Starting phenix.real_space_refine on Thu Apr 11 00:55:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1s_36800/04_2024/8k1s_36800_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1s_36800/04_2024/8k1s_36800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1s_36800/04_2024/8k1s_36800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1s_36800/04_2024/8k1s_36800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1s_36800/04_2024/8k1s_36800_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1s_36800/04_2024/8k1s_36800_updated.pdb" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 16 5.49 5 S 76 5.16 5 C 13712 2.51 5 N 3398 2.21 5 O 3794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 21000 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "B" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "C" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1047 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain: "D" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "E" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1047 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain: "F" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "G" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1047 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain: "H" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "I" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3111 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3111 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3111 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3111 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.49, per 1000 atoms: 0.55 Number of scatterers: 21000 At special positions: 0 Unit cell: (176.79, 115.37, 90.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 76 16.00 P 16 15.00 O 3794 8.00 N 3398 7.00 C 13712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.67 Conformation dependent library (CDL) restraints added in 3.8 seconds 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4958 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 12 sheets defined 59.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 removed outlier: 3.557A pdb=" N SER A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 60 through 66 Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.689A pdb=" N GLU A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 Processing helix chain 'A' and resid 124 through 138 removed outlier: 3.546A pdb=" N GLY A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 28 removed outlier: 3.557A pdb=" N SER B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 60 through 66 Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.690A pdb=" N GLU B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 124 through 138 removed outlier: 3.547A pdb=" N GLY B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 131 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 28 removed outlier: 3.557A pdb=" N SER C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 82 through 94 removed outlier: 3.690A pdb=" N GLU C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 116 Processing helix chain 'C' and resid 124 through 139 removed outlier: 3.547A pdb=" N GLY C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN C 134 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 28 removed outlier: 3.557A pdb=" N SER D 20 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 60 through 66 Processing helix chain 'D' and resid 68 through 70 No H-bonds generated for 'chain 'D' and resid 68 through 70' Processing helix chain 'D' and resid 82 through 94 removed outlier: 3.690A pdb=" N GLU D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 116 Processing helix chain 'D' and resid 124 through 138 removed outlier: 3.546A pdb=" N GLY D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 131 " --> pdb=" O ASP D 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.556A pdb=" N SER E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 60 through 66 Processing helix chain 'E' and resid 68 through 70 No H-bonds generated for 'chain 'E' and resid 68 through 70' Processing helix chain 'E' and resid 82 through 94 removed outlier: 3.690A pdb=" N GLU E 94 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 116 Processing helix chain 'E' and resid 124 through 139 removed outlier: 3.546A pdb=" N GLY E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS E 131 " --> pdb=" O ASP E 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 134 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 