Starting phenix.real_space_refine on Wed Apr 8 08:32:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x28_32961/04_2026/7x28_32961_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x28_32961/04_2026/7x28_32961.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/cci-nas-00/data/ceres_data/7x28_32961/04_2026/7x28_32961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x28_32961/04_2026/7x28_32961.map" model { file = "/net/cci-nas-00/data/ceres_data/7x28_32961/04_2026/7x28_32961_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x28_32961/04_2026/7x28_32961_neut.cif" } 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 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 Anisotropic ADP refinement not supported. Converting 5870 atoms to isotropic. 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 155 5.16 5 C 20027 2.51 5 N 5245 2.21 5 O 6156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31583 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 1633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1655 Chain: "D" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 8947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8947 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 58, 'TRANS': 1098} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 8852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 8852 Classifications: {'peptide': 1147} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 58, 'TRANS': 1086} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1655 Chain: "I" Number of atoms: 7316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 947, 7316 Classifications: {'peptide': 947} Link IDs: {'PTRANS': 44, 'TRANS': 902} Chain breaks: 5 Chain: "K" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 7.56, per 1000 atoms: 0.24 Number of scatterers: 31583 At special positions: 0 Unit cell: (149.385, 200.262, 239.232, 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 155 16.00 O 6156 8.00 N 5245 7.00 C 20027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=55, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 203 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 30 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS F 176 " - pdb=" SG CYS F 214 " distance=2.03 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 339 " - pdb=" SG CYS F 349 " distance=2.03 Simple disulfide: pdb=" SG CYS F 383 " - pdb=" SG CYS F 407 " distance=2.04 Simple disulfide: pdb=" SG CYS F 425 " - pdb=" SG CYS F 478 " distance=2.04 Simple disulfide: pdb=" SG CYS F 437 " - pdb=" SG CYS F 585 " distance=2.03 Simple disulfide: pdb=" SG CYS F 503 " - pdb=" SG CYS F 526 " distance=2.03 Simple disulfide: pdb=" SG CYS F 603 " - pdb=" SG CYS F 654 " distance=2.04 Simple disulfide: pdb=" SG CYS F 620 " - pdb=" SG CYS F 650 " distance=2.03 Simple disulfide: pdb=" SG CYS F 679 " - pdb=" SG CYS F 713 " distance=2.04 Simple disulfide: pdb=" SG CYS F 727 " - pdb=" SG CYS F 736 " distance=2.03 Simple disulfide: pdb=" SG CYS F 806 " - pdb=" SG CYS F 828 " distance=2.04 Simple disulfide: pdb=" SG CYS F 811 " - pdb=" SG CYS F 817 " distance=2.03 Simple disulfide: pdb=" SG CYS F 912 " - pdb=" SG CYS F 925 " distance=2.03 Simple disulfide: pdb=" SG CYS F1106 " - pdb=" SG CYS F1117 " distance=2.03 Simple disulfide: pdb=" SG CYS F1156 " - pdb=" SG CYS F1164 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS G 185 " - pdb=" SG CYS G 237 " distance=2.03 Simple disulfide: pdb=" SG CYS G 339 " - pdb=" SG CYS G 349 " distance=2.03 Simple disulfide: pdb=" SG CYS G 383 " - pdb=" SG CYS G 407 " distance=2.04 Simple disulfide: pdb=" SG CYS G 425 " - pdb=" SG CYS G 478 " distance=2.04 Simple disulfide: pdb=" SG CYS G 437 " - pdb=" SG CYS G 585 " distance=2.03 Simple disulfide: pdb=" SG CYS G 503 " - pdb=" SG CYS G 526 " distance=2.04 Simple disulfide: pdb=" SG CYS G 603 " - pdb=" SG CYS G 654 " distance=2.04 Simple disulfide: pdb=" SG CYS G 620 " - pdb=" SG CYS G 650 " distance=2.03 Simple disulfide: pdb=" SG CYS G 679 " - pdb=" SG CYS G 713 " distance=2.04 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=2.04 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 H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS I 679 " - pdb=" SG CYS I 713 " 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=2.04 Simple disulfide: pdb=" SG CYS I 912 " - pdb=" SG CYS I 925 " distance=2.04 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 K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.5 seconds 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7620 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 71 sheets defined 21.3% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'C' and resid 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 268 through 273 removed outlier: 3.752A pdb=" N LEU F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 352 Processing helix chain 'F' and resid 410 through 418 removed outlier: 3.737A pdb=" N LEU F 414 " --> pdb=" O ASN F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 435 Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 524 through 528 removed outlier: 4.413A pdb=" N SER F 528 " --> pdb=" O PRO F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 682 Processing helix chain 'F' and resid 805 through 811 Processing helix chain 'F' and resid 815 through 824 Processing helix chain 'F' and resid 825 through 854 Processing helix chain 'F' and resid 888 through 898 Processing helix chain 'F' and resid 907 through 916 removed outlier: 3.735A pdb=" N GLN F 914 " --> pdb=" O ASP F 910 " (cutoff:3.500A) Processing helix chain 'F' and resid 922 through 931 Processing helix chain 'F' and resid 940 through 959 removed outlier: 3.560A pdb=" N ALA F 956 " --> pdb=" O LEU F 952 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY F 957 " --> pdb=" O GLY F 953 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY F 959 " --> pdb=" O ILE F 955 " (cutoff:3.500A) Processing helix chain 'F' and resid 971 through 984 Processing helix chain 'F' and resid 986 through 993 Processing helix chain 'F' and resid 993 through 1010 Processing helix chain 'F' and resid 1016 through 1042 Processing helix chain 'F' and resid 1051 through 1057 removed outlier: 3.804A pdb=" N ILE F1055 " --> pdb=" O ILE F1051 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN F1056 " --> pdb=" O GLY F1052 " (cutoff:3.500A) Processing helix chain 'F' and resid 1059 through 1066 removed outlier: 3.521A pdb=" N GLN F1063 " --> pdb=" O ASP F1059 " (cutoff:3.500A) Processing helix chain 'F' and resid 1067 through 1106 Processing helix chain 'F' and resid 1198 through 1200 No H-bonds generated for 'chain 'F' and resid 1198 through 1200' Processing helix chain 'G' and resid 36 through 41 Processing helix chain 'G' and resid 209 through 214 Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 268 through 273 removed outlier: 4.190A pdb=" N LEU G 273 " --> pdb=" O ARG G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 352 Processing helix chain 'G' and resid 385 through 390 Processing helix chain 'G' and resid 410 through 418 removed outlier: 3.665A pdb=" N LEU G 414 " --> pdb=" O ASN G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 435 Processing helix chain 'G' and resid 449 through 453 removed outlier: 3.567A pdb=" N MET G 452 " --> pdb=" O PRO G 449 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 468 Processing helix chain 'G' and resid 678 through 682 Processing helix chain 'G' and resid 805 through 811 Processing helix chain 'G' and resid 814 through 825 Processing helix chain 'G' and resid 826 through 854 Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 907 through 916 Processing helix chain 'G' and resid 922 through 931 removed outlier: 3.529A pdb=" N TYR G 928 " --> pdb=" O ILE G 924 " (cutoff:3.500A) Processing helix chain 'G' and resid 940 through 959 removed outlier: 3.768A pdb=" N ALA G 956 " --> pdb=" O LEU G 952 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY G 957 " --> pdb=" O GLY G 953 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY G 959 " --> pdb=" O ILE G 955 " (cutoff:3.500A) Processing helix chain 'G' and resid 971 through 983 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1010 Processing helix chain 'G' and resid 1016 through 1041 removed outlier: 3.512A pdb=" N LEU G1040 " --> pdb=" O LEU G1036 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER G1041 " --> pdb=" O ALA G1037 " (cutoff:3.500A) Processing helix chain 'G' and resid 1050 through 1058 Processing helix chain 'G' and resid 1059 through 1106 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 161 through 165 Processing helix chain 'I' and resid 222 through 231 Processing helix chain 'I' and resid 342 through 352 Processing helix chain 'I' and resid 608 through 611 Processing helix chain 'I' and resid 805 through 810 Processing helix chain 'I' and resid 814 through 825 Processing helix chain 'I' and resid 826 through 854 Processing helix chain 'I' and resid 888 through 898 Processing helix chain 'I' and resid 907 through 916 Processing helix chain 'I' and resid 922 through 931 removed outlier: 3.517A pdb=" N TYR I 928 " --> pdb=" O ILE I 924 " (cutoff:3.500A) Processing helix chain 'I' and resid 940 through 959 removed outlier: 3.875A pdb=" N ALA I 956 " --> pdb=" O LEU I 952 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY I 957 " --> pdb=" O GLY I 953 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY I 959 " --> pdb=" O ILE I 955 " (cutoff:3.500A) Processing helix chain 'I' and resid 971 through 984 Processing helix chain 'I' and resid 986 through 993 Processing helix chain 'I' and resid 993 through 1010 Processing helix chain 'I' and resid 1016 through 1042 removed outlier: 3.547A pdb=" N SER I1041 " --> pdb=" O ALA I1037 " (cutoff:3.500A) Processing helix chain 'I' and resid 1050 through 1058 Processing helix chain 'I' and resid 1059 through 1106 Processing helix chain 'I' and resid 1219 through 1223 Processing helix chain 'K' and resid 122 through 128 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.812A pdb=" N VAL C 5 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.538A pdb=" N THR C 117 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 34 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 127 through 128 Processing sheet with id=AA4, first strand: chain 'C' and resid 144 through 146 Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 160 removed outlier: 4.482A pdb=" N CYS C 203 " --> pdb=" O LYS C 216 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS C 216 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS C 207 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR C 212 " --> pdb=" O HIS C 207 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AA7, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AA8, first strand: chain 'D' and resid 54 through 55 removed outlier: 3.621A pdb=" N SER D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.536A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 154 through 155 removed outlier: 3.601A pdb=" N LYS D 146 " --> pdb=" O THR D 198 