " pdb=" CG LYS J 698 " pdb=" CD LYS J 698 " ideal model delta sigma weight residual 111.30 121.17 -9.87 2.30e+00 1.89e-01 1.84e+01 angle pdb=" CA CYS I 650 " pdb=" CB CYS I 650 " pdb=" SG CYS I 650 " ideal model delta sigma weight residual 114.40 124.25 -9.85 2.30e+00 1.89e-01 1.83e+01 ... (remaining 31663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11854 17.97 - 35.94: 1376 35.94 - 53.92: 466 53.92 - 71.89: 125 71.89 - 89.86: 57 Dihedral angle restraints: 13878 sinusoidal: 5316 harmonic: 8562 Sorted by residual: dihedral pdb=" CB CYS I 176 " pdb=" SG CYS I 176 " pdb=" SG CYS I 214 " pdb=" CB CYS I 214 " ideal model delta sinusoidal sigma weight residual -86.00 -160.84 74.84 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CB CYS I 30 " pdb=" SG CYS I 30 " pdb=" SG CYS I 195 " pdb=" CB CYS I 195 " ideal model delta sinusoidal sigma weight residual -86.00 -154.46 68.46 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CB CYS G 30 " pdb=" SG CYS G 30 " pdb=" SG CYS G 195 " pdb=" CB CYS G 195 " ideal model delta sinusoidal sigma weight residual -86.00 -154.19 68.19 1 1.00e+01 1.00e-02 6.03e+01 ... (remaining 13875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2410 0.038 - 0.077: 782 0.077 - 0.115: 289 0.115 - 0.153: 38 0.153 - 0.192: 6 Chirality restraints: 3525 Sorted by residual: chirality pdb=" CA GLN G 377 " pdb=" N GLN G 377 " pdb=" C GLN G 377 " pdb=" CB GLN G 377 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA ASP G 593 " pdb=" N ASP G 593 " pdb=" C ASP G 593 " pdb=" CB ASP G 593 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA PRO J1131 " pdb=" N PRO J1131 " pdb=" C PRO J1131 " pdb=" CB PRO J1131 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 3522 not shown) Planarity restraints: 4140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN I 377 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLN I 377 " -0.057 2.00e-02 2.50e+03 pdb=" O GLN I 377 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA I 378 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU I 284 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO I 285 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO I 285 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO I 285 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 284 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO J 285 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO J 285 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 285 " 0.031 5.00e-02 4.00e+02 ... (remaining 4137 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 1 1.82 - 2.59: 222 2.59 - 3.36: 28051 3.36 - 4.13: 55344 4.13 - 4.90: 101433 Nonbonded interactions: 185051 Sorted by model distance: nonbonded pdb=" OE2 GLU I 376 " pdb=" NZ LYS I 595 " model vdw 1.052 2.520 nonbonded pdb=" OG1 THR G 667 " pdb=" OG1 THR G 669 " model vdw 2.135 2.440 nonbonded pdb=" O THR I 594 " pdb=" OG1 THR I 594 " model vdw 2.160 2.440 nonbonded pdb=" NH2 ARG J 181 " pdb=" O ARG J 221 " model vdw 2.164 2.520 nonbonded pdb=" N ASP J 216 " pdb=" OD1 ASP J 216 " model vdw 2.171 2.520 ... (remaining 185046 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 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 8.000 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 64.780 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.150 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 : 0.004 0.050 23289 Z= 0.239 Angle : 0.752 12.987 31668 Z= 0.447 Chirality : 0.044 0.192 3525 Planarity : 0.005 0.058 4140 Dihedral : 18.743 89.861 8310 Min Nonbonded Distance : 1.052 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 9.19 % Allowed : 23.94 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.20 (0.15), residues: 2925 helix: 1.45 (0.21), residues: 639 sheet: -0.85 (0.20), residues: 543 loop : -1.73 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 310 HIS 0.007 0.001 HIS G 194 PHE 0.022 0.002 PHE J 156 TYR 0.023 0.001 TYR J 635 ARG 0.011 0.001 ARG G 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 180 time to evaluate : 2.655 Fit side-chains REVERT: I 592 ASN cc_start: 0.6283 (OUTLIER) cc_final: 0.5629 (t0) REVERT: I 1090 GLU cc_start: 0.8000 (tp30) cc_final: 0.7688 (tp30) REVERT: I 1137 MET cc_start: 0.8645 (mtm) cc_final: 0.8401 (mtm) REVERT: J 666 GLU cc_start: 0.8068 (tp30) cc_final: 0.7856 (mm-30) REVERT: J 1008 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8098 (tpp) REVERT: J 1090 GLU cc_start: 0.7928 (tp30) cc_final: 0.7684 (tp30) outliers start: 230 outliers final: 180 residues processed: 394 average time/residue: 0.9013 time to fit residues: 431.2149 Evaluate side-chains 330 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 148 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 110 LYS Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 343 ASP Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 604 VAL Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 677 VAL Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 694 ARG Chi-restraints excluded: chain G residue 704 TYR Chi-restraints excluded: chain G residue 717 LEU Chi-restraints excluded: chain G residue 720 SER Chi-restraints excluded: chain G residue 729 LEU Chi-restraints excluded: chain G residue 781 SER Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 804 VAL