28 removed outlier: 3.557A pdb=" N SER F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 60 through 66 Processing helix chain 'F' and resid 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.689A pdb=" N GLU F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 116 Processing helix chain 'F' and resid 124 through 138 removed outlier: 3.546A pdb=" N GLY F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS F 131 " --> pdb=" O ASP F 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN F 134 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 28 removed outlier: 3.558A pdb=" N SER G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 Processing helix chain 'G' and resid 60 through 66 Processing helix chain 'G' and resid 68 through 70 No H-bonds generated for 'chain 'G' and resid 68 through 70' Processing helix chain 'G' and resid 82 through 94 removed outlier: 3.689A pdb=" N GLU G 94 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 116 Processing helix chain 'G' and resid 124 through 139 removed outlier: 3.547A pdb=" N GLY G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS G 131 " --> pdb=" O ASP G 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN G 134 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 28 removed outlier: 3.558A pdb=" N SER H 20 " --> pdb=" O ARG H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 Processing helix chain 'H' and resid 60 through 66 Processing helix chain 'H' and resid 68 through 70 No H-bonds generated for 'chain 'H' and resid 68 through 70' Processing helix chain 'H' and resid 82 through 94 removed outlier: 3.690A pdb=" N GLU H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 116 Processing helix chain 'H' and resid 124 through 138 removed outlier: 3.547A pdb=" N GLY H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS H 131 " --> pdb=" O ASP H 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN H 134 " --> pdb=" O VAL H 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 36 removed outlier: 3.602A pdb=" N MET I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 58 Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 74 through 101 Processing helix chain 'I' and resid 128 through 156 removed outlier: 3.569A pdb=" N VAL I 132 " --> pdb=" O GLY I 128 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG I 151 " --> pdb=" O ILE I 147 " (cutoff:3.500A) Proline residue: I 154 - end of helix Processing helix chain 'I' and resid 158 through 173 Processing helix chain 'I' and resid 186 through 188 No H-bonds generated for 'chain 'I' and resid 186 through 188' Processing helix chain 'I' and resid 192 through 204 Processing helix chain 'I' and resid 209 through 218 Processing helix chain 'I' and resid 221 through 223 No H-bonds generated for 'chain 'I' and resid 221 through 223' Processing helix chain 'I' and resid 226 through 249 removed outlier: 3.504A pdb=" N LEU I 236 " --> pdb=" O LEU I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 274 Processing helix chain 'I' and resid 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 291 through 302 removed outlier: 3.578A pdb=" N LEU I 299 " --> pdb=" O VAL I 295 " (cutoff:3.500A) Processing helix chain 'I' and resid 316 through 330 Processing helix chain 'I' and resid 345 through 372 Processing helix chain 'I' and resid 377 through 388 Processing helix chain 'I' and resid 403 through 418 Processing helix chain 'I' and resid 420 through 427 removed outlier: 3.746A pdb=" N PHE I 427 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 36 removed outlier: 3.602A pdb=" N MET J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 58 Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 74 through 101 Processing helix chain 'J' and resid 128 through 156 removed outlier: 3.567A pdb=" N VAL J 132 " --> pdb=" O GLY J 128 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG J 151 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Proline residue: J 154 - end of helix Processing helix chain 'J' and resid 158 through 173 Processing helix chain 'J' and resid 186 through 188 No H-bonds generated for 'chain 'J' and resid 186 through 188' Processing helix chain 'J' and resid 192 through 204 Processing helix chain 'J' and resid 209 through 218 Processing helix chain 'J' and resid 221 through 223 No H-bonds generated for 'chain 'J' and resid 221 through 223' Processing helix chain 'J' and resid 226 through 249 removed outlier: 3.503A pdb=" N LEU J 236 " --> pdb=" O LEU J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 274 Processing