Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 11 04:36:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x27_32960/07_2023/7x27_32960_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x27_32960/07_2023/7x27_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_32960/07_2023/7x27_32960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x27_32960/07_2023/7x27_32960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x27_32960/07_2023/7x27_32960_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x27_32960/07_2023/7x27_32960_neut.pdb" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 11.60, per 1000 atoms: 0.51 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: 8.55 Conformation dependent library (CDL) restraints added in 4.3 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: 1.70 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: 10.01 Time building geometry restraints manager: 9.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 0.010 Normalize map: mean=0, sd=1: 1.630 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: 8.960 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 60.440 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.120 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.060 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.830 Fit side-chains outliers start: 230 outliers final: 180 residues processed: 394 average time/residue: 0.8765 time to fit residues: 420.2641 Evaluate side-chains 327 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 147 time to evaluate : 2.579 Switching outliers to nearest non-outliers outliers start: 180 outliers final: 173 residues processed: 7 average time/residue: 0.4321 time to fit residues: 7.7298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 140 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.8488 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 23289 Z= 0.301 Angle : 0.614 8.173 31668 Z= 0.327 Chirality : 0.044 0.199 3525 Planarity : 0.005 0.055 4140 Dihedral : 4.885 33.228 3207 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.46 % Favored : 93.47 % Rotamer Outliers : 9.83 % 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: -0.95 (0.15), residues: 2925 helix: 1.37 (0.21), residues: 666 sheet: -0.59 (0.20), residues: 597 loop : -1.55 (0.15), residues: 1662 *********************** 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 407 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 161 time to evaluate : 2.710 Fit side-chains outliers start: 246 outliers final: 183 residues processed: 387 average time/residue: 0.9732 time to fit residues: 453.0469 Evaluate side-chains 331 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 148 time to evaluate : 2.687 Switching outliers to nearest non-outliers outliers start: 183 outliers final: 177 residues processed: 8 average time/residue: 0.4386 time to fit residues: 8.5706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 222 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 267 optimal weight: 0.0980 chunk 288 optimal weight: 0.9980 chunk 238 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 628 GLN G 815 GLN G 819 GLN I 194 HIS J 194 HIS J 628 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 23289 Z= 0.306 Angle : 0.600 7.922 31668 Z= 0.318 Chirality : 0.044 0.190 3525 Planarity : 0.005 0.051 4140 Dihedral : 4.840 32.435 3207 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.87 % Favored : 93.09 % Rotamer Outliers : 9.35 % 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: -0.85 (0.15), residues: 2925 helix: 1.42 (0.21), residues: 666 sheet: -0.57 (0.20), residues: 603 loop : -1.45 (0.15), residues: 1656 *********************** 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 392 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 158 time to evaluate : 2.555 Fit side-chains outliers start: 234 outliers final: 183 residues processed: 376 average time/residue: 0.9414 time to fit residues: 430.2556 Evaluate side-chains 327 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 144 time to evaluate : 2.622 Switching outliers to nearest non-outliers outliers start: 183 outliers final: 177 residues processed: 7 average time/residue: 0.6640 time to fit residues: 9.3948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 254 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 628 GLN G 819 GLN I 194 HIS J 194 HIS J 808 GLN J1160 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 23289 Z= 0.362 Angle : 0.617 8.393 31668 Z= 0.327 Chirality : 0.045 0.204 3525 Planarity : 0.005 0.048 4140 Dihedral : 4.902 32.265 3207 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.74 % Favored : 93.20 % Rotamer Outliers : 8.95 % 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: -0.81 (0.15), residues: 2925 helix: 1.42 (0.20), residues: 669 sheet: -0.60 (0.19), residues: 615 loop : -1.39 (0.15), residues: 1641 *********************** 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 376 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 152 time to evaluate : 2.499 Fit side-chains outliers start: 224 outliers final: 184 residues processed: 357 average time/residue: 0.9213 time to fit residues: 399.6630 Evaluate side-chains 326 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 142 time to evaluate : 2.796 Switching outliers to nearest non-outliers outliers start: 184 outliers final: 176 residues processed: 9 average time/residue: 0.7642 time to fit residues: 12.3591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 242 optimal weight: 0.0670 chunk 196 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 0.6980 chunk 255 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 628 GLN G1129 ASN I 194 HIS I 628 GLN J 194 HIS J1097 GLN J1145 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 23289 Z= 0.207 Angle : 0.561 9.021 31668 Z= 0.297 Chirality : 0.042 0.164 3525 Planarity : 0.004 0.050 4140 Dihedral : 4.632 32.185 3207 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer Outliers : 8.47 % 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: -0.67 (0.15), residues: 2925 helix: 1.65 (0.21), residues: 666 sheet: -0.55 (0.20), residues: 609 loop : -1.32 (0.15), residues: 1650 *********************** 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 374 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 162 time to evaluate : 2.661 Fit side-chains outliers start: 212 outliers final: 171 residues processed: 363 average time/residue: 0.9150 time to fit residues: 405.9846 Evaluate side-chains 317 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 146 time to evaluate : 2.878 Switching outliers to nearest non-outliers outliers start: 171 outliers final: 167 residues processed: 5 average time/residue: 0.6549 time to fit residues: 7.6277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 284 optimal weight: 0.9980 chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 628 GLN G1042 ASN I 194 HIS I 628 GLN J 194 HIS J 628 GLN J 808 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1390 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= 0.179 Angle : 0.551 9.603 31668 Z= 0.290 Chirality : 0.042 0.161 3525 Planarity : 0.004 0.048 4140 Dihedral : 