Chi-restraints excluded: chain G residue 853 VAL Chi-restraints excluded: chain G residue 856 SER Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 859 SER Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 873 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 877 VAL Chi-restraints excluded: chain G residue 924 ILE Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 985 ILE Chi-restraints excluded: chain G residue 1010 THR Chi-restraints excluded: chain G residue 1034 SER Chi-restraints excluded: chain G residue 1038 SER Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1055 ILE Chi-restraints excluded: chain G residue 1077 THR Chi-restraints excluded: chain G residue 1089 SER Chi-restraints excluded: chain G residue 1095 SER Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1203 LYS Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain G residue 1226 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 110 LYS Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 214 CYS Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 343 ASP Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 377 GLN Chi-restraints excluded: chain I residue 592 ASN Chi-restraints excluded: chain I residue 596 ILE Chi-restraints excluded: chain I residue 604 VAL Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 669 THR Chi-restraints excluded: chain I residue 679 CYS Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 704 TYR Chi-restraints excluded: chain I residue 717 LEU Chi-restraints excluded: chain I residue 720 SER Chi-restraints excluded: chain I residue 729 LEU Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 804 VAL Chi-restraints excluded: chain I residue 829 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 856 SER Chi-restraints excluded: chain I residue 858 SER Chi-restraints excluded: chain I residue 859 SER Chi-restraints excluded: chain I residue 872 THR Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 893 LEU Chi-restraints excluded: chain I residue 910 ASP Chi-restraints excluded: chain I residue 924 ILE Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 965 SER Chi-restraints excluded: chain I residue 975 SER Chi-restraints excluded: chain I residue 994 GLN Chi-restraints excluded: chain I residue 1010 THR Chi-restraints excluded: chain I residue 1015 THR Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1054 ILE Chi-restraints excluded: chain I residue 1055 ILE Chi-restraints excluded: chain I residue 1082 VAL Chi-restraints excluded: chain I residue 1089 SER Chi-restraints excluded: chain I residue 1091 SER Chi-restraints excluded: chain I residue 1095 SER Chi-restraints excluded: chain I residue 1112 LYS Chi-restraints excluded: chain I residue 1175 THR Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1209 VAL Chi-restraints excluded: chain I residue 1216 THR Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 294 SER Chi-restraints excluded: chain J residue 302 SER Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 604 VAL Chi-restraints excluded: chain J residue 620 CYS Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 669 THR Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 704 TYR Chi-restraints excluded: chain J residue 720 SER Chi-restraints excluded: chain J residue 729 LEU Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 829 SER Chi-restraints excluded: chain J residue 856 SER Chi-restraints excluded: chain J residue 858 SER Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 872 THR Chi-restraints excluded: chain J residue 873 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 910 ASP Chi-restraints excluded: chain J residue 924 ILE Chi-restraints excluded: chain J residue 948 THR Chi-restraints excluded: chain J residue 1008 MET Chi-restraints excluded: chain J residue 1010 THR Chi-restraints excluded: chain J residue 1034 SER Chi-restraints excluded: chain J residue 1038 SER Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1055 ILE Chi-restraints excluded: chain J residue 1089 SER Chi-restraints excluded: chain J residue 1091 SER Chi-restraints excluded: chain J residue 1095 SER Chi-restraints excluded: chain J residue 1111 SER Chi-restraints excluded: chain J residue 1112 LYS Chi-restraints excluded: chain J residue 1131 PRO Chi-restraints excluded: chain J residue 1175 THR Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1226 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 230 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 266 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 37 GLN I 194 HIS I 377 GLN J 628 GLN J1129 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23289 Z= 0.334 Angle : 0.623 8.229 31668 Z= 0.332 Chirality : 0.045 0.209 3525 Planarity : 0.005 0.054 4140 Dihedral : 10.187 69.868 3486 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.43 % Favored : 93.47 % Rotamer: Outliers : 7.31 % Allowed : 23.02 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.97 (0.15), residues: 2925 helix: 1.34 (0.21), residues: 666 sheet: -0.61 (0.20), residues: 597 loop : -1.54 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 310 HIS 0.008 0.001 HIS G 194 PHE 0.015 0.002 PHE I 865 TYR 0.023 0.002 TYR G 184 ARG 0.008 0.001 ARG I 652 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 161 time to evaluate : 