helix chain 'J' and resid 286 through 288 No H-bonds generated for 'chain 'J' and resid 286 through 288' Processing helix chain 'J' and resid 291 through 300 removed outlier: 3.578A pdb=" N LEU J 299 " --> pdb=" O VAL J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 330 Processing helix chain 'J' and resid 345 through 372 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 403 through 418 Processing helix chain 'J' and resid 420 through 427 removed outlier: 3.745A pdb=" N PHE J 427 " --> pdb=" O PHE J 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 36 removed outlier: 3.602A pdb=" N MET K 36 " --> pdb=" O ALA K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 58 Processing helix chain 'K' and resid 68 through 71 No H-bonds generated for 'chain 'K' and resid 68 through 71' Processing helix chain 'K' and resid 74 through 101 Processing helix chain 'K' and resid 128 through 156 removed outlier: 3.569A pdb=" N VAL K 132 " --> pdb=" O GLY K 128 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG K 151 " --> pdb=" O ILE K 147 " (cutoff:3.500A) Proline residue: K 154 - end of helix Processing helix chain 'K' and resid 158 through 173 Processing helix chain 'K' and resid 186 through 188 No H-bonds generated for 'chain 'K' and resid 186 through 188' Processing helix chain 'K' and resid 192 through 204 Processing helix chain 'K' and resid 209 through 218 Processing helix chain 'K' and resid 221 through 223 No H-bonds generated for 'chain 'K' and resid 221 through 223' Processing helix chain 'K' and resid 226 through 249 removed outlier: 3.504A pdb=" N LEU K 236 " --> pdb=" O LEU K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 274 Processing helix chain 'K' and resid 286 through 288 No H-bonds generated for 'chain 'K' and resid 286 through 288' Processing helix chain 'K' and resid 291 through 302 removed outlier: 3.577A pdb=" N LEU K 299 " --> pdb=" O VAL K 295 " (cutoff:3.500A) Processing helix chain 'K' and resid 316 through 330 Processing helix chain 'K' and resid 345 through 372 Processing helix chain 'K' and resid 377 through 388 Processing helix chain 'K' and resid 403 through 418 Processing helix chain 'K' and resid 420 through 427 removed outlier: 3.745A pdb=" N PHE K 427 " --> pdb=" O PHE K 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 36 removed outlier: 3.602A pdb=" N MET L 36 " --> pdb=" O ALA L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 58 Processing helix chain 'L' and resid 68 through 71 No H-bonds generated for 'chain 'L' and resid 68 through 71' Processing helix chain 'L' and resid 74 through 101 Processing helix chain 'L' and resid 128 through 156 removed outlier: 3.569A pdb=" N VAL L 132 " --> pdb=" O GLY L 128 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG L 151 " --> pdb=" O ILE L 147 " (cutoff:3.500A) Proline residue: L 154 - end of helix Processing helix chain 'L' and resid 158 through 173 Processing helix chain 'L' and resid 186 through 188 No H-bonds generated for 'chain 'L' and resid 186 through 188' Processing helix chain 'L' and resid 192 through 204 Processing helix chain 'L' and resid 209 through 218 Processing helix chain 'L' and resid 221 through 223 No H-bonds generated for 'chain 'L' and resid 221 through 223' Processing helix chain 'L' and resid 226 through 249 removed outlier: 3.504A pdb=" N LEU L 236 " --> pdb=" O LEU L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 274 Processing helix chain 'L' and resid 286 through 288 No H-bonds generated for 'chain 'L' and resid 286 through 288' Processing helix chain 'L' and resid 291 through 302 removed outlier: 3.578A pdb=" N LEU L 299 " --> pdb=" O VAL L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 316 through 330 Processing helix chain 'L' and resid 345 through 372 Processing helix chain 'L' and resid 377 through 388 Processing helix chain 'L' and resid 403 through 418 Processing helix chain 'L' and resid 420 through 427 removed outlier: 3.744A pdb=" N PHE L 427 " --> pdb=" O PHE L 423 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.861A pdb=" N TYR A 73 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU A 31 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL A 11 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU A 33 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS A 51 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ASP A 36 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 53 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.861A pdb=" N TYR B 73 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU B 31 " --> pdb=" O PHE B 9 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL B 11 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU B 33 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS B 51 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASP B 36 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 53 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.860A pdb=" N TYR C 73 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU C 31 " --> pdb=" O PHE C 9 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL C 11 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU C 33 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS C 51 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ASP C 36 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL C 53 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.861A pdb=" N TYR D 73 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU D 31 " --> pdb=" O PHE D 9 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL D 11 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU D 33 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS D 51 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASP D 36 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL D 53 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.861A pdb=" N TYR E 73 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU E 31 " --> pdb=" O PHE E 9 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL E 11 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU E 33 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS E 51 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASP E 36 " --> pdb=" O HIS E 51 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL E 53 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 120 through 122 removed outlier: 3.860A pdb=" N TYR F 73 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU F 31 " --> pdb=" O PHE F 9 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL F 11 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU F 33 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS F 51 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASP F 36 " --> pdb=" O HIS F 51 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL F 53 " --> pdb=" O ASP F 36 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.861A pdb=" N TYR G 73 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU G 31 " --> pdb=" O PHE G 9 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL G 11 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU G 33 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS G 51 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASP G 36 " --> pdb=" O HIS G 51 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL G 53 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 120 through 122 removed outlier: 3.861A pdb=" N TYR H 73 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU H 31 " --> pdb=" O PHE H 9 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL H 11 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU H 33 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS H 51 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ASP H 36 " --> pdb=" O HIS H 51 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL H 53 " --> pdb=" O ASP H 36 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 336 through 338 removed outlier: 4.739A pdb=" N THR I 336 " --> pdb=" O ILE I 343 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 336 through 338 removed outlier: 4.739A pdb=" N THR J 336 " --> pdb=" O ILE J 343 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 336 through 338 removed outlier: 4.739A pdb=" N THR K 336 " --> pdb=" O ILE K 343 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 336 through 338 removed outlier: 4.739A pdb=" N THR L 336 " --> pdb=" O ILE L 343 " (cutoff:3.500A) 1117 hydrogen bonds defined for protein. 3315 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: 7.25 Time building geometry restraints manager: 9.