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 33 through 34 Processing sheet with id=AB3, first strand: chain 'F' and resid 63 through 64 removed outlier: 6.787A pdb=" N THR F 63 " --> pdb=" O TYR I 632 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL I 631 " --> pdb=" O VAL I 639 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL I 639 " --> pdb=" O LEU I 651 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE I 617 " --> pdb=" O ASN I 602 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN I 602 " --> pdb=" O PHE I 617 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 68 through 75 removed outlier: 4.214A pdb=" N ARG F 335 " --> pdb=" O ASP F 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 83 through 86 removed outlier: 5.753A pdb=" N SER F 267 " --> pdb=" O GLN F 280 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLN F 280 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 88 through 89 removed outlier: 7.051A pdb=" N SER F 88 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR F 206 " --> pdb=" O SER F 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 92 through 93 Processing sheet with id=AB8, first strand: chain 'F' and resid 110 through 111 removed outlier: 4.487A pdb=" N ALA F 146 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER F 151 " --> pdb=" O HIS F 167 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N HIS F 167 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL F 153 " --> pdb=" O PHE F 165 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE F 165 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N PHE F 164 " --> pdb=" O PRO F 189 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN F 166 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU F 187 " --> pdb=" O ASN F 166 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU F 180 " --> pdb=" O TYR F 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR F 241 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA F 182 " --> pdb=" O PHE F 239 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE F 239 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR F 184 " --> pdb=" O CYS F 237 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N CYS F 237 " --> pdb=" O TYR F 184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 127 through 129 Processing sheet with id=AC1, first strand: chain 'F' and resid 359 through 366 removed outlier: 4.578A pdb=" N VAL F 659 " --> pdb=" O VAL F 363 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER F 365 " --> pdb=" O VAL F 657 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL F 657 " --> pdb=" O SER F 365 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR F 669 " --> pdb=" O ASP F 664 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 373 through 374 removed outlier: 6.937A pdb=" N VAL F 374 " --> pdb=" O SER F 607 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL F 639 " --> pdb=" O LEU F 651 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 400 through 404 removed outlier: 6.339A pdb=" N THR F 483 " --> pdb=" O VAL F 420 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL F 420 " --> pdb=" O THR F 483 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 513 through 515 removed outlier: 3.712A pdb=" N TYR F 497 " --> pdb=" O VAL F 561 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER F 557 " --> pdb=" O ASN F 501 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N CYS F 503 " --> pdb=" O VAL F 555 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL F 555 " --> pdb=" O CYS F 503 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ARG F 505 " --> pdb=" O TRP F 553 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP F 553 " --> pdb=" O ARG F 505 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 707 through 708 Processing sheet with id=AC6, first strand: chain 'F' and resid 718 through 724 removed outlier: 9.075A pdb=" N VAL F 718 " --> pdb=" O GLY F 755 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET F 757 " --> pdb=" O VAL F 718 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER F 720 " --> pdb=" O MET F 757 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU F 759 " --> pdb=" O SER F 720 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU F 722 " --> pdb=" O LEU F 759 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER F 761 " --> pdb=" O LEU F 722 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU F 756 " --> pdb=" O ASP F 740 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP F 740 " --> pdb=" O GLU F 756 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY F 732 " --> pdb=" O LEU F 735 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ALA F 737 " --> pdb=" O PRO F 730 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 768 through 769 removed outlier: 5.484A pdb=" N ILE F 768 " --> pdb=" O SER G 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 1121 through 1128 removed outlier: 5.674A pdb=" N HIS F1122 " --> pdb=" O TYR F1141 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR F1141 " --> pdb=" O HIS F1122 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE F1172 " --> pdb=" O ALA F1152 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY F1188 " --> pdb=" O ALA F1193 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ALA F1193 " --> pdb=" O GLY F1188 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 1121 through 1128 removed outlier: 5.674A pdb=" N HIS F1122 " --> pdb=" O TYR F1141 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR F1141 " --> pdb=" O HIS F1122 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS F1146 " --> pdb=" O PRO F 783 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU F1148 " --> pdb=" O SER F 781 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER F 781 " --> pdb=" O GLU F1148 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL F1150 " --> pdb=" O LYS F 779 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LYS F 779 " --> pdb=" O VAL F1150 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 801 through 803 removed outlier: 4.363A pdb=" N LYS F 801 " --> pdb=" O LEU F 935 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 857 through 858 Processing sheet with id=AD3, first strand: chain 'F' and resid 967 through 968 removed outlier: 6.737A pdb=" N LYS I 779 " --> pdb=" O VAL I1150 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL I1150 " --> pdb=" O LYS I 779 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER I 781 " --> pdb=" O GLU I1148 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU I1148 " --> pdb=" O SER I 781 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N HIS I1146 " --> pdb=" O PRO I 783 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR I1135 " --> pdb=" O VAL I1127 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL I1127 " --> pdb=" O TYR I1135 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N MET I1137 " --> pdb=" O SER I1125 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER I1125 " --> pdb=" O MET I1137 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL I1139 " --> pdb=" O ILE I1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 967 through 968 removed outlier: 6.737A pdb=" N LYS I 779 " --> pdb=" O VAL I1150 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL I1150 " --> pdb=" O LYS I 779 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER I 781 " --> pdb=" O GLU I1148 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU I1148 " --> pdb=" O SER I 781 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N HIS I1146 " --> pdb=" O PRO I 783 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE I1172 " --> pdb=" O ALA I1152 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 1202 through 1204 Processing sheet with id=AD6, first strand: chain 'G' and resid 33 through 34 Processing sheet with id=AD7, first strand: chain 'G' and resid 68 through 75 removed outlier: 3.533A pdb=" N ILE G 69 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY G 115 " --> pdb=" O LEU G 318 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER G 267 " --> pdb=" O GLN G 280 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLN G 280 " --> pdb=" O SER G 267 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 83 through 86 removed outlier: 4.087A pdb=" N ARG G 335 " --> pdb=" O ASP G 326 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 88 through 89 removed outlier: 7.090A pdb=" N SER G 88 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR G 206 " --> pdb=" O SER G 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'G' and resid 92 through 93 Processing sheet with id=AE2, first strand: chain 'G' and resid 110 through 111 removed outlier: 4.516A pdb=" N ALA G 146 " --> pdb=" O ILE G 296 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR G 184 " --> pdb=" O PHE G 239 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE G 239 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE G 186 " --> pdb=" O CYS G 237 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N CYS G 237 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU G 188 " --> pdb=" O ARG G 235 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG G 235 " --> pdb=" O GLU G 188 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 127 through 129 Processing sheet with id=AE4, first strand: chain 'G' and resid 359 through 366 removed outlier: 4.562A pdb=" N VAL G 659 " --> pdb=" O VAL G 363 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER G 365 " --> pdb=" O VAL G 657 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL G 657 " --> pdb=" O SER G 365 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR G 669 " --> pdb=" O ASP G 664 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 373 through 374 removed outlier: 7.004A pdb=" N VAL G 374 " --> pdb=" O SER G 607 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL G 639 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE G 630 " --> pdb=" O THR I 63 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 400 through 404 removed outlier: 6.353A pdb=" N THR G 483 " --> pdb=" O VAL G 420 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL G 420 " --> pdb=" O THR G 483 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 408 through 409 Processing sheet with id=AE8, first strand: chain 'G' and resid 513 through 515 removed outlier: 5.743A pdb=" N SER G 498 " --> pdb=" O VAL G 561 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL G 561 " --> pdb=" O SER G 498 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE G 500 " --> pdb=" O SER G 559 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N SER G 559 " --> pdb=" O ILE G 500 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS G 502 " --> pdb=" O SER G 557 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP G 553 " --> pdb=" O LEU G 506 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 718 through 724 removed outlier: 7.077A pdb=" N VAL G 718 " --> pdb=" O LEU G 759 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N SER G 761 " --> pdb=" O VAL G 718 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N SER G 720 " --> pdb=" O