2.576 Fit side-chains REVERT: G 110 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7769 (mttp) REVERT: G 184 TYR cc_start: 0.6023 (OUTLIER) cc_final: 0.5053 (m-80) REVERT: G 628 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.6248 (mt0) REVERT: G 907 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6586 (pp30) REVERT: G 960 TRP cc_start: 0.6507 (OUTLIER) cc_final: 0.5755 (m-90) REVERT: I 110 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7465 (mtpt) REVERT: I 367 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7309 (mp0) REVERT: I 1090 GLU cc_start: 0.8039 (tp30) cc_final: 0.7747 (tp30) REVERT: J 110 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7698 (mtpt) REVERT: J 184 TYR cc_start: 0.6147 (OUTLIER) cc_final: 0.5260 (m-80) REVERT: J 240 MET cc_start: 0.8282 (tmt) cc_final: 0.8037 (tmt) REVERT: J 292 TYR cc_start: 0.8687 (m-80) cc_final: 0.8406 (m-80) REVERT: J 808 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: J 820 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8976 (mm) outliers start: 183 outliers final: 115 residues processed: 327 average time/residue: 1.0855 time to fit residues: 419.6321 Evaluate side-chains 263 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 138 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 110 LYS Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 343 ASP Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 628 GLN Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 677 VAL Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 704 TYR Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 804 VAL Chi-restraints excluded: chain G residue 812 ASN Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 859 SER Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 877 VAL Chi-restraints excluded: chain G residue 907 GLN Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 1038 SER Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1055 ILE Chi-restraints excluded: chain G residue 1094 LEU Chi-restraints excluded: chain G residue 1095 SER Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1203 LYS Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 LYS Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 214 CYS Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 343 ASP Chi-restraints excluded: chain I residue 377 GLN Chi-restraints excluded: chain I residue 596 ILE Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 669 THR Chi-restraints excluded: chain I residue 679 CYS Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 704 TYR Chi-restraints excluded: chain I residue 804 VAL Chi-restraints excluded: chain I residue 829 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 859 SER Chi-restraints excluded: chain I residue 872 THR Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1054 ILE Chi-restraints excluded: chain I residue 1055 ILE Chi-restraints excluded: chain I residue 1095 SER Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1209 VAL Chi-restraints excluded: chain I residue 1216 THR Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 131 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 669 THR Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 704 TYR Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 808 GLN Chi-restraints excluded: chain J residue 820 LEU Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 858 SER Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 872 THR Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 941 VAL Chi-restraints excluded: chain J residue 948 THR Chi-restraints excluded: chain J residue 1038 SER Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1095 SER Chi-restraints excluded: chain J residue 1111 SER Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 267 optimal weight: 6.9990 chunk 288 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 265 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 815 GLN G 819 GLN I 194 HIS J 628 GLN J1217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23289 Z= 0.257 Angle : 0.575 7.754 31668 Z= 0.306 Chirality : 0.043 0.179 3525 Planarity : 0.004 0.050 4140 Dihedral : 8.389 70.452 3353 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.92 % Allowed : 22.82 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.79 (0.15), residues: 2925 helix: 1.51 (0.21), residues: 666 sheet: -0.54 (0.20), residues: 603 loop : -1.42 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 310 HIS 0.006 0.001 HIS G 194 PHE 0.015 0.002 PHE I 112 TYR 0.017 0.001 TYR J1141 ARG 0.009 0.000 ARG I 652 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 163 time to evaluate : 2.770 Fit side-chains REVERT: G 628 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6193 (mt0) REVERT: G 728 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8415 (mmmt) REVERT: G 907 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6351 (pp30) REVERT: G 960 TRP cc_start: 0.6514 (OUTLIER) cc_final: 0.5780 (m-90) REVERT: I 110 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7404 (mtpt) REVERT: I 367 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7080 (mt-10) REVERT: I 669 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8344 (p) REVERT: I 1090 GLU cc_start: 0.8051 (tp30) cc_final: 0.7774 (tp30) REVERT: J 184 TYR cc_start: 0.6056 (OUTLIER) cc_final: 0.5253 (m-80) REVERT: J 289 THR cc_start: 0.9225 (m) cc_final: 0.8992 (t) REVERT: J 292 TYR cc_start: 0.8682 (m-80) cc_final: 0.8342 (m-80) REVERT: J 608 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8433 (mt) REVERT: J 628 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6123 (mt0) REVERT: J 808 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7721 (tt0) outliers start: 148 outliers final: 87 residues processed: 298 average time/residue: 1.1574 time to fit residues: 404.0265 Evaluate side-chains 246 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 149 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 343 ASP Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 628 GLN Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 704 TYR Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 812 ASN Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 859 SER Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 877 VAL Chi-restraints excluded: chain G residue 907 GLN Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 1031 GLN Chi-restraints excluded: chain G residue 1038 SER Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1203 LYS Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 LYS Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 343 ASP Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 669 THR Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 704 TYR Chi-restraints excluded: chain I residue 829 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 872 THR Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 1054 ILE Chi-restraints excluded: chain I residue 1055 ILE Chi-restraints excluded: chain I residue 1112 LYS Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 608 LEU Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 628 GLN Chi-restraints excluded: chain J residue 669 THR Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 808 GLN Chi-restraints excluded: chain J residue 812 ASN Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 948 THR Chi-restraints excluded: chain J residue 1038 SER Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1111 SER Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 179 optimal weight: 0.0370 chunk 268 optimal weight: 1.9990 chunk 284 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 254 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 819 GLN G1129 ASN I 194 HIS I 819 GLN J 808 GLN J1097 GLN J1145 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23289 Z= 0.167 Angle : 0.543 8.261 31668 Z= 0.287 Chirality : 0.042 0.156 3525 Planarity : 0.004 0.049 4140 Dihedral : 7.293 71.629 3310 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.44 % Allowed : 24.70 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.58 (0.15), residues: 2925 helix: 1.99 (0.21), residues: 651 sheet: -0.52 (0.20), residues: 615 loop : -1.36 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 310 HIS 0.005 0.001 HIS G 194 PHE 0.015 0.001 PHE G 164 TYR 0.015 0.001 TYR J1141 ARG 0.008 0.000 ARG I 652 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 163 time to evaluate : 2.589 Fit side-chains REVERT: G 164 PHE cc_start: 0.8208 (m-80) cc_final: 0.8006 (m-80) REVERT: G 728 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8377 (mmmt) REVERT: G 960 TRP cc_start: 0.6497 (OUTLIER) cc_final: 0.5714 (m-90) REVERT: G 1035 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8180 (tppp) REVERT: I 181 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7020 (ptm160) REVERT: I 1090 GLU cc_start: 0.8044 (tp30) cc_final: 0.7777 (tp30) REVERT: J 289 THR cc_start: 0.9219 (m) cc_final: 0.9007 (t) REVERT: J 292 TYR cc_start: 0.8692 (m-80) cc_final: 0.8345 (m-80) REVERT: J 608 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8402 (mt) REVERT: J 1090 GLU cc_start: 0.8016 (tp30) cc_final: 0.7750 (tp30) outliers start: 111 outliers final: 72 residues processed: 262 average time/residue: 1.1481 time to fit residues: 353.2485 Evaluate side-chains 225 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 149 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 704 TYR Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 812 ASN Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 859 SER Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 877 VAL Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 181 ARG Chi-restraints excluded: chain I residue 214 CYS Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 343 ASP Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 704 TYR Chi-restraints excluded: chain I residue 812 ASN Chi-restraints excluded: chain I residue 829 SER Chi-restraints excluded: chain I residue 844 ASP Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 893 LEU Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 1054 ILE Chi-restraints excluded: chain I residue 1112 LYS Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 227 SER Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 608 LEU Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain J residue 812 ASN Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 941 VAL Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1042 ASN I 194 HIS I 819 GLN J 194 HIS J 628 GLN J1160 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 23289 Z= 0.494 Angle : 0.665 