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3301 1.31 - 1.44: 5658 1.44 - 1.56: 12302 1.56 - 1.68: 27 1.68 - 1.81: 140 Bond restraints: 21428 Sorted by residual: bond pdb=" CA LYS J 315 " pdb=" C LYS J 315 " ideal model delta sigma weight residual 1.528 1.447 0.081 1.28e-02 6.10e+03 4.02e+01 bond pdb=" CA LYS L 315 " pdb=" C LYS L 315 " ideal model delta sigma weight residual 1.528 1.452 0.076 1.33e-02 5.65e+03 3.25e+01 bond pdb=" CA ALA J 305 " pdb=" C ALA J 305 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.34e-02 5.57e+03 1.68e+01 bond pdb=" CA GLY I 306 " pdb=" C GLY I 306 " ideal model delta sigma weight residual 1.516 1.468 0.048 1.18e-02 7.18e+03 1.67e+01 bond pdb=" N LYS J 315 " pdb=" CA LYS J 315 " ideal model delta sigma weight residual 1.454 1.407 0.047 1.17e-02 7.31e+03 1.63e+01 ... (remaining 21423 not shown) Histogram of bond angle deviations from ideal: 94.17 - 102.58: 78 102.58 - 110.99: 8796 110.99 - 119.39: 9419 119.39 - 127.80: 10652 127.80 - 136.21: 188 Bond angle restraints: 29133 Sorted by residual: angle pdb=" N ILE J 314 " pdb=" CA ILE J 314 " pdb=" C ILE J 314 " ideal model delta sigma weight residual 109.63 94.17 15.46 1.44e+00 4.82e-01 1.15e+02 angle pdb=" N ILE L 314 " pdb=" CA ILE L 314 " pdb=" C ILE L 314 " ideal model delta sigma weight residual 109.30 96.69 12.61 1.31e+00 5.83e-01 9.27e+01 angle pdb=" N ILE I 314 " pdb=" CA ILE I 314 " pdb=" C ILE I 314 " ideal model delta sigma weight residual 109.51 98.85 10.66 1.43e+00 4.89e-01 5.55e+01 angle pdb=" O SER I 312 " pdb=" C SER I 312 " pdb=" N GLY I 313 " ideal model delta sigma weight residual 122.78 114.25 8.53 1.33e+00 5.65e-01 4.12e+01 angle pdb=" CA SER K 312 " pdb=" C SER K 312 " pdb=" N GLY K 313 " ideal model delta sigma weight residual 116.01 125.06 -9.05 1.45e+00 4.76e-01 3.90e+01 ... (remaining 29128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.79: 12333 28.79 - 57.57: 134 57.57 - 86.36: 8 86.36 - 115.14: 4 115.14 - 143.93: 8 Dihedral angle restraints: 12487 sinusoidal: 4782 harmonic: 7705 Sorted by residual: dihedral pdb=" O2A ADP H 301 " pdb=" O3A ADP H 301 " pdb=" PA ADP H 301 " pdb=" PB ADP H 301 " ideal model delta sinusoidal sigma weight residual -60.00 83.93 -143.93 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O2A ADP E 301 " pdb=" O3A ADP E 301 " pdb=" PA ADP E 301 " pdb=" PB ADP E 301 " ideal model delta sinusoidal sigma weight residual -60.00 83.93 -143.93 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O2A ADP D 301 " pdb=" O3A ADP D 301 " pdb=" PA ADP D 301 " pdb=" PB ADP D 301 " ideal model delta sinusoidal sigma weight residual -60.00 83.89 -143.89 1 2.00e+01 2.50e-03 4.34e+01 ... (remaining 12484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3049 0.057 - 0.115: 445 0.115 - 0.172: 35 0.172 - 0.230: 11 0.230 - 0.287: 3 Chirality restraints: 3543 Sorted by residual: chirality pdb=" CA SER J 307 " pdb=" N SER J 307 " pdb=" C SER J 307 " pdb=" CB SER J 307 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA SER L 307 " pdb=" N SER L 307 " pdb=" C SER L 307 " pdb=" CB SER L 307 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA SER K 307 " pdb=" N SER K 307 " pdb=" C SER K 307 " pdb=" CB SER K 307 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3540 not shown) Planarity restraints: 3542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET K 301 " -0.019 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C MET K 301 " 0.064 2.00e-02 2.50e+03 pdb=" O MET K 301 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE K 302 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET J 301 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C MET J 301 " -0.063 2.00e-02 2.50e+03 pdb=" O MET J 301 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE J 302 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET I 301 " 0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C MET I 301 " -0.057 2.00e-02 2.50e+03 pdb=" O MET I 301 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE I 302 " 0.020 2.00e-02 2.50e+03 ... (remaining 3539 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.85: 7091 2.85 - 3.42: 24057 3.42 - 3.99: 40626 3.99 - 4.57: 58577 4.57 - 5.14: 83423 Nonbonded interactions: 213774 Sorted by model distance: nonbonded pdb=" OE2 GLU E 94 " pdb=" NZ LYS G 115 " model vdw 2.272 2.520 nonbonded pdb=" O ALA L 55 " pdb=" OG1 THR L 59 " model vdw 2.294 2.440 nonbonded pdb=" O ALA I 55 " pdb=" OG1 THR I 59 " model vdw 2.294 2.440 nonbonded pdb=" O ALA K 55 " pdb=" OG1 THR K 59 " model vdw 2.294 2.440 nonbonded pdb=" O ALA J 55 " pdb=" OG1 THR J 59 " model vdw 2.294 2.440 ... (remaining 213769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 7 through 139 or resid 301)) selection = chain 'D' selection = (chain 'E' and (resid 7 through 139 or resid 301)) selection = chain 'F' selection = (chain 'G' and (resid 7 through 139 or resid 301)) selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.190 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 59.440 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 21428 Z= 0.242 Angle : 0.610 15.459 29133 