SER G 761 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLU G 756 " --> pdb=" O ASP G 740 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP G 740 " --> pdb=" O GLU G 756 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY G 732 " --> pdb=" O LEU G 735 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ALA G 737 " --> pdb=" O PRO G 730 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 768 through 769 removed outlier: 5.492A pdb=" N ILE G 768 " --> pdb=" O SER I 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'G' and resid 1121 through 1130 removed outlier: 5.864A pdb=" N HIS G1122 " --> pdb=" O TYR G1141 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N TYR G1141 " --> pdb=" O HIS G1122 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G1124 " --> pdb=" O VAL G1139 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY G1188 " --> pdb=" O ALA G1193 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA G1193 " --> pdb=" O GLY G1188 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 1121 through 1130 removed outlier: 5.864A pdb=" N HIS G1122 " --> pdb=" O TYR G1141 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N TYR G1141 " --> pdb=" O HIS G1122 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G1124 " --> pdb=" O VAL G1139 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N HIS G1146 " --> pdb=" O PRO G 783 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU G1148 " --> pdb=" O SER G 781 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER G 781 " --> pdb=" O GLU G1148 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL G1150 " --> pdb=" O LYS G 779 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS G 779 " --> pdb=" O VAL G1150 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 801 through 803 removed outlier: 4.308A pdb=" N LYS G 801 " --> pdb=" O LEU G 935 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 1202 through 1204 Processing sheet with id=AF6, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.701A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.039A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 127 through 128 removed outlier: 4.118A pdb=" N ASP H 151 " --> pdb=" O TYR H 183 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 143 through 145 Processing sheet with id=AG1, first strand: chain 'H' and resid 158 through 160 Processing sheet with id=AG2, first strand: chain 'I' and resid 33 through 34 Processing sheet with id=AG3, first strand: chain 'I' and resid 68 through 75 removed outlier: 4.396A pdb=" N ARG I 335 " --> pdb=" O ASP I 326 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 83 through 85 removed outlier: 5.955A pdb=" N SER I 267 " --> pdb=" O GLN I 280 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLN I 280 " --> pdb=" O SER I 267 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 88 through 89 removed outlier: 3.943A pdb=" N SER I 88 " --> pdb=" O HIS I 298 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE I 300 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR I 206 " --> pdb=" O SER I 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'I' and resid 92 through 93 Processing sheet with id=AG7, first strand: chain 'I' and resid 110 through 111 removed outlier: 4.579A pdb=" N SER I 151 " --> pdb=" O HIS I 167 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N HIS I 167 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL I 153 " --> pdb=" O PHE I 165 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE I 165 " --> pdb=" O VAL I 153 " (cutoff:3.500A) removed outlier: 11.534A pdb=" N PHE I 164 " --> pdb=" O PRO I 189 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN I 166 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU I 187 " --> pdb=" O ASN I 166 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU I 180 " --> pdb=" O TYR I 241 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR I 241 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA I 182 " --> pdb=" O PHE I 239 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE I 239 " --> pdb=" O ALA I 182 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR I 184 " --> pdb=" O CYS I 237 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N CYS I 237 " --> pdb=" O TYR I 184 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 127 through 129 Processing sheet with id=AG9, first strand: chain 'I' and resid 659 through 664 removed outlier: 3.879A pdb=" N THR I 669 " --> pdb=" O ASP I 664 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 707 through 709 Processing sheet with id=AH2, first strand: chain 'I' and resid 718 through 724 removed outlier: 7.536A pdb=" N SER I 761 " --> pdb=" O SER I 720 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU I 722 " --> pdb=" O SER I 761 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU I 756 " --> pdb=" O ASP I 740 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP I 740 " --> pdb=" O GLU I 756 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU I 729 " --> pdb=" O ALA I 737 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 801 through 803 removed outlier: 4.483A pdb=" N LYS I 801 " --> pdb=" O LEU I 935 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 1202 through 1204 Processing sheet with id=AH5, first strand: chain 'K' and resid 11 through 13 removed outlier: 3.569A pdb=" N LEU K 11 " --> pdb=" O LYS K 104 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU K 106 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 19 through 24 removed outlier: 3.879A pdb=" N ASP K 71 " --> pdb=" O SER K 68 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 115 through 119 removed outlier: 3.539A pdb=" N VAL K 134 " --> pdb=" O PHE K 119 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 154 through 155 removed outlier: 3.731A pdb=" N LYS K 146 " --> pdb=" O THR K 198 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3373 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: 8.19 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5348 1.32 - 1.44: 8881 1.44 - 1.57: 17879 1.57 - 1.69: 9 1.69 - 1.81: 200 Bond restraints: 32317 Sorted by residual: bond pdb=" C SER H 160 " pdb=" O SER H 160 " ideal model delta sigma weight residual 1.235 1.366 -0.131 1.14e-02 7.69e+03 1.32e+02 bond pdb=" C SER C 160 " pdb=" O SER C 160 " ideal model delta sigma weight residual 1.236 1.365 -0.129 1.20e-02 6.94e+03 1.16e+02 bond pdb=" C SER C 186 " pdb=" O SER C 186 " ideal model delta sigma weight residual 1.236 1.363 -0.128 1.20e-02 6.94e+03 1.14e+02 bond pdb=" C SER H 186 " pdb=" O SER H 186 " ideal model delta sigma weight residual 1.236 1.364 -0.128 1.21e-02 6.83e+03 1.12e+02 bond pdb=" N CYS F 585 " pdb=" CA CYS F 585 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.92e+01 ... (remaining 32312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.36: 43778 4.36 - 8.73: 186 8.73 - 13.09: 11 13.09 - 17.46: 5 17.46 - 21.82: 2 Bond angle restraints: 43982 Sorted by residual: angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA BSER H 186 " ideal model delta sigma weight residual 120.38 132.34 -11.96 1.09e+00 8.42e-01 1.20e+02 angle pdb=" O SER C 186 " pdb=" C SER C 186 " pdb=" CA ASER C 186 " ideal model delta sigma weight residual 120.36 132.15 -11.79 1.08e+00 8.57e-01 1.19e+02 angle pdb=" O SER C 186 " pdb=" C SER C 186 " pdb=" CA BSER C 186 " ideal model delta sigma weight residual 120.36 132.15 -11.79 1.08e+00 8.57e-01 1.19e+02 angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA ASER H 186 " ideal model delta sigma weight residual 120.38 132.25 -11.87 1.09e+00 8.42e-01 1.19e+02 angle pdb=" O SER C 160 " pdb=" C SER C 160 " pdb=" CA BSER C 160 " ideal model delta sigma weight residual 120.36 131.97 -11.61 1.08e+00 8.57e-01 1.16e+02 ... (remaining 43977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 17659 17.86 - 35.72: 1234 35.72 - 53.58: 308 53.58 - 71.44: 80 71.44 - 89.31: 12 Dihedral angle restraints: 19293 sinusoidal: 7344 harmonic: 11949 Sorted by residual: dihedral pdb=" CB CYS F 811 " pdb=" SG CYS F 811 " pdb=" SG CYS F 817 " pdb=" CB CYS F 817 " ideal model delta sinusoidal sigma weight residual -86.00 -165.04 79.04 1 1.00e+01 1.00e-02 7.77e+01 dihedral pdb=" CA LEU G 548 " pdb=" C LEU G 548 " pdb=" N GLU G 549 " pdb=" CA GLU G 549 " ideal model delta harmonic sigma weight residual 0.00 33.07 -33.07 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CB CYS F 806 " pdb=" SG CYS F 806 " pdb=" SG CYS F 828 " pdb=" CB CYS F 828 " ideal model delta sinusoidal sigma weight residual 93.00 45.76 47.24 1 1.00e+01 1.00e-02 3.08e+01 ... (remaining 19290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 3901 0.140 - 0.279: 1010 0.279 - 0.419: 17 0.419 - 0.559: 4 0.559 - 0.698: 2 Chirality restraints: 4934 Sorted by residual: chirality pdb=" CG LEU F1222 " pdb=" CB LEU F1222 " pdb=" CD1 LEU F1222 " pdb=" CD2 LEU F1222 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CG LEU G1222 " pdb=" CB LEU G1222 " pdb=" CD1 LEU G1222 " pdb=" CD2 LEU G1222 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA BSER H 186 " pdb=" N SER H 186 " pdb=" C SER H 186 " pdb=" CB BSER H 186 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.77e+00 ... (remaining 4931 not shown) Planarity restraints: 5708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F1066 " -0.013 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C GLN F1066 " 0.048 2.00e-02 2.50e+03 pdb=" O GLN F1066 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE F1067 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G1192 " 0.032 2.00e-02 2.50e+03 1.73e-02 6.01e+00 pdb=" CG TYR G1192 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR G1192 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR G1192 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR G1192 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR G1192 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR G1192 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR G1192 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F1192 " -0.032 2.00e-02 2.50e+03 1.73e-02 5.98e+00 pdb=" CG TYR F1192 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR F1192 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR F1192 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR F1192 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR F1192 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR F1192 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F1192 " -0.026 2.00e-02 2.50e+03 ... (remaining 5705 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 1 2.27 - 2.92: 13044 2.92 - 3.58: 45182 3.58 - 4.24: 78178 4.24 - 4.90: 127790 Nonbonded interactions: 264195 Sorted by model distance: nonbonded pdb=" CB ALA F1130 " pdb=" O GLY F1133 " model vdw 1.606 3.460 nonbonded pdb=" CA ALA G 53 " pdb=" CD1 ILE G 56 " model vdw 2.265 3.890 nonbonded pdb=" CB ALA G 53 " pdb=" CD1 ILE G 56 " model vdw 2.367 3.880 nonbonded pdb=" O SER F 546 " pdb=" O GLU F 549 " model vdw 2.421 3.040 nonbonded pdb=" N GLY I 90 " pdb=" O ILE I 300 " model vdw 2.439 3.120 ... (remaining 264190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 