9.177 31668 Z= 0.352 Chirality : 0.047 0.233 3525 Planarity : 0.005 0.050 4140 Dihedral : 7.430 76.868 3281 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.94 % Favored : 92.96 % Rotamer: Outliers : 6.00 % Allowed : 23.38 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.15), residues: 2925 helix: 1.44 (0.20), residues: 666 sheet: -0.60 (0.19), residues: 618 loop : -1.34 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 960 HIS 0.008 0.001 HIS G1138 PHE 0.016 0.002 PHE I 850 TYR 0.028 0.002 TYR J 184 ARG 0.009 0.001 ARG I 652 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 156 time to evaluate : 2.676 Fit side-chains REVERT: G 184 TYR cc_start: 0.5876 (OUTLIER) cc_final: 0.4760 (m-80) REVERT: G 240 MET cc_start: 0.8147 (tmt) cc_final: 0.7722 (tmt) REVERT: G 628 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.6421 (mt0) REVERT: G 728 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8439 (mmmt) REVERT: G 960 TRP cc_start: 0.6405 (OUTLIER) cc_final: 0.5841 (m-90) REVERT: I 110 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7562 (mtpt) REVERT: I 184 TYR cc_start: 0.6151 (OUTLIER) cc_final: 0.5440 (m-80) REVERT: I 628 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6106 (mt0) REVERT: I 669 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8401 (p) REVERT: I 960 TRP cc_start: 0.6492 (OUTLIER) cc_final: 0.5232 (m-90) REVERT: I 1090 GLU cc_start: 0.8039 (tp30) cc_final: 0.7720 (tp30) REVERT: J 184 TYR cc_start: 0.6096 (OUTLIER) cc_final: 0.5332 (m-80) REVERT: J 289 THR cc_start: 0.9251 (m) cc_final: 0.9030 (t) REVERT: J 292 TYR cc_start: 0.8716 (m-80) cc_final: 0.8349 (m-80) REVERT: J 608 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8504 (mt) REVERT: J 808 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: J 820 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9035 (mm) REVERT: J 960 TRP cc_start: 0.6740 (OUTLIER) cc_final: 0.5639 (m-90) outliers start: 150 outliers final: 93 residues processed: 286 average time/residue: 1.0780 time to fit residues: 365.8647 Evaluate side-chains 251 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 144 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 628 GLN Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 704 TYR Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 812 ASN Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 859 SER Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 877 VAL Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 965 SER Chi-restraints excluded: chain G residue 1031 GLN Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1055 ILE Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 LYS Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 184 TYR Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 214 CYS Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 343 ASP Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 628 GLN Chi-restraints excluded: chain I residue 669 THR Chi-restraints excluded: chain I residue 679 CYS Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 704 TYR Chi-restraints excluded: chain I residue 829 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 893 LEU Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 960 TRP Chi-restraints excluded: chain I residue 1010 THR Chi-restraints excluded: chain I residue 1054 ILE Chi-restraints excluded: chain I residue 1112 LYS Chi-restraints excluded: chain I residue 1175 THR Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 203 SER Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 227 SER Chi-restraints excluded: chain J residue 294 SER Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 608 LEU Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 669 THR Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain J residue 808 GLN Chi-restraints excluded: chain J residue 812 ASN Chi-restraints excluded: chain J residue 820 LEU Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 948 THR Chi-restraints excluded: chain J residue 960 TRP Chi-restraints excluded: chain J residue 1031 GLN Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1089 SER Chi-restraints excluded: chain J residue 1175 THR Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 0.9990 chunk 255 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 284 optimal weight: 0.6980 chunk 236 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 815 GLN G 819 GLN I 194 HIS I 819 GLN J 194 HIS J 628 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23289 Z= 0.197 Angle : 0.556 9.754 31668 Z= 0.294 Chirality : 0.042 0.159 3525 Planarity : 0.004 0.050 4140 Dihedral : 6.755 79.958 3279 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.28 % Allowed : 25.22 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.58 (0.15), residues: 2925 helix: 1.72 (0.21), residues: 663 sheet: -0.40 (0.20), residues: 603 loop : -1.30 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 310 HIS 0.005 0.001 HIS G 194 PHE 0.016 0.001 PHE I 112 TYR 0.016 0.001 TYR J1141 ARG 0.009 0.000 ARG I 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 155 time to evaluate : 2.978 Fit side-chains REVERT: G 628 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.5954 (mm-40) REVERT: G 728 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8371 (mmmt) REVERT: G 960 TRP