Z= 0.326 Chirality : 0.043 0.287 3543 Planarity : 0.003 0.037 3542 Dihedral : 10.425 143.931 7529 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.76 % Allowed : 4.10 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.16), residues: 2663 helix: 1.47 (0.12), residues: 1647 sheet: 0.88 (0.30), residues: 296 loop : -0.93 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 158 HIS 0.003 0.001 HIS E 110 PHE 0.024 0.001 PHE J 202 TYR 0.003 0.001 TYR F 73 ARG 0.002 0.000 ARG I 417 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 639 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7263 (mp0) REVERT: A 111 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7530 (mmpt) REVERT: B 23 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7738 (mtmm) REVERT: B 126 LYS cc_start: 0.7648 (ttmt) cc_final: 0.7416 (ttpp) REVERT: B 134 GLN cc_start: 0.7508 (tp40) cc_final: 0.7225 (mt0) REVERT: C 35 VAL cc_start: 0.8311 (p) cc_final: 0.8104 (m) REVERT: C 111 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7454 (mmpt) REVERT: E 111 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7592 (mmpt) REVERT: F 23 LYS cc_start: 0.7995 (mtpp) cc_final: 0.7787 (mtpt) REVERT: F 59 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6279 (mt-10) REVERT: F 126 LYS cc_start: 0.7629 (ttmt) cc_final: 0.7356 (ttpp) REVERT: F 127 ASP cc_start: 0.7602 (m-30) cc_final: 0.7354 (m-30) REVERT: G 16 ARG cc_start: 0.8351 (mtm180) cc_final: 0.8070 (mtm-85) REVERT: G 35 VAL cc_start: 0.8303 (p) cc_final: 0.8069 (t) REVERT: G 111 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7381 (mmpt) REVERT: I 158 TRP cc_start: 0.6190 (m100) cc_final: 0.5471 (t60) REVERT: I 331 ARG cc_start: 0.7533 (mtp85) cc_final: 0.7236 (mtm-85) REVERT: I 360 PHE cc_start: 0.6889 (t80) cc_final: 0.6603 (m-10) REVERT: I 394 THR cc_start: 0.8226 (t) cc_final: 0.7854 (t) REVERT: J 81 MET cc_start: 0.7231 (ttm) cc_final: 0.7019 (ttt) REVERT: J 196 LEU cc_start: 0.8001 (mt) cc_final: 0.7445 (tp) REVERT: J 394 THR cc_start: 0.7429 (t) cc_final: 0.6965 (t) REVERT: K 81 MET cc_start: 0.7254 (ttm) cc_final: 0.6979 (ttt) REVERT: K 196 LEU cc_start: 0.8054 (mt) cc_final: 0.7491 (tp) REVERT: K 394 THR cc_start: 0.7357 (t) cc_final: 0.6902 (t) REVERT: L 158 TRP cc_start: 0.6127 (m100) cc_final: 0.5509 (t60) REVERT: L 331 ARG cc_start: 0.7465 (mtp85) cc_final: 0.7175 (mtm-85) REVERT: L 333 LYS cc_start: 0.7933 (mmtm) cc_final: 0.7714 (mmpt) REVERT: L 394 THR cc_start: 0.8366 (t) cc_final: 0.8042 (t) outliers start: 17 outliers final: 2 residues processed: 648 average time/residue: 1.2387 time to fit residues: 915.9321 Evaluate side-chains 441 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 435 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain G residue 111 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.0570 chunk 200 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 68 optimal weight: 0.2980 chunk 134 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 206 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 239 optimal weight: 2.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 61 ASN B 70 ASN B 83 GLN C 38 ASN C 70 ASN C 110 HIS D 51 HIS ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN F 61 ASN F 70 ASN F 83 GLN F 106 ASN F 110 HIS G 38 ASN G 70 ASN G 110 HIS H 38 ASN I 174 ASN I 434 ASN J 239 ASN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21428 Z= 0.225 Angle : 0.615 7.095 29133 Z= 0.298 Chirality : 0.043 0.158 3543 Planarity : 0.004 0.034 3542 Dihedral : 9.457 131.986 2927 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.92 % Allowed : 14.22 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.16), residues: 2663 helix: 2.26 (0.12), residues: 1661 sheet: 1.01 (0.29), residues: 288 loop : -1.04 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 181 HIS 0.003 0.001 HIS A 110 PHE 0.035 0.002 PHE J 202 TYR 0.014 0.001 TYR I 270 ARG 0.006 0.001 ARG J 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 475 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.7635 (t) cc_final: 0.7323 (m) REVERT: A 127 ASP cc_start: 0.8011 (m-30) cc_final: 0.7431 (m-30) REVERT: B 23 LYS cc_start: 0.7913 (mtpp) cc_final: 0.7700 (mtpt) REVERT: B 108 TYR cc_start: 0.6985 (m-10) cc_final: 0.6460 (m-80) REVERT: B 127 ASP cc_start: 0.8073 (m-30) cc_final: 0.7757 (m-30) REVERT: C 59 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6884 (mm-30) REVERT: C 111 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7383 (mmpt) REVERT: D 83 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: D 