159 or resid 161 through 185 or resid 187 throug \ h 221)) selection = (chain 'H' and (resid 1 through 159 or resid 161 through 185 or resid 187 throug \ h 221)) } ncs_group { reference = chain 'D' selection = chain 'K' } ncs_group { reference = (chain 'F' and (resid 18 through 153 or resid 166 through 1224)) selection = chain 'G' } 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=0.40 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 30.980 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3881 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 : 0.013 0.141 32372 Z= 1.016 Angle : 1.521 21.819 44092 Z= 1.180 Chirality : 0.109 0.698 4934 Planarity : 0.004 0.035 5708 Dihedral : 13.241 89.306 11508 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.72 % Favored : 97.03 % Rotamer: Outliers : 7.98 % Allowed : 8.27 % Favored : 83.75 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.13), residues: 4081 helix: 4.14 (0.17), residues: 800 sheet: 1.74 (0.16), residues: 1068 loop : 0.35 (0.12), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 629 TYR 0.032 0.002 TYR F1192 PHE 0.016 0.002 PHE G 895 TRP 0.019 0.002 TRP F1184 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.01337 (32317) covalent geometry : angle 1.52155 (43982) SS BOND : bond 0.00519 ( 55) SS BOND : angle 1.14090 ( 110) hydrogen bonds : bond 0.20003 ( 1218) hydrogen bonds : angle 8.48759 ( 3373) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 277 poor density : 516 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 190 HIS cc_start: -0.2560 (OUTLIER) cc_final: -0.2951 (t-90) REVERT: G 809 TYR cc_start: 0.3194 (t80) cc_final: 0.2731 (t80) REVERT: G 909 TYR cc_start: -0.0661 (OUTLIER) cc_final: -0.1350 (t80) REVERT: K 147 VAL cc_start: -0.0187 (OUTLIER) cc_final: -0.0421 (t) outliers start: 277 outliers final: 44 residues processed: 740 average time/residue: 0.5021 time to fit residues: 457.7888 Evaluate side-chains 337 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 290 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain F residue 71 TYR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 219 TYR Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 590 PHE Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 831 ILE Chi-restraints excluded: chain F residue 836 HIS Chi-restraints excluded: chain F residue 909 TYR Chi-restraints excluded: chain F residue 1150 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 422 ASP Chi-restraints excluded: chain G residue 909 TYR Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 1015 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 254 PHE Chi-restraints excluded: chain I residue 278 MET Chi-restraints excluded: chain I residue 608 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 1015 THR Chi-restraints excluded: chain I residue 1149 VAL Chi-restraints excluded: chain K residue 33 TYR Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 148 GLN Chi-restraints excluded: chain K residue 184 LYS Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 190 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN C 112 GLN C 178 GLN C 199 GLN C 204 ASN F 36 GLN F 166 ASN F 236 ASN F 521 ASN F 582 ASN F 592 ASN ** F 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 628 GLN F 733 GLN F 815 GLN F 819 GLN ** F 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 981 ASN F1009 GLN F1042 ASN F1063 GLN F1066 GLN F1085 GLN F1213 ASN G 78 GLN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 HIS G 236 ASN G 521 ASN G 576 GLN G 599 GLN ** G 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 628 GLN G 681 HIS G 839 ASN ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 981 ASN G1072 ASN G1213 ASN H 6 GLN H 162 ASN H 178 GLN I 166 ASN I 208 HIS ** I 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 ASN I 277 ASN I 280 GLN I 599 GLN ** I 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 766 HIS I 769 GLN I 812 ASN ** I 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 981 ASN I1020 GLN ** I1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1072 ASN I1213 ASN I1217 ASN K 43 GLN K 148 GLN K 161 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5022 r_free = 0.5022 target = 0.206716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.184499 restraints weight = 190254.875| |-----------------------------------------------------------------------------| r_work (start): 0.4469 rms_B_bonded: 4.13 r_work: 0.4239 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4205 r_free = 0.4205 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4205 r_free = 0.4205 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 32372 Z= 0.182 Angle : 0.712 19.870 44092 Z= 0.373 Chirality : 0.047 0.312 4934 Planarity : 0.005 0.057 5708 Dihedral : 6.238 59.549 4537 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.82 % Favored : 98.06 % Rotamer: Outliers : 4.55 % Allowed : 15.70 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.12), residues: 4081 helix: 2.38 (0.18), residues: 791 sheet: 1.15 (0.15), residues: 1126 loop : -0.01 (0.12), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 50 TYR 0.037 0.002 TYR G 824 PHE 0.028 0.002 PHE G 827 TRP 0.042 0.003 TRP C 47 HIS 0.012 0.001 HIS I 836 Details of bonding type rmsd covalent geometry : bond 0.00395 (32317) covalent geometry : angle 0.70352 (43982) SS BOND : bond 0.00600 ( 55) SS BOND : angle 2.30990 ( 110) hydrogen bonds : bond 0.06194 ( 1218) hydrogen bonds : angle 6.75976 ( 3373) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 321 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ARG cc_start: 0.5757 (ttp-110) cc_final: 0.5554 (tmm-80) REVERT: C 48 MET cc_start: 0.8185 (mtp) cc_final: 0.7253 (mpp) REVERT: C 205 VAL cc_start: 0.7345 (p) cc_final: 0.7029 (m) REVERT: D 39 GLN cc_start: -0.1017 (OUTLIER) cc_final: -0.1525 (tm-30) REVERT: D 190 HIS cc_start: -0.1013 (OUTLIER) cc_final: -0.1691 (t-90) REVERT: F 219 TYR cc_start: 0.6385 (p90) cc_final: 0.5611 (p90) REVERT: F 252 GLU cc_start: 0.5663 (tt0) cc_final: 0.5304 (tp30) REVERT: F 408 ASN cc_start: 0.7226 (t0) cc_final: 0.6929 (t0) REVERT: F 417 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7691 (pp) REVERT: F 563 MET cc_start: 0.3646 (tpp) cc_final: 0.3437 (tpp) REVERT: G 141 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6946 (mtp85) REVERT: G 259 THR cc_start: 0.6652 (p) cc_final: 0.6340 (t) REVERT: G 481 LEU cc_start: 0.8800 (mm) cc_final: 0.8499 (tm) REVERT: G 841 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7210 (mpp-170) REVERT: G 909 TYR cc_start: 0.2246 (OUTLIER) cc_final: 0.1760 (t80) REVERT: I 84 MET cc_start: 0.2811 (OUTLIER) cc_final: 0.2533 (tmt) REVERT: I 156 PHE cc_start: 0.3155 (m-80) cc_final: 0.2764 (m-80) REVERT: I 174 ASP cc_start: 0.0817 (OUTLIER) cc_final: 0.0249 (m-30) REVERT: I 346 GLN cc_start: 0.7375 (mt0) cc_final: 0.7147 (tt0) REVERT: I 352 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7377 (tp30) REVERT: I 642 TYR cc_start: -0.0281 (m-80) cc_final: -0.1008 (t80) REVERT: I 757 MET cc_start: 0.3482 (OUTLIER) cc_final: 0.3029 (mpt) REVERT: I 810 VAL cc_start: 0.6561 (t) cc_final: 0.6221 (t) REVERT: I 1035 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8137 (tppp) REVERT: I 1039 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7976 (mm-30) REVERT: I 1090 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: K 33 TYR cc_start: 0.8346 (m-10) cc_final: 0.7956 (m-10) outliers start: 159 outliers final: 59 residues processed: 447 average time/residue: 0.5023 time to fit residues: 278.6885 Evaluate side-chains 309 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 240 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 532 SER Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 590 PHE Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 655 VAL Chi-restraints excluded: chain F residue 909 TYR Chi-restraints excluded: chain F residue 1150 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 141 ARG Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 303 ILE Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 443 LEU Chi-restraints excluded: chain G residue 458 VAL Chi-restraints excluded: chain G residue 828 CYS Chi-restraints excluded: chain G residue 841 ARG Chi-restraints excluded: chain G residue 854 LYS Chi-restraints excluded: chain G residue 909 TYR Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 254 PHE Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 608 LEU Chi-restraints excluded: chain I residue 757 MET Chi-restraints excluded: chain I residue 821 LEU Chi-restraints excluded: chain I residue 1090 GLU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 184 LYS Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 190 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 170 optimal weight: 2.9990 chunk 8 optimal weight: 30.0000 chunk 374 optimal weight: 1.9990 chunk 322 optimal weight: 0.8980 chunk 243 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 375 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 334 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 839 ASN ** F 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 GLN G 408 ASN ** G 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 670 HIS ** G 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 839 ASN G 927 GLN G1056 GLN H 204 ASN I 733 GLN ** I 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1132 ASN I1217 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.192581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.169644 restraints weight = 173278.902| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 4.88 r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4343 r_free = 0.4343 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4343 r_free = 0.4343 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.5935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 32372 Z= 0.295 Angle : 0.858 16.315 44092 Z= 0.462 Chirality : 0.053 0.355 4934 Planarity : 0.007 0.188 5708 Dihedral : 6.405 59.452 4496 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.02 % Favored : 96.84 % Rotamer: Outliers : 5.23 % Allowed : 15.82 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.12), residues: 4081 helix: 0.78 (0.18), residues: 800 sheet: 0.53 (0.15), residues: 1060 loop : -0.47 (0.12), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG C 50 TYR 0.032 0.003 TYR F 932 PHE 0.052 0.003 PHE I 354 TRP 0.058 0.003 TRP K 36 HIS 0.013 0.003 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00652 (32317) covalent geometry : angle 0.85320 (43982) SS BOND : bond 0.01326 ( 55) SS BOND : angle 1.98774 ( 110) hydrogen bonds : bond 0.07422 ( 1218) hydrogen bonds : angle 6.82324 ( 3373) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 314 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 190 HIS cc_start: -0.2512 (OUTLIER) cc_final: -0.2989 (t-90) REVERT: F 84 MET cc_start: 0.6618 (tmm) cc_final: 0.6261 (tmm) REVERT: F 318 LEU cc_start: 0.5461 (OUTLIER) cc_final: 0.4790 (mp) REVERT: F 529 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7635 (mp) REVERT: F 541 TYR cc_start: 0.6142 (m-80) cc_final: 0.5823 (m-10) REVERT: F 1008 MET cc_start: 0.7841 (tmm) cc_final: 0.7474 (ttp) REVERT: F 1174 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8765 (ttpt) REVERT: G 63 THR cc_start: 0.3109 (OUTLIER) cc_final: 0.2870 (t) REVERT: G 330 ASP cc_start: 0.3369 (OUTLIER) cc_final: 0.3047 (p0) REVERT: G 563 MET cc_start: 0.4350 (tpp) cc_final: 0.3653 (tpt) REVERT: G 668 LYS cc_start: 0.7365 (tptt) cc_final: 0.7152 (tppp) REVERT: G 757 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6804 (mtp) REVERT: G 827 PHE cc_start: 0.6268 (OUTLIER) cc_final: 0.6023 (p90) REVERT: G 841 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7255 (mpp-170) REVERT: G 988 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: G 995 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8331 (mppt) REVERT: H 145 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.6052 (pp) REVERT: I 84 MET cc_start: 0.4576 (OUTLIER) cc_final: 0.4255 (tpt) REVERT: I 174 ASP cc_start: 0.2188 (OUTLIER) cc_final: 0.1754 (m-30) REVERT: I 757 MET cc_start: 0.5414 (OUTLIER) cc_final: 0.5181 (mpt) outliers start: 183 outliers final: 59 residues processed: 455 average time/residue: 0.5291 time to fit residues: 295.8534 Evaluate side-chains 309 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 235 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 496 LYS Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 900 ILE Chi-restraints excluded: chain F residue 909 TYR Chi-restraints excluded: chain F residue 958 VAL Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain F residue 1174 LYS Chi-restraints excluded: chain F residue 1185 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 243 TYR Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 330 ASP Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 466 GLN Chi-restraints excluded: chain G residue 662 ILE Chi-restraints excluded: chain G residue 670 HIS Chi-restraints excluded: chain G residue 717 LEU Chi-restraints excluded: chain G residue 757 MET Chi-restraints excluded: chain G residue 821 LEU Chi-restraints excluded: chain G residue 827 PHE Chi-restraints excluded: chain G residue 828 CYS Chi-restraints excluded: chain G residue 841 ARG Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 988 GLN Chi-restraints excluded: chain G residue 995 LYS Chi-restraints excluded: chain G residue 1090 GLU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain H residue 155 GLU Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 657 VAL Chi-restraints excluded: chain I residue 718 VAL Chi-restraints excluded: chain I residue 757 MET Chi-restraints excluded: chain I residue 995 LYS Chi-restraints excluded: chain I residue 1090 GLU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 78 ARG Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 190 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 1 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 52 optimal weight: 0.0980 chunk 241 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 27 optimal weight: 30.0000 chunk 31 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 385 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 HIS D 148 GLN F 78 GLN F 319 GLN F 346 GLN F 733 GLN ** F 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 914 GLN ** F 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 466 GLN ** G 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 812 ASN G 826 GLN G 927 GLN I 348 HIS ** I 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 708 GLN I 733 GLN I 808 GLN ** I 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 988 GLN ** I1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1079 ASN K 27 GLN K 91 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.191796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.168365 restraints weight = 183204.693| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 5.05 r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4337 r_free = 0.4337 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4337 r_free = 0.4337 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 32372 Z= 0.161 Angle : 0.670 13.930 44092 Z= 0.348 Chirality : 0.045 0.311 4934 Planarity : 0.005 0.058 5708 Dihedral : 5.600 58.875 4481 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.65 % Favored : 97.23 % Rotamer: Outliers : 3.72 % Allowed : 17.88 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.12), residues: 4081 helix: 1.41 (0.19), residues: 784 sheet: 0.45 (0.16), residues: 1021 loop : -0.47 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 38 TYR 0.033 0.002 TYR G 497 PHE 0.031 0.002 PHE G 571 TRP 0.045 0.002 TRP C 47 HIS 0.020 0.001 HIS G 670 Details of bonding type rmsd covalent geometry : bond 0.00354 (32317) covalent geometry : angle 0.66731 (43982) SS BOND : bond 0.00375 ( 55) SS BOND : angle 1.41275 ( 110) hydrogen bonds : bond 0.05337 ( 1218) hydrogen bonds : angle 6.22456 ( 3373) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 273 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 LEU cc_start: 0.6435 (tm) cc_final: 0.6063 (tm) REVERT: D 190 HIS cc_start: -0.2565 (OUTLIER) cc_final: -0.2899 (t-90) REVERT: F 529 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7659 (mp) REVERT: F 541 TYR cc_start: 0.6218 (m-80) cc_final: 0.5898 (m-10) REVERT: F 569 MET cc_start: 0.4816 (mpp) cc_final: 0.4590 (mpp) REVERT: F 636 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7149 (tp-100) REVERT: G 232 PHE cc_start: 0.4583 (OUTLIER) cc_final: 0.4338 (m-10) REVERT: G 563 MET cc_start: 0.4191 (OUTLIER) cc_final: 0.3545 (tpt) REVERT: G 757 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6630 (ptp) REVERT: G 923 LEU cc_start: 0.7554 (pt) cc_final: 0.7222 (mt) REVERT: G 988 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: G 1090 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: H 145 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6269 (pp) REVERT: I 84 MET cc_start: 0.4148 (OUTLIER) cc_final: 0.3061 (tmt) REVERT: I 174 ASP cc_start: 0.1664 (OUTLIER) cc_final: 0.1110 (m-30) REVERT: I 346 GLN cc_start: 0.7880 (tt0) cc_final: 0.7559 (tt0) REVERT: I 1090 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7246 (mp0) outliers start: 130 outliers final: 54 residues processed: 375 average time/residue: 0.5117 time to fit residues: 238.1142 Evaluate side-chains 300 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 235 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 635 TYR Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 810 VAL Chi-restraints excluded: chain F residue 909 TYR Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 458 VAL Chi-restraints excluded: chain G residue 563 MET Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 757 MET Chi-restraints excluded: chain G residue 758 ARG Chi-restraints excluded: chain G residue 821 LEU Chi-restraints excluded: chain G residue 827 PHE Chi-restraints excluded: chain G residue 854 LYS Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 988 GLN Chi-restraints excluded: chain G residue 1090 GLU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 132 ILE Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 718 VAL Chi-restraints excluded: chain I residue 854 LYS Chi-restraints excluded: chain I residue 900 ILE Chi-restraints excluded: chain I residue 1090 GLU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 33 TYR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 190 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 310 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 397 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 376 optimal weight: 0.9990 chunk 41 optimal weight: 30.0000 chunk 272 optimal weight: 30.0000 chunk 199 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN C 65 GLN C 171 HIS F 277 ASN F 466 GLN ** F 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 681 HIS ** F 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 815 GLN ** F 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS ** G 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 GLN G 348 HIS G 544 GLN G 566 GLN ** G 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 826 GLN G 836 HIS G1056 GLN G1132 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS I 194 HIS I 298 HIS I 348 HIS I 377 GLN I 628 GLN ** I 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.164593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.123985 restraints weight = 181571.940| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 6.94 r_work: 0.3405 rms_B_bonded: 5.49 restraints_weight: 2.0000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.9340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.187 32372 Z= 0.617 Angle : 1.173 21.341 44092 Z= 0.638 Chirality : 0.069 0.533 4934 Planarity : 0.009 0.116 5708 Dihedral : 7.386 55.652 4481 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 24.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.40 % Favored : 94.38 % Rotamer: Outliers : 6.04 % Allowed : 16.48 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.12), residues: 4081 helix: 0.07 (0.17), residues: 764 sheet: -0.11 (0.15), residues: 1037 loop : -1.25 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.002 ARG I 119 TYR 0.091 0.005 TYR I 316 PHE 0.040 0.005 PHE F 814 TRP 0.050 0.005 TRP C 47 HIS 0.065 0.006 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.01459 (32317) covalent geometry : angle 1.16515 (43982) SS BOND : bond 0.01835 ( 55) SS BOND : angle 2.88871 ( 110) hydrogen bonds : bond 0.09678 ( 1218) hydrogen bonds : angle 7.36635 ( 3373) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 303 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7453 (pp20) cc_final: 0.7103 (pp20) REVERT: C 80 TYR cc_start: 0.7054 (OUTLIER) cc_final: 0.6497 (m-80) REVERT: F 41 ASP cc_start: 0.7524 (m-30) cc_final: 0.7247 (m-30) REVERT: F 63 THR cc_start: 0.1681 (OUTLIER) cc_final: -0.0110 (p) REVERT: F 101 PHE cc_start: 0.6920 (t80) cc_final: 0.5263 (t80) REVERT: F 141 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6641 (mmm160) REVERT: F 219 TYR cc_start: 0.6067 (p90) cc_final: 0.5828 (p90) REVERT: F 232 PHE cc_start: 0.3496 (OUTLIER) cc_final: 0.2920 (m-10) REVERT: F 278 MET cc_start: 0.1907 (OUTLIER) cc_final: 0.1610 (mpp) REVERT: F 466 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8119 (mm110) REVERT: F 636 GLN cc_start: 0.8676 (mm-40) cc_final: 0.7838 (tp-100) REVERT: F 680 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.5186 (mm-30) REVERT: F 757 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7749 (mtm) REVERT: F 805 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7918 (p0) REVERT: F 824 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.6024 (p90) REVERT: F 1008 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8641 (ttp) REVERT: F 1064 ASP cc_start: 0.8314 (t0) cc_final: 0.7898 (m-30) REVERT: F 1174 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9117 (ttpt) REVERT: G 140 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7989 (mm) REVERT: G 180 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8375 (mt) REVERT: G 232 PHE cc_start: 0.4106 (OUTLIER) cc_final: 0.3889 (m-10) REVERT: G 240 MET cc_start: 0.7596 (tmt) cc_final: 0.7382 (tmt) REVERT: G 291 LYS cc_start: 0.8672 (mttt) cc_final: 0.8173 (mppt) REVERT: G 292 TYR cc_start: 0.8632 (m-80) cc_final: 0.8373 (m-80) REVERT: G 332 TYR cc_start: 0.7915 (m-10) cc_final: 0.7335 (m-80) REVERT: G 357 GLU cc_start: 0.8867 (pt0) cc_final: 0.8583 (pm20) REVERT: G 481 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8204 (tm) REVERT: G 499 TYR cc_start: 0.8563 (p90) cc_final: 0.8191 (p90) REVERT: G 542 ARG cc_start: 0.5263 (OUTLIER) cc_final: 0.3418 (ttp80) REVERT: G 583 SER cc_start: 0.8078 (OUTLIER) cc_final: 0.7871 (p) REVERT: G 635 TYR cc_start: 0.8258 (m-80) cc_final: 0.8033 (m-80) REVERT: G 827 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7573 (p90) REVERT: G 923 LEU cc_start: 0.8464 (pt) cc_final: 0.8185 (mm) REVERT: H 147 CYS cc_start: -0.1997 (OUTLIER) cc_final: -0.2378 (p) REVERT: I 111 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8759 (mp10) REVERT: I 291 LYS cc_start: 0.8743 (mttt) cc_final: 0.8432 (mppt) REVERT: I 332 TYR cc_start: 0.3348 (m-80) cc_final: 0.2853 (m-80) REVERT: I 821 LEU cc_start: 0.4763 (OUTLIER) cc_final: 0.4353 (pp) REVERT: I 827 PHE cc_start: 0.8723 (m-10) cc_final: 0.8512 (m-80) REVERT: I 1008 MET cc_start: 0.8794 (tmm) cc_final: 0.8366 (ttp) REVERT: I 1063 GLN cc_start: 0.3205 (OUTLIER) cc_final: 0.2900 (pt0) REVERT: K 79 LEU cc_start: 0.7216 (pp) cc_final: 0.6772 (mm) outliers start: 211 outliers final: 94 residues processed: 478 average time/residue: 0.4947 time to fit residues: 293.9758 Evaluate side-chains 360 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 244 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 119 ARG Chi-restraints excluded: chain F residue 141 ARG Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 466 GLN Chi-restraints excluded: chain F residue 467 PHE Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain F residue 521 ASN Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 590 PHE Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 635 TYR Chi-restraints excluded: chain F residue 680 GLU Chi-restraints excluded: chain F residue 757 MET Chi-restraints excluded: chain F residue 805 ASP Chi-restraints excluded: chain F residue 807 LYS Chi-restraints excluded: chain F residue 810 VAL Chi-restraints excluded: chain F residue 824 TYR Chi-restraints excluded: chain F residue 900 ILE Chi-restraints excluded: chain F residue 1008 MET Chi-restraints excluded: chain F residue 1067 ILE Chi-restraints excluded: chain F residue 1068 ASP Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain F residue 1131 PRO Chi-restraints excluded: chain F residue 1174 LYS Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 303 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 396 VAL Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 458 VAL Chi-restraints excluded: chain G residue 478 CYS Chi-restraints excluded: chain G residue 481 LEU Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 542 ARG Chi-restraints excluded: chain G residue 583 SER Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 642 TYR Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 821 LEU Chi-restraints excluded: chain G residue 827 PHE Chi-restraints excluded: chain G residue 853 VAL Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 943 MET Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 988 GLN Chi-restraints excluded: chain G residue 1043 THR Chi-restraints excluded: chain G residue 1090 GLU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 155 GLU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 664 ASP Chi-restraints excluded: chain I residue 736 CYS Chi-restraints excluded: chain I residue 821 LEU Chi-restraints excluded: chain I residue 854 LYS Chi-restraints excluded: chain I residue 923 LEU Chi-restraints excluded: chain I residue 1047 ILE Chi-restraints excluded: chain I residue 1063 GLN Chi-restraints excluded: chain I residue 1090 GLU Chi-restraints excluded: chain I residue 1127 VAL Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 33 TYR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 190 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 226 optimal weight: 0.6980 chunk 283 optimal weight: 5.9990 chunk 357 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 chunk 278 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 352 optimal weight: 0.8980 chunk 326 optimal weight: 0.9990 chunk 185 optimal weight: 8.9990 chunk 101 optimal weight: 0.4980 chunk 16 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 72 GLN F 277 ASN F 348 HIS ** F 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1132 ASN ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 398 ASN G 826 GLN G1129 ASN I 91 HIS ** I 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN I 377 GLN I 915 GLN I1063 GLN K 27 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.174582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.137221 restraints weight = 133203.980| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 5.37 r_work: 0.3533 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.9378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32372 Z= 0.162 Angle : 0.717 10.662 44092 Z= 0.378 Chirality : 0.046 0.276 4934 Planarity : 0.005 0.058 5708 Dihedral : 6.092 55.164 4478 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.98 % Rotamer: Outliers : 3.26 % Allowed : 19.91 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.12), residues: 4081 helix: 0.92 (0.18), residues: 784 sheet: -0.09 (0.16), residues: 1040 loop : -1.04 (0.12), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 62 TYR 0.033 0.002 TYR G 497 PHE 0.030 0.002 PHE G 204 TRP 0.059 0.002 TRP C 47 HIS 0.016 0.002 HIS F 670 Details of bonding type rmsd covalent geometry : bond 0.00347 (32317) covalent geometry : angle 0.71514 (43982) SS BOND : bond 0.00315 ( 55) SS BOND : angle 1.21580 ( 110) hydrogen bonds : bond 0.05884 ( 1218) hydrogen bonds : angle 6.36668 ( 3373) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 262 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.7668 (mptt) cc_final: 0.7347 (mmmm) REVERT: C 46 GLU cc_start: 0.7085 (pp20) cc_final: 0.5291 (pm20) REVERT: C 47 TRP cc_start: 0.7900 (t60) cc_final: 0.7145 (t60) REVERT: C 59 ARG cc_start: 0.8373 (ptm160) cc_final: 0.8110 (ptm160) REVERT: C 80 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: D 190 HIS cc_start: -0.0098 (OUTLIER) cc_final: -0.1006 (t-90) REVERT: F 41 ASP cc_start: 0.7415 (m-30) cc_final: 0.6716 (p0) REVERT: F 101 PHE cc_start: 0.6262 (t80) cc_final: 0.5299 (t80) REVERT: F 172 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.5673 (tp) REVERT: F 219 TYR cc_start: 0.5830 (p90) cc_final: 0.5606 (p90) REVERT: F 232 PHE cc_start: 0.3074 (OUTLIER) cc_final: 0.2347 (m-10) REVERT: F 344 LEU cc_start: 0.8614 (mt) cc_final: 0.8370 (mm) REVERT: F 848 ASN cc_start: 0.8972 (m-40) cc_final: 0.8710 (t0) REVERT: F 988 GLN cc_start: 0.8857 (tt0) cc_final: 0.8530 (tp40) REVERT: G 119 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.7660 (ttm110) REVERT: G 167 HIS cc_start: 0.3513 (OUTLIER) cc_final: 0.2405 (t-90) REVERT: G 180 LEU cc_start: 0.8349 (mm) cc_final: 0.8126 (mt) REVERT: G 232 PHE cc_start: 0.4781 (OUTLIER) cc_final: 0.4383 (m-10) REVERT: G 261 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: G 332 TYR cc_start: 0.8070 (m-10) cc_final: 0.7482 (m-80) REVERT: G 357 GLU cc_start: 0.9020 (pt0) cc_final: 0.8739 (pm20) REVERT: G 398 ASN cc_start: 0.9646 (OUTLIER) cc_final: 0.9406 (p0) REVERT: G 499 TYR cc_start: 0.8521 (p90) cc_final: 0.8112 (p90) REVERT: G 583 SER cc_start: 0.7981 (OUTLIER) cc_final: 0.7739 (p) REVERT: G 635 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7771 (m-10) REVERT: G 960 TRP cc_start: 0.6838 (t60) cc_final: 0.6551 (t60) REVERT: G 1044 PHE cc_start: 0.8734 (m-80) cc_final: 0.8507 (m-80) REVERT: H 147 CYS cc_start: -0.1836 (OUTLIER) cc_final: -0.2265 (p) REVERT: I 252 GLU cc_start: 0.7889 (pt0) cc_final: 0.7184 (pt0) REVERT: I 291 LYS cc_start: 0.8613 (mttt) cc_final: 0.8352 (mtmt) REVERT: I 310 TRP cc_start: 0.6936 (m100) cc_final: 0.6730 (m100) REVERT: I 357 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7670 (tp30) REVERT: I 635 TYR cc_start: 0.6775 (m-80) cc_final: 0.6528 (m-80) REVERT: I 757 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.7970 (mtt) REVERT: I 1008 MET cc_start: 0.8422 (tmm) cc_final: 0.7938 (ttp) REVERT: I 1090 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: K 27 GLN cc_start: 0.4550 (OUTLIER) cc_final: 0.4345 (pp30) REVERT: K 28 SER cc_start: 0.8314 (p) cc_final: 0.8079 (m) REVERT: K 79 LEU cc_start: 0.6901 (pp) cc_final: 0.6558 (mm) outliers start: 114 outliers final: 52 residues processed: 351 average time/residue: 0.5021 time to fit residues: 217.9696 Evaluate side-chains 301 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 234 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 119 ARG Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 635 TYR Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 810 VAL Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain G residue 261 GLN Chi-restraints excluded: chain G residue 303 ILE Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 458 VAL Chi-restraints excluded: chain G residue 478 CYS Chi-restraints excluded: chain G residue 583 SER Chi-restraints excluded: chain G residue 635 TYR Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 827 PHE Chi-restraints excluded: chain G residue 900 ILE Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 943 MET Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 673 LEU Chi-restraints excluded: chain I residue 736 CYS Chi-restraints excluded: chain I residue 757 MET Chi-restraints excluded: chain I residue 808 GLN Chi-restraints excluded: chain I residue 1090 GLU Chi-restraints excluded: chain I residue 1127 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 190 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 111 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 294 optimal weight: 8.9990 chunk 352 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 279 optimal weight: 30.0000 chunk 161 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 826 GLN G 927 GLN G1063 GLN I 348 HIS I 377 GLN I1129 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.175061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.146063 restraints weight = 148850.039| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 5.60 r_work: 0.3505 rms_B_bonded: 5.28 restraints_weight: 2.0000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.9631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 32372 Z= 0.176 Angle : 0.701 13.175 44092 Z= 0.365 Chirality : 0.045 0.207 4934 Planarity : 0.005 0.061 5708 Dihedral : 5.827 56.315 4478 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.22 % Favored : 95.68 % Rotamer: Outliers : 3.32 % Allowed : 20.28 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.12), residues: 4081 helix: 1.15 (0.19), residues: 781 