4.455 31.097 3207 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer Outliers : 8.03 % 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: -0.51 (0.15), residues: 2925 helix: 2.05 (0.21), residues: 651 sheet: -0.42 (0.20), residues: 606 loop : -1.33 (0.15), residues: 1668 *********************** 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 364 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 163 time to evaluate : 2.893 Fit side-chains outliers start: 201 outliers final: 164 residues processed: 354 average time/residue: 0.9459 time to fit residues: 404.6663 Evaluate side-chains 312 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 148 time to evaluate : 2.718 Switching outliers to nearest non-outliers outliers start: 164 outliers final: 160 residues processed: 4 average time/residue: 0.6397 time to fit residues: 6.5820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 160 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 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: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 GLN G 628 GLN I 194 HIS I 628 GLN I 819 GLN J 166 ASN J 194 HIS J 628 GLN J1160 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 23289 Z= 0.369 Angle : 0.617 10.759 31668 Z= 0.324 Chirality : 0.045 0.206 3525 Planarity : 0.005 0.047 4140 Dihedral : 4.719 30.583 3207 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 8.07 % 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: -0.59 (0.15), residues: 2925 helix: 1.67 (0.21), residues: 663 sheet: -0.45 (0.20), residues: 618 loop : -1.27 (0.15), residues: 1644 *********************** 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 355 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 153 time to evaluate : 2.569 Fit side-chains outliers start: 202 outliers final: 172 residues processed: 344 average time/residue: 0.9091 time to fit residues: 382.0280 Evaluate side-chains 316 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 144 time to evaluate : 2.623 Switching outliers to nearest non-outliers outliers start: 172 outliers final: 166 residues processed: 6 average time/residue: 0.8377 time to fit residues: 9.7302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 169 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 140 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 222 optimal weight: 0.0070 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 628 GLN I 194 HIS J 194 HIS J 628 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1507 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= 0.171 Angle : 0.556 10.477 31668 Z= 0.290 Chirality : 0.042 0.154 3525 Planarity : 0.004 0.050 4140 Dihedral : 4.448 30.957 3207 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 7.43 % 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 (0.16), residues: 2925 helix: 2.01 (0.21), residues: 666 sheet: -0.37 (0.20), residues: 627 loop : -1.29 (0.15), residues: 1632 *********************** 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 339 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 153 time to evaluate : 2.789 Fit side-chains outliers start: 186 outliers final: 168 residues processed: 335 average time/residue: 0.9071 time to fit residues: 371.4084 Evaluate side-chains 313 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 145 time to evaluate : 2.617 Switching outliers to nearest non-outliers outliers start: 168 outliers final: 165 residues processed: 4 average time/residue: 0.7125 time to fit residues: 7.1713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 0.2980 chunk 271 optimal weight: 0.8980 chunk 247 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 chunk 249 optimal weight: 0.9980 chunk 263 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 628 GLN I 194 HIS J 194 HIS J 628 GLN J1217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1532 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= 0.224 Angle : 0.577 12.429 31668 Z= 0.300 Chirality : 0.042 0.175 3525 Planarity : 0.004 0.049 4140 Dihedral : 4.473 29.833 3207 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 6.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2925 helix: 2.02 (0.20), residues: 666 sheet: -0.38 (0.20), residues: 618 loop : -1.21 (0.15), residues: 1641 *********************** 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 330 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 155 time to evaluate : 2.715 Fit side-chains outliers start: 175 outliers final: 164 residues processed: 324 average time/residue: 0.8955 time to fit residues: 357.0153 Evaluate side-chains 308 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 144 time to evaluate : 2.656 Switching outliers to nearest non-outliers outliers start: 164 outliers final: 164 residues processed: 1 average time/residue: 0.4093 time to fit residues: 4.1213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 0.8980 chunk 279 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 292 optimal weight: 0.8980 chunk 269 optimal weight: 0.7980 chunk 233 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 628 GLN I 194 HIS J 194 HIS J 628 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 23289 Z= 0.263 Angle : 0.597 12.896 31668 Z= 0.310 Chirality : 0.043 0.182 3525 Planarity : 0.004 0.049 4140 Dihedral : 4.555 30.124 3207 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 6.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.40 (0.16), residues: 2925 helix: 1.99 (0.20), residues: 666 sheet: -0.37 (0.20), residues: 618 loop : -1.21 (0.15), residues: 1641 ********************** 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 323 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 149 time to evaluate : 2.814 Fit side-chains outliers start: 174 outliers final: 167 residues processed: 321 average time/residue: 0.9032 time to fit residues: 355.0609 Evaluate side-chains 310 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 143 time to evaluate : 2.794 Switching outliers to nearest non-outliers outliers start: 167 outliers final: 166 residues processed: 2 average time/residue: 1.1410 time to fit residues: 6.3808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 233 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 239 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 628 GLN I 194 HIS J 628 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.109296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.072937 restraints weight = 36464.856| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.60 r_work: 0.2842 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1603 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= 0.197 Angle : 0.566 11.758 31668 Z= 0.295 Chirality : 0.042 0.164 3525 Planarity : 0.004 0.049 4140 Dihedral : 4.431 29.911 3207 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 6.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2925 helix: 2.08 (0.20), residues: 666 sheet: -0.34 (0.20), residues: 627 loop : -1.28 (0.15), residues: 1632 =============================================================================== Job complete usr+sys time: 7662.94 seconds wall clock time: 137 minutes 25.21 seconds (8245.21 seconds total)