cc_start: 0.6498 (OUTLIER) cc_final: 0.5799 (m-90) REVERT: I 1090 GLU cc_start: 0.8049 (tp30) cc_final: 0.7769 (tp30) REVERT: J 166 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.7326 (p0) REVERT: J 289 THR cc_start: 0.9225 (m) cc_final: 0.9024 (t) REVERT: J 292 TYR cc_start: 0.8688 (m-80) cc_final: 0.8373 (m-80) REVERT: J 608 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8378 (mt) REVERT: J 614 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7769 (ttm170) REVERT: J 960 TRP cc_start: 0.6739 (OUTLIER) cc_final: 0.5561 (m-90) outliers start: 107 outliers final: 75 residues processed: 246 average time/residue: 1.1568 time to fit residues: 334.5995 Evaluate side-chains 225 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 143 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 628 GLN Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1089 SER Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 214 CYS Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 343 ASP Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 679 CYS Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 812 ASN Chi-restraints excluded: chain I residue 844 ASP Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 1010 THR Chi-restraints excluded: chain I residue 1054 ILE Chi-restraints excluded: chain I residue 1055 ILE Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 166 ASN Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 365 SER Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 608 LEU Chi-restraints excluded: chain J residue 614 ARG Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 812 ASN Chi-restraints excluded: chain J residue 816 LYS Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 948 THR Chi-restraints excluded: chain J residue 960 TRP Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1175 THR Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 160 optimal weight: 0.4980 chunk 239 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 283 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 819 GLN I 194 HIS I 819 GLN J 194 HIS J 628 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23289 Z= 0.226 Angle : 0.568 10.568 31668 Z= 0.298 Chirality : 0.042 0.176 3525 Planarity : 0.004 0.049 4140 Dihedral : 6.553 81.727 3270 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.64 % Allowed : 25.02 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.45 (0.15), residues: 2925 helix: 2.02 (0.21), residues: 651 sheet: -0.37 (0.20), residues: 603 loop : -1.27 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 310 HIS 0.005 0.001 HIS G 194 PHE 0.016 0.001 PHE I 204 TYR 0.016 0.001 TYR J1141 ARG 0.010 0.000 ARG G 652 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 156 time to evaluate : 2.955 Fit side-chains REVERT: G 184 TYR cc_start: 0.5724 (OUTLIER) cc_final: 0.4673 (m-80) REVERT: G 628 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.6035 (mm-40) REVERT: G 728 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8389 (mmmt) REVERT: G 960 TRP cc_start: 0.6364 (OUTLIER) cc_final: 0.5665 (m-90) REVERT: I 669 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8362 (p) REVERT: I 960 TRP cc_start: 0.6398 (OUTLIER) cc_final: 0.5146 (m-90) REVERT: I 1090 GLU cc_start: 0.8045 (tp30) cc_final: 0.7779 (tp30) REVERT: J 166 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7407 (p0) REVERT: J 169 LEU cc_start: 0.8544 (tp) cc_final: 0.8327 (tp) REVERT: J 184 TYR cc_start: 0.6098 (OUTLIER) cc_final: 0.5281 (m-80) REVERT: J 289 THR cc_start: 0.9225 (m) cc_final: 0.9021 (t) REVERT: J 292 TYR cc_start: 0.8693 (m-80) cc_final: 0.8307 (m-80) REVERT: J 608 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8401 (mt) REVERT: J 614 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7770 (ttm170) REVERT: J 960 TRP cc_start: 0.6752 (OUTLIER) cc_final: 0.5585 (m-90) REVERT: J 1008 MET cc_start: 0.8439 (mtm) cc_final: 0.8170 (ttp) REVERT: J 1090 GLU cc_start: 0.7960 (tp30) cc_final: 0.7660 (tp30) outliers start: 116 outliers final: 84 residues processed: 259 average time/residue: 1.0771 time to fit residues: 330.5681 Evaluate side-chains 242 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 147 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 628 GLN Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1055 ILE Chi-restraints excluded: chain G residue 1089 SER Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 125 ASN Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 214 CYS Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 669 THR Chi-restraints excluded: chain I residue 679 CYS Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 960 TRP Chi-restraints excluded: chain I residue 1010 THR Chi-restraints excluded: chain I residue 1031 GLN Chi-restraints excluded: chain I residue 1054 ILE Chi-restraints excluded: chain I residue 1055 ILE Chi-restraints excluded: chain I residue 1112 LYS Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 166 ASN Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 227 SER Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 365 SER Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 608 LEU Chi-restraints excluded: chain J residue 614 ARG Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 628 GLN Chi-restraints excluded: chain J residue 