sheet: -0.10 (0.16), residues: 1027 loop : -0.99 (0.12), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 269 TYR 0.041 0.002 TYR D 88 PHE 0.024 0.002 PHE G 571 TRP 0.050 0.002 TRP C 47 HIS 0.016 0.002 HIS F 670 Details of bonding type rmsd covalent geometry : bond 0.00394 (32317) covalent geometry : angle 0.69378 (43982) SS BOND : bond 0.00452 ( 55) SS BOND : angle 2.12715 ( 110) hydrogen bonds : bond 0.05704 ( 1218) hydrogen bonds : angle 6.13364 ( 3373) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 243 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.7815 (mptt) cc_final: 0.7468 (mmmm) REVERT: C 46 GLU cc_start: 0.7576 (pp20) cc_final: 0.6440 (pm20) REVERT: C 47 TRP cc_start: 0.7478 (t60) cc_final: 0.6647 (t60) REVERT: C 80 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.6900 (m-80) REVERT: F 41 ASP cc_start: 0.7505 (m-30) cc_final: 0.7132 (m-30) REVERT: F 219 TYR cc_start: 0.5604 (p90) cc_final: 0.5380 (p90) REVERT: F 230 GLU cc_start: 0.2855 (mt-10) cc_final: 0.2498 (tm-30) REVERT: F 232 PHE cc_start: 0.3034 (OUTLIER) cc_final: 0.2671 (m-10) REVERT: F 344 LEU cc_start: 0.8847 (mt) cc_final: 0.8305 (mt) REVERT: F 569 MET cc_start: 0.7802 (mpp) cc_final: 0.7136 (mpp) REVERT: F 932 TYR cc_start: 0.8452 (p90) cc_final: 0.7871 (p90) REVERT: G 119 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.7702 (ttm110) REVERT: G 167 HIS cc_start: 0.4189 (OUTLIER) cc_final: 0.3050 (t-90) REVERT: G 232 PHE cc_start: 0.4867 (OUTLIER) cc_final: 0.4611 (m-10) REVERT: G 261 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: G 332 TYR cc_start: 0.8557 (m-10) cc_final: 0.8310 (m-80) REVERT: G 499 TYR cc_start: 0.8515 (p90) cc_final: 0.8191 (p90) REVERT: G 569 MET cc_start: 0.9000 (tmm) cc_final: 0.8735 (tmm) REVERT: G 635 TYR cc_start: 0.8249 (m-80) cc_final: 0.7985 (m-10) REVERT: G 642 TYR cc_start: 0.3804 (OUTLIER) cc_final: 0.3515 (t80) REVERT: G 729 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8657 (pp) REVERT: G 827 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6865 (m-80) REVERT: H 147 CYS cc_start: -0.1420 (OUTLIER) cc_final: -0.1760 (p) REVERT: I 151 SER cc_start: 0.7573 (OUTLIER) cc_final: 0.7049 (p) REVERT: I 176 CYS cc_start: 0.6518 (OUTLIER) cc_final: 0.6181 (m) REVERT: I 291 LYS cc_start: 0.8580 (mttt) cc_final: 0.8164 (mppt) REVERT: I 356 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8556 (p) REVERT: I 357 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7382 (tp30) REVERT: I 635 TYR cc_start: 0.7040 (m-80) cc_final: 0.6747 (m-80) REVERT: I 673 LEU cc_start: 0.6291 (OUTLIER) cc_final: 0.6000 (tm) REVERT: I 757 MET cc_start: 0.8925 (mtt) cc_final: 0.8364 (mtt) REVERT: I 1008 MET cc_start: 0.8365 (tmm) cc_final: 0.7892 (ttp) REVERT: I 1090 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8344 (mp0) REVERT: K 28 SER cc_start: 0.8092 (p) cc_final: 0.7879 (m) REVERT: K 79 LEU cc_start: 0.6660 (pp) cc_final: 0.6351 (mm) outliers start: 116 outliers final: 59 residues processed: 338 average time/residue: 0.4857 time to fit residues: 204.4104 Evaluate side-chains 298 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 224 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 119 ARG Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 635 TYR Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 810 VAL Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 261 GLN Chi-restraints excluded: chain G residue 303 ILE Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 458 VAL Chi-restraints excluded: chain G residue 478 CYS Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 642 TYR Chi-restraints excluded: chain G residue 729 LEU Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 827 PHE Chi-restraints excluded: chain G residue 900 ILE Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 964 LEU Chi-restraints excluded: chain G residue 988 GLN Chi-restraints excluded: chain G residue 995 LYS Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 673 LEU Chi-restraints excluded: chain I residue 808 GLN Chi-restraints excluded: chain I residue 913 MET Chi-restraints excluded: chain I residue 1090 GLU Chi-restraints excluded: chain I residue 1127 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 190 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 355 optimal weight: 5.9990 chunk 217 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 chunk 320 optimal weight: 0.6980 chunk 369 optimal weight: 3.9990 chunk 395 optimal weight: 50.0000 chunk 62 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 218 optimal weight: 0.2980 chunk 111 optimal weight: 3.9990 chunk 393 optimal weight: 20.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 72 GLN F 348 HIS F 708 GLN G 72 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 HIS G 826 GLN G 927 GLN ** I 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 GLN I 808 GLN I 927 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.168787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.125292 restraints weight = 128234.132| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 4.72 r_work: 0.3480 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 1.0156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 32372 Z= 0.207 Angle : 0.747 25.087 44092 Z= 0.389 Chirality : 0.047 0.356 4934 Planarity : 0.005 0.071 5708 Dihedral : 5.843 56.282 4478 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.44 % Favored : 95.46 % Rotamer: Outliers : 3.09 % Allowed : 20.22 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.12), residues: 4081 helix: 1.11 (0.19), residues: 770 sheet: -0.09 (0.16), residues: 1007 loop : -0.99 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 235 TYR 0.050 0.002 TYR I 351 PHE 0.029 0.002 PHE F 814 TRP 0.050 0.003 TRP G 553 HIS 0.012 0.002 HIS F 264 Details of bonding type rmsd covalent geometry : bond 0.00476 (32317) covalent geometry : angle 0.73742 (43982) SS BOND : bond 0.00573 ( 55) SS BOND : angle 2.55680 ( 110) hydrogen bonds : bond 0.06013 ( 1218) hydrogen bonds : angle 6.15159 ( 3373) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 240 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.7720 (mptt) cc_final: 0.7387 (mmmm) REVERT: C 46 GLU cc_start: 0.7608 (pp20) cc_final: 0.6281 (pm20) REVERT: C 80 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.6789 (m-80) REVERT: D 190 HIS cc_start: -0.0018 (OUTLIER) cc_final: -0.0911 (t-90) REVERT: F 101 PHE cc_start: 0.6431 (t80) cc_final: 0.6167 (t80) REVERT: F 219 TYR cc_start: 0.5898 (p90) cc_final: 0.5666 (p90) REVERT: F 230 GLU cc_start: 0.3326 (mt-10) cc_final: 0.2917 (tm-30) REVERT: F 232 PHE cc_start: 0.3038 (OUTLIER) cc_final: 0.2423 (m-10) REVERT: F 330 ASP cc_start: 0.0338 (OUTLIER) cc_final: -0.0162 (p0) REVERT: F 569 MET cc_start: 0.7037 (mpp) cc_final: 0.6540 (mpp) REVERT: F 573 ILE cc_start: 0.9382 (mp) cc_final: 0.8720 (tp) REVERT: F 680 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7352 (mm-30) REVERT: G 119 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.7644 (ttm110) REVERT: G 167 HIS cc_start: 0.4234 (OUTLIER) cc_final: 0.3415 (t-90) REVERT: G 499 TYR cc_start: 0.8484 (p90) cc_final: 0.8029 (p90) REVERT: G 553 TRP cc_start: 0.5184 (t-100) cc_final: 0.4937 (t-100) REVERT: G 1090 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8254 (mp0) REVERT: H 147 CYS cc_start: -0.1921 (OUTLIER) cc_final: -0.2368 (p) REVERT: I 151 SER cc_start: 0.7666 (m) cc_final: 0.7040 (p) REVERT: I 176 CYS cc_start: 0.6347 (OUTLIER) cc_final: 0.5919 (m) REVERT: I 181 ARG cc_start: 0.7836 (ttm110) cc_final: 0.7317 (mtt90) REVERT: I 278 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.6716 (mpp) REVERT: I 291 LYS cc_start: 0.8747 (mttt) cc_final: 0.8477 (mtmt) REVERT: I 635 TYR cc_start: 0.7062 (m-80) cc_final: 0.6809 (m-80) REVERT: I 1090 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: K 79 LEU cc_start: 0.7179 (pp) cc_final: 0.6866 (mm) outliers start: 108 outliers final: 61 residues processed: 330 average time/residue: 0.4998 time to fit residues: 205.1948 Evaluate side-chains 289 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 216 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 496 LYS Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain F residue 521 ASN Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 635 TYR Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 680 GLU Chi-restraints excluded: chain F residue 718 VAL Chi-restraints excluded: chain F residue 810 VAL Chi-restraints excluded: chain F residue 900 ILE Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 303 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 458 VAL Chi-restraints excluded: chain G residue 478 CYS Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 564 THR Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 900 ILE Chi-restraints excluded: chain G residue 988 GLN Chi-restraints excluded: chain G residue 995 LYS Chi-restraints excluded: chain G residue 1090 GLU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 278 MET Chi-restraints excluded: chain I residue 673 LEU Chi-restraints excluded: chain I residue 854 LYS Chi-restraints excluded: chain I residue 1090 GLU Chi-restraints excluded: chain I residue 1127 VAL Chi-restraints excluded: chain I residue 1174 LYS Chi-restraints excluded: chain K residue 33 TYR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 190 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 223 optimal weight: 0.5980 chunk 195 optimal weight: 30.0000 chunk 140 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 192 optimal weight: 4.9990 chunk 377 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 281 optimal weight: 20.0000 chunk 320 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 280 optimal weight: 40.