126 LYS cc_start: 0.7460 (ttpt) cc_final: 0.6874 (mmtp) REVERT: E 127 ASP cc_start: 0.7992 (m-30) cc_final: 0.7418 (m-30) REVERT: F 23 LYS cc_start: 0.7862 (mtpp) cc_final: 0.7651 (mtpt) REVERT: F 60 GLU cc_start: 0.7730 (tp30) cc_final: 0.7487 (tp30) REVERT: F 108 TYR cc_start: 0.6982 (m-10) cc_final: 0.6473 (m-80) REVERT: F 128 MET cc_start: 0.8561 (tpt) cc_final: 0.8095 (tpt) REVERT: G 59 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6872 (mm-30) REVERT: G 111 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7450 (mmtt) REVERT: G 128 MET cc_start: 0.8093 (mmm) cc_final: 0.7883 (mmp) REVERT: H 126 LYS cc_start: 0.7501 (ttpt) cc_final: 0.6872 (mmtp) REVERT: I 150 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7433 (pt) REVERT: I 243 MET cc_start: 0.7817 (ttt) cc_final: 0.7521 (ttp) REVERT: I 267 TRP cc_start: 0.7473 (m100) cc_final: 0.7265 (m100) REVERT: I 331 ARG cc_start: 0.7630 (mtp85) cc_final: 0.7388 (mtm-85) REVERT: I 394 THR cc_start: 0.8440 (t) cc_final: 0.8211 (t) REVERT: J 196 LEU cc_start: 0.8083 (mt) cc_final: 0.7546 (tp) REVERT: J 243 MET cc_start: 0.7724 (ttp) cc_final: 0.7437 (ttt) REVERT: J 340 ARG cc_start: 0.7442 (ttm-80) cc_final: 0.7161 (mtt-85) REVERT: K 196 LEU cc_start: 0.8054 (mt) cc_final: 0.7494 (tp) REVERT: K 243 MET cc_start: 0.7706 (ttp) cc_final: 0.7456 (ttt) REVERT: K 334 LYS cc_start: 0.8039 (mptt) cc_final: 0.7802 (mptt) REVERT: L 150 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7183 (pt) REVERT: L 243 MET cc_start: 0.7799 (ttt) cc_final: 0.7498 (ttp) REVERT: L 267 TRP cc_start: 0.7584 (m100) cc_final: 0.7308 (m100) REVERT: L 331 ARG cc_start: 0.7599 (mtp85) cc_final: 0.7312 (mtm-85) REVERT: L 333 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7735 (mmpt) outliers start: 88 outliers final: 35 residues processed: 526 average time/residue: 1.3590 time to fit residues: 806.1966 Evaluate side-chains 473 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 431 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 269 SER Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 150 ILE Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 150 ILE Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 237 MET Chi-restraints excluded: chain L residue 269 SER Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 283 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 chunk 163 optimal weight: 0.0170 chunk 66 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 213 optimal weight: 0.0980 chunk 238 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 134 GLN B 70 ASN B 106 ASN D 38 ASN D 56 ASN E 105 GLN F 70 ASN F 106 ASN H 38 ASN H 56 ASN I 434 ASN ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 ASN L 434 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21428 Z= 0.190 Angle : 0.592 8.157 29133 Z= 0.283 Chirality : 0.042 0.160 3543 Planarity : 0.003 0.031 3542 Dihedral : 9.193 132.987 2915 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.83 % Allowed : 16.45 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.16), residues: 2663 helix: 2.47 (0.12), residues: 1658 sheet: 1.20 (0.30), residues: 278 loop : -1.02 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 181 HIS 0.003 0.001 HIS H 110 PHE 0.031 0.001 PHE J 202 TYR 0.012 0.001 TYR I 270 ARG 0.007 0.001 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 460 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8077 (m-30) cc_final: 0.7511 (m-30) REVERT: B 23 LYS cc_start: 0.7863 (mtpp) cc_final: 0.7636 (mtpt) REVERT: B 60 GLU cc_start: 0.7613 (tp30) cc_final: 0.7333 (tp30) REVERT: B 108 TYR cc_start: 0.6973 (m-80) cc_final: 0.6494 (m-80) REVERT: B 127 ASP cc_start: 0.8050 (m-30) cc_final: 0.7715 (m-30) REVERT: C 16 ARG cc_start: 0.8206 (mtm-85) cc_final: 0.7988 (mtp180) REVERT: C 59 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6873 (mm-30) REVERT: C 111 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7380 (mmpt) REVERT: D 126 LYS cc_start: 0.7442 (ttpt) cc_final: 0.6900 (mmtp) REVERT: E 127 ASP cc_start: 0.7900 (m-30) cc_final: 0.7367 (m-30) REVERT: F 23 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7637 (mtpt) REVERT: F 60 GLU cc_start: 0.7680 (tp30) cc_final: 0.7362 (tp30) REVERT: F 108 TYR cc_start: 0.6996 (m-80) cc_final: 0.6513 (m-80) REVERT: F 127 ASP cc_start: 0.7989 (m-30) cc_final: 0.7554 (m-30) REVERT: F 128 MET cc_start: 0.8514 (tpt) cc_final: 0.8146 (tpt) REVERT: G 16 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7989 (mtp180) REVERT: G 59 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6773 (mm-30) REVERT: G 111 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7428 (mmtt) REVERT: G 128 MET cc_start: 0.8102 (mmm) cc_final: 0.7901 (mmp) REVERT: H 23 LYS cc_start: 0.7680 (mttp) cc_final: 0.7467 (mttm) REVERT: H 59 GLU cc_start: 0.7958 (mp0) cc_final: 0.7678 (mp0) REVERT: H 126 LYS cc_start: 0.7464 (ttpt) cc_final: 0.6909 (mmtp) REVERT: I 150 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7365 (pt) REVERT: I 267 TRP cc_start: 0.7454 (m100) cc_final: 0.7221 (m100) REVERT: I 394 THR cc_start: 0.8440 (t) cc_final: 0.8173 (t) REVERT: J 143 ILE cc_start: 0.8149 (mt) cc_final: 0.7948 (mm) REVERT: J 196 LEU cc_start: 0.8028 (mt) cc_final: 0.7504 (tp) REVERT: J 243 MET cc_start: 0.7689 (ttp) cc_final: 0.7394 (ttt) REVERT: J 340 ARG cc_start: 0.7536 (ttm-80) cc_final: 0.7319 (mtp85) REVERT: J 395 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7903 (mtp) REVERT: K 81 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6402 (ttm) REVERT: K 196 LEU cc_start: 0.8012 (mt) cc_final: 0.7486 (tp) REVERT: K 253 ASN cc_start: 0.8308 (t0) cc_final: 0.7860 (t0) REVERT: K 334 LYS cc_start: 0.8058 (mptt) cc_final: 0.7805 (mptt) REVERT: K 395 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7973 (mtp) REVERT: L 243 MET cc_start: 0.7720 (ttt) cc_final: 0.7508 (ttp) REVERT: L 267 TRP cc_start: 0.7568 (m100) cc_final: 0.7315 (m100) REVERT: L 331 ARG cc_start: 0.7607 (mtp85) cc_final: 0.7334 (mtm-85) REVERT: L 333 LYS cc_start: 0.8078 (mmtm) cc_final: 0.7783 (mmpt) outliers start: 86 outliers final: 38 residues processed: 516 average time/residue: 1.3589 time to fit residues: 792.2813 Evaluate side-chains 472 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 426 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 269 SER Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 395 MET Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 395 MET Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 269 SER Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 283 SER Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.8980 chunk 180 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 228 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 70 ASN B 106 ASN D 38 ASN E 105 GLN F 51 HIS F 70 ASN F 106 ASN H 38 ASN ** J 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 21428 Z= 0.412 Angle : 0.704 9.215 29133 Z= 0.343 Chirality : 0.047 0.176 3543 Planarity : 0.004 0.040 3542 Dihedral : 9.786 134.341 2915 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.48 % Allowed : 16.18 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.16), residues: 2663 helix: 1.95 (0.12), residues: 1677 sheet: 0.73 (0.30), residues: 288 loop : -1.26 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 181 HIS 0.006 0.001 HIS F 30 PHE 0.037 0.002 PHE J 202 TYR 0.011 0.002 TYR F 107 ARG 0.006 0.001 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 455 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8113 (m-30) cc_final: 0.7572 (m-30) REVERT: B 23 LYS cc_start: 0.7918 (mtpp) cc_final: 0.7624 (mtmp) REVERT: B 60 GLU cc_start: 0.7688 (tp30) cc_final: 0.7305 (tp30) REVERT: B 108 TYR cc_start: 0.7071 (m-10) cc_final: 0.6548 (m-80) REVERT: B 127 ASP cc_start: 0.8064 (m-30) cc_final: 0.7761 (m-30) REVERT: C 16 ARG cc_start: 0.8250 (mtm-85) cc_final: 0.8031 (mtp180) REVERT: C 59 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6921 (mm-30) REVERT: C 111 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7840 (mtpt) REVERT: C 127 ASP cc_start: 0.7708 (m-30) cc_final: 0.7501 (m-30) REVERT: D 83 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7448 (mt0) REVERT: D 126 LYS cc_start: 0.7609 (ttpt) cc_final: 0.7007 (mttp) REVERT: E 72 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7287 (tp30) REVERT: E 127 ASP cc_start: 0.8099 (m-30) cc_final: 0.7598 (m-30) REVERT: F 23 LYS cc_start: 0.7937 (mtpp) cc_final: 0.7618 (mtmp) REVERT: F 60 GLU cc_start: 0.7619 (tp30) cc_final: 0.7249 (tp30) REVERT: F 108 TYR cc_start: 0.7073 (m-10) cc_final: 0.6532 (m-80) REVERT: F 134 GLN cc_start: 0.7458 (tp40) cc_final: 0.7203 (mt0) REVERT: G 16 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.8021 (mtp180) REVERT: G 27 ARG cc_start: 0.7696 (ttp80) cc_final: 0.7339 (ttp80) REVERT: G 59 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7265 (mt-10) REVERT: G 62 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7359 (mt-10) REVERT: G 111 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7876 (mtpt) REVERT: G 115 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7936 (mttp) REVERT: H 126 LYS cc