669 THR Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 812 ASN Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 948 THR Chi-restraints excluded: chain J residue 960 TRP Chi-restraints excluded: chain J residue 1031 GLN Chi-restraints excluded: chain J residue 1038 SER Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1175 THR Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 169 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 194 HIS I 819 GLN J 194 HIS J 628 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23289 Z= 0.201 Angle : 0.562 10.735 31668 Z= 0.294 Chirality : 0.042 0.165 3525 Planarity : 0.004 0.051 4140 Dihedral : 6.319 83.144 3261 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.36 % Allowed : 25.38 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.36 (0.16), residues: 2925 helix: 1.99 (0.21), residues: 666 sheet: -0.25 (0.20), residues: 594 loop : -1.22 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 310 HIS 0.005 0.001 HIS G 194 PHE 0.015 0.001 PHE I 156 TYR 0.016 0.001 TYR J1141 ARG 0.012 0.000 ARG G 652 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 159 time to evaluate : 2.851 Fit side-chains REVERT: G 184 TYR cc_start: 0.5863 (OUTLIER) cc_final: 0.4786 (m-80) REVERT: G 628 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.5997 (mm-40) REVERT: G 728 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8388 (mmmt) REVERT: G 960 TRP cc_start: 0.6348 (OUTLIER) cc_final: 0.5649 (m-90) REVERT: G 1035 LYS cc_start: 0.8449 (ttmm) cc_final: 0.8204 (tppp) REVERT: I 110 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7492 (mtpt) REVERT: I 669 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8387 (p) REVERT: I 960 TRP cc_start: 0.6385 (OUTLIER) cc_final: 0.5049 (m-90) REVERT: I 1090 GLU cc_start: 0.8047 (tp30) cc_final: 0.7769 (tp30) REVERT: J 184 TYR cc_start: 0.6106 (OUTLIER) cc_final: 0.5289 (m-80) REVERT: J 292 TYR cc_start: 0.8684 (m-80) cc_final: 0.8315 (m-80) REVERT: J 608 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8388 (mt) REVERT: J 614 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7763 (ttm170) REVERT: J 960 TRP cc_start: 0.6758 (OUTLIER) cc_final: 0.5590 (m-90) REVERT: J 1090 GLU cc_start: 0.7978 (tp30) cc_final: 0.7705 (tp30) outliers start: 109 outliers final: 83 residues processed: 256 average time/residue: 1.1520 time to fit residues: 348.5210 Evaluate side-chains 243 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 149 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 628 GLN Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 1055 ILE Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 LYS Chi-restraints excluded: chain I residue 125 ASN Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 156 PHE Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 214 CYS Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 669 THR Chi-restraints excluded: chain I residue 679 CYS Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 960 TRP Chi-restraints excluded: chain I residue 1010 THR Chi-restraints excluded: chain I residue 1055 ILE Chi-restraints excluded: chain I residue 1112 LYS Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 156 PHE Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 227 SER Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 365 SER Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 608 LEU Chi-restraints excluded: chain J residue 614 ARG Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 669 THR Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain J residue 812 ASN Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 941 VAL Chi-restraints excluded: chain J residue 948 THR Chi-restraints excluded: chain J residue 960 TRP Chi-restraints excluded: chain J residue 1031 GLN Chi-restraints excluded: chain J residue 1038 SER Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1175 THR Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 0.0870 chunk 271 optimal weight: 0.6980 chunk 247 optimal weight: 0.8980 chunk 264 optimal weight: 0.9990 chunk 158 optimal weight: 0.4980 chunk 115 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 238 optimal weight: 0.0570 chunk 249 optimal weight: 0.3980 chunk 263 optimal weight: 5.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 GLN I 194 HIS I 819 GLN I1129 ASN J 194 HIS J 628 GLN J1217 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23289 Z= 0.145 Angle : 0.538 11.944 31668 Z= 0.280 Chirality : 0.041 0.149 3525 Planarity : 0.004 0.051 4140 Dihedral : 5.746 84.252 3254 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.52 % Allowed : 27.34 % Favored : 70.14 % 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: -0.28 (0.16), residues: 2925 helix: 2.21 (0.21), residues: 666 sheet: -0.16 (0.20), residues: 612 loop : -1.26 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 253 HIS 0.004 0.001 HIS G 194 PHE 0.018 0.001 PHE I 112 TYR 0.016 0.001 TYR J1141 ARG 0.011 0.000 ARG G 652 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 175 time to evaluate : 2.400 Fit side-chains REVERT: G 164 PHE cc_start: 0.8077 (m-80) cc_final: 0.7868 (m-80) REVERT: G 219 TYR cc_start: 0.8593 (m-80) cc_final: 0.8299 (m-80) REVERT: G 728 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8379 (mmmt) REVERT: G 771 ASP cc_start: 0.8074 (m-30) cc_final: 0.7844 (m-30) REVERT: G 1035 LYS cc_start: 0.8408 (ttmm) cc_final: 0.8194 (tppp) REVERT: I 960 TRP cc_start: 0.6333 (OUTLIER) cc_final: 0.5015 (m-90) REVERT: I 1008 MET cc_start: 0.8383 (ttp) cc_final: 0.8125 (ttp) REVERT: I 1090 GLU cc_start: 0.8032 (tp30) cc_final: 0.7780 (tp30) REVERT: J 84 MET cc_start: 0.8473 (ttp) cc_final: 0.8239 (ttp) REVERT: J 376 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8167 (mm-30) REVERT: J 614 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7775 (ttm170) REVERT: J 734 SER cc_start: 0.7289 (m) cc_final: 0.6834 (t) REVERT: J 960 TRP cc_start: 0.6694 (OUTLIER) cc_final: 0.5446 (m-90) REVERT: J 1090 GLU cc_start: 0.7998 (tp30) cc_final: 0.7751 (tp30) outliers start: 63 outliers final: 38 residues processed: 232 average time/residue: 1.2047 time to fit residues: 327.3734 Evaluate side-chains 199 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 156 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 1089 SER Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 214 CYS Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 960 TRP Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 614 ARG Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain J residue 812 ASN Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 960 TRP Chi-restraints excluded: chain J residue 1175 THR Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 132 optimal weight: 0.0970 chunk 194 optimal weight: 0.9980 chunk 292 optimal weight: 0.2980 chunk 269 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 194 HIS I 819 GLN I1145 ASN J 194 HIS J 628 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23289 Z= 0.173 Angle : 0.558 12.479 31668 Z= 0.289 Chirality : 0.042 0.157 3525 Planarity : 0.004 0.082 4140 Dihedral : 5.530 85.415 3243 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.12 % Allowed : 27.86 % Favored : 70.02 % 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: -0.24 (0.16), residues: 2925 helix: 2.26 (0.21), residues: 666 sheet: -0.11 (0.20), residues: 612 loop : -1.25 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 310 HIS 0.005 0.001 HIS G 194 PHE 0.016 0.001 PHE G 112 TYR 0.016 0.001 TYR J1141 ARG 0.024 0.000 ARG I 652 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 161 time to evaluate : 2.746 Fit side-chains REVERT: G 666 GLU cc_start: 0.7680 (pm20) cc_final: 0.7449 (pm20) REVERT: G 728 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8356 (mmmt) REVERT: G 960 TRP cc_start: 0.6382 (OUTLIER) cc_final: 0.5608 (m-90) REVERT: G 1035 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8207 (tppp) REVERT: I 110 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7590 (mtpt) REVERT: I 235 ARG cc_start: 0.7532 (mmp80) cc_final: 0.7148 (tpp80) REVERT: I 669 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8340 (p) REVERT: I 960 TRP cc_start: 0.6358 (OUTLIER) cc_final: 0.5036 (m-90) REVERT: I 1008 MET cc_start: 0.8475 (ttp) cc_final: 0.8212 (ttp) REVERT: I 1090 GLU cc_start: 0.8024 (tp30) cc_final: 0.7781 (tp30) REVERT: J 84 MET cc_start: 0.8514 (ttp) cc_final: 0.8273 (ttp) REVERT: J 376 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8223 (mm-30) REVERT: J 614 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7742 (ttm170) REVERT: J 960 TRP cc_start: 0.6724 (OUTLIER) cc_final: 0.5469 (m-90) REVERT: J 1090 GLU cc_start: 0.8004 (tp30) cc_final: 0.7760 (tp30) outliers start: 53 outliers final: 41 residues processed: 211 average time/residue: 1.2637 time to fit residues: 312.0073 Evaluate side-chains 203 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 154 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 1089 SER Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 LYS Chi-restraints excluded: chain I residue 156 PHE Chi-restraints excluded: chain I residue 214 CYS Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 669 THR Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 960 TRP Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 156 PHE Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 614 ARG Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain J residue 812 ASN Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 960 TRP Chi-restraints excluded: chain J residue 1175 THR Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 239 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 194 HIS I 819 GLN J 628 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.071767 restraints weight = 36264.219| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.58 r_work: 0.2793 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23289 Z= 0.235 Angle : 0.581 12.847 31668 Z= 0.302 Chirality : 0.043 0.176 3525 Planarity : 0.004 0.089 4140 Dihedral : 5.416 51.606 3240 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.52 % Allowed : 27.46 % Favored : 70.02 % 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: -0.20 (0.16), residues: 2925 helix: 2.20 (0.21), residues: 666 sheet: -0.10 (0.20), residues: 594 loop : -1.17 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 310 HIS 0.009 0.001 HIS J 194 PHE 0.014 0.001 PHE I 156 TYR 0.016 0.001 TYR J1141 ARG 0.020 0.000 ARG I 652 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7748.54 seconds wall clock time: 140 minutes 20.20 seconds (8420.20 seconds total)