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 36 GLN F 377 GLN G 208 HIS G 486 HIS G 826 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 GLN I 808 GLN K 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.161564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.119761 restraints weight = 145269.126| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 5.32 r_work: 0.3405 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 1.0591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 32372 Z= 0.228 Angle : 0.757 21.917 44092 Z= 0.393 Chirality : 0.047 0.338 4934 Planarity : 0.005 0.064 5708 Dihedral : 5.837 56.699 4477 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 2.72 % Allowed : 21.22 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.13), residues: 4081 helix: 1.00 (0.19), residues: 770 sheet: -0.10 (0.16), residues: 1015 loop : -1.01 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG F 119 TYR 0.032 0.002 TYR I 351 PHE 0.128 0.002 PHE G 399 TRP 0.050 0.002 TRP C 47 HIS 0.016 0.002 HIS I 298 Details of bonding type rmsd covalent geometry : bond 0.00532 (32317) covalent geometry : angle 0.74401 (43982) SS BOND : bond 0.00918 ( 55) SS BOND : angle 2.91430 ( 110) hydrogen bonds : bond 0.06127 ( 1218) hydrogen bonds : angle 6.17729 ( 3373) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 232 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.7741 (mptt) cc_final: 0.7398 (mmmm) REVERT: C 46 GLU cc_start: 0.7674 (pp20) cc_final: 0.6559 (pm20) REVERT: C 80 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6996 (m-80) REVERT: D 190 HIS cc_start: 0.0154 (OUTLIER) cc_final: -0.0805 (t-90) REVERT: F 63 THR cc_start: 0.1162 (OUTLIER) cc_final: -0.0791 (p) REVERT: F 101 PHE cc_start: 0.6844 (t80) cc_final: 0.6357 (t80) REVERT: F 219 TYR cc_start: 0.5936 (p90) cc_final: 0.5632 (p90) REVERT: F 230 GLU cc_start: 0.3946 (mt-10) cc_final: 0.3185 (tm-30) REVERT: F 232 PHE cc_start: 0.3240 (OUTLIER) cc_final: 0.2467 (m-10) REVERT: F 240 MET cc_start: 0.6319 (OUTLIER) cc_final: 0.5673 (tmt) REVERT: F 252 GLU cc_start: 0.7331 (tp30) cc_final: 0.6851 (tm-30) REVERT: F 330 ASP cc_start: 0.0469 (OUTLIER) cc_final: -0.0051 (p0) REVERT: F 334 ARG cc_start: 0.4950 (mmt-90) cc_final: 0.4746 (tpp-160) REVERT: F 569 MET cc_start: 0.7302 (mpp) cc_final: 0.5917 (mmp) REVERT: F 573 ILE cc_start: 0.9468 (mp) cc_final: 0.8825 (tp) REVERT: F 758 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8512 (mtm180) REVERT: F 913 MET cc_start: 0.7486 (ppp) cc_final: 0.7210 (ppp) REVERT: F 1068 ASP cc_start: 0.8210 (t0) cc_final: 0.7883 (t70) REVERT: G 119 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.7695 (ttm110) REVERT: G 167 HIS cc_start: 0.5060 (OUTLIER) cc_final: 0.3800 (t-90) REVERT: G 499 TYR cc_start: 0.8489 (p90) cc_final: 0.8038 (p90) REVERT: G 729 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8724 (pp) REVERT: H 29 PHE cc_start: 0.5608 (OUTLIER) cc_final: 0.5326 (m-80) REVERT: H 147 CYS cc_start: -0.1931 (OUTLIER) cc_final: -0.2312 (p) REVERT: I 62 ARG cc_start: 0.7069 (ptp90) cc_final: 0.6848 (ptp90) REVERT: I 151 SER cc_start: 0.7875 (OUTLIER) cc_final: 0.7317 (p) REVERT: I 171 LEU cc_start: 0.8452 (tp) cc_final: 0.8227 (mt) REVERT: I 176 CYS cc_start: 0.6738 (OUTLIER) cc_final: 0.6375 (m) REVERT: I 291 LYS cc_start: 0.8817 (mttt) cc_final: 0.8529 (mtmt) REVERT: I 346 GLN cc_start: 0.8880 (tt0) cc_final: 0.8500 (tt0) REVERT: I 635 TYR cc_start: 0.7125 (m-80) cc_final: 0.6448 (m-80) REVERT: I 665 LYS cc_start: 0.8961 (tttt) cc_final: 0.8667 (tttp) REVERT: I 758 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8747 (mtm180) REVERT: I 1008 MET cc_start: 0.8467 (tmm) cc_final: 0.7946 (ttp) REVERT: I 1090 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8369 (mp0) REVERT: K 79 LEU cc_start: 0.7221 (pp) cc_final: 0.6920 (mm) outliers start: 95 outliers final: 58 residues processed: 314 average time/residue: 0.5228 time to fit residues: 202.4308 Evaluate side-chains 289 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 215 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 296 ILE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 496 LYS Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain F residue 521 ASN Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 596 ILE Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 635 TYR Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 718 VAL Chi-restraints excluded: chain F residue 758 ARG Chi-restraints excluded: chain F residue 810 VAL Chi-restraints excluded: chain F residue 900 ILE Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 458 VAL Chi-restraints excluded: chain G residue 478 CYS Chi-restraints excluded: chain G residue 729 LEU Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 900 ILE Chi-restraints excluded: chain G residue 988 GLN Chi-restraints excluded: chain G residue 995 LYS Chi-restraints excluded: chain G residue 1051 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 673 LEU Chi-restraints excluded: chain I residue 758 ARG Chi-restraints excluded: chain I residue 854 LYS Chi-restraints excluded: chain I residue 1090 GLU Chi-restraints excluded: chain I residue 1127 VAL Chi-restraints excluded: chain K residue 33 TYR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 190 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 38 optimal weight: 40.0000 chunk 213 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 400 optimal weight: 50.0000 chunk 12 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 274 optimal weight: 30.0000 chunk 306 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 GLN G 91 HIS ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN G 826 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 277 ASN I 280 GLN I 377 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.162775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.120625 restraints weight = 138103.758| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 5.74 r_work: 0.3308 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 1.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 32372 Z= 0.287 Angle : 0.859 20.988 44092 Z= 0.451 Chirality : 0.051 0.326 4934 Planarity : 0.006 0.066 5708 Dihedral : 6.238 57.384 4477 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.00 % Favored : 94.90 % Rotamer: Outliers : 2.46 % Allowed : 21.77 % Favored : 75.77 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 4081 helix: 0.87 (0.18), residues: 776 sheet: -0.15 (0.15), residues: 1025 loop : -1.13 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 269 TYR 0.040 0.003 TYR G 809 PHE 0.050 0.003 PHE C 106 TRP 0.061 0.003 TRP C 47 HIS 0.028 0.002 HIS F 836 Details of bonding type rmsd covalent geometry : bond 0.00668 (32317) covalent geometry : angle 0.84528 (43982) SS BOND : bond 0.00987 ( 55) SS BOND : angle 3.15082 ( 110) hydrogen bonds : bond 0.06991 ( 1218) hydrogen bonds : angle 6.39949 ( 3373) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 247 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7405 (pp20) cc_final: 0.6143 (pm20) REVERT: C 80 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.7040 (m-80) REVERT: D 190 HIS cc_start: 0.0507 (OUTLIER) cc_final: -0.0554 (t-90) REVERT: F 34 ASP cc_start: 0.5711 (t0) cc_final: 0.4775 (t0) REVERT: F 63 THR cc_start: 0.2930 (OUTLIER) cc_final: 0.0722 (p) REVERT: F 219 TYR cc_start: 0.5918 (p90) cc_final: 0.5540 (p90) REVERT: F 230 GLU cc_start: 0.5197 (mt-10) cc_final: 0.3966 (tm-30) REVERT: F 232 PHE cc_start: 0.3603 (OUTLIER) cc_final: 0.2824 (m-10) REVERT: F 291 LYS cc_start: 0.7550 (mttt) cc_final: 0.7238 (mppt) REVERT: F 330 ASP cc_start: 0.0932 (OUTLIER) cc_final: -0.1382 (m-30) REVERT: F 563 MET cc_start: 0.4047 (tpp) cc_final: 0.3689 (tpp) REVERT: F 569 MET cc_start: 0.7019 (mpp) cc_final: 0.5946 (mmp) REVERT: F 573 ILE cc_start: 0.9435 (mp) cc_final: 0.8839 (tp) REVERT: F 754 PRO cc_start: 0.8342 (Cg_exo) cc_final: 0.8061 (Cg_endo) REVERT: F 913 MET cc_start: 0.7691 (ppp) cc_final: 0.7365 (ppp) REVERT: F 924 ILE cc_start: 0.6704 (OUTLIER) cc_final: 0.6086 (mm) REVERT: F 988 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8597 (tp40) REVERT: F 1068 ASP cc_start: 0.8305 (t0) cc_final: 0.7984 (t70) REVERT: G 119 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.7672 (ttm110) REVERT: G 245 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8596 (pp) REVERT: G 261 GLN cc_start: 0.7766 (tm130) cc_final: 0.7546 (tm-30) REVERT: G 306 ASP cc_start: 0.8773 (m-30) cc_final: 0.8546 (p0) REVERT: G 499 TYR cc_start: 0.8491 (p90) cc_final: 0.8212 (p90) REVERT: G 500 ILE cc_start: 0.9529 (mt) cc_final: 0.9287 (tp) REVERT: G 553 TRP cc_start: 0.5618 (t-100) cc_final: 0.5207 (t-100) REVERT: G 642 TYR cc_start: 0.3706 (OUTLIER) cc_final: 0.3365 (m-10) REVERT: G 729 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8800 (pp) REVERT: I 240 MET cc_start: 0.7883 (tmt) cc_final: 0.7659 (tmt) REVERT: I 246 THR cc_start: 0.8373 (m) cc_final: 0.7894 (t) REVERT: I 635 TYR cc_start: 0.7540 (m-80) cc_final: 0.6664 (m-10) REVERT: I 758 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8786 (mtm180) REVERT: I 1008 MET cc_start: 0.8517 (tmm) cc_final: 0.8069 (ttp) REVERT: I 1090 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8449 (mp0) REVERT: K 79 LEU cc_start: 0.7220 (pp) cc_final: 0.6915 (mm) outliers start: 86 outliers final: 56 residues processed: 319 average time/residue: 0.5224 time to fit residues: 205.3162 Evaluate side-chains 276 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 496 LYS Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain F residue 521 ASN Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 635 TYR Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 718 VAL Chi-restraints excluded: chain F residue 810 VAL Chi-restraints excluded: chain F residue 900 ILE Chi-restraints excluded: chain F residue 924 ILE Chi-restraints excluded: chain F residue 988 GLN Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 397 TYR Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 458 VAL Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 642 TYR Chi-restraints excluded: chain G residue 729 LEU Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 900 ILE Chi-restraints excluded: chain G residue 988 GLN Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 758 ARG Chi-restraints excluded: chain I residue 854 LYS Chi-restraints excluded: chain I residue 1090 GLU Chi-restraints excluded: chain I residue 1127 VAL Chi-restraints excluded: chain I residue 1174 LYS Chi-restraints excluded: chain K residue 33 TYR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 188 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 372 optimal weight: 0.0470 chunk 91 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 302 optimal weight: 5.9990 chunk 348 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 92 optimal weight: 0.0000 chunk 38 optimal weight: 40.0000 chunk 101 optimal weight: 0.0030 chunk 20 optimal weight: 2.9990 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 36 GLN F 72 GLN ** F 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 HIS G 826 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 277 ASN I 377 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.168167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.136457 restraints weight = 142462.211| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 6.46 r_work: 0.3347 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 1.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 32372 Z= 0.144 Angle : 0.718 13.018 44092 Z= 0.366 Chirality : 0.045 0.250 4934 Planarity : 0.005 0.067 5708 Dihedral : 5.679 57.824 4474 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.08 % Rotamer: Outliers : 1.77 % Allowed : 23.20 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.13), residues: 4081 helix: 1.20 (0.19), residues: 770 sheet: -0.07 (0.16), residues: 1019 loop : -1.09 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 119 TYR 0.040 0.002 TYR G 438 PHE 0.035 0.002 PHE G 571 TRP 0.070 0.002 TRP C 47 HIS 0.010 0.001 HIS F 91 Details of bonding type rmsd covalent geometry : bond 0.00326 (32317) covalent geometry : angle 0.70898 (43982) SS BOND : bond 0.00636 ( 55) SS BOND : angle 2.35837 ( 110) hydrogen bonds : bond 0.05194 ( 1218) hydrogen bonds : angle 5.94184 ( 3373) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18836.24 seconds wall clock time: 319 minutes 18.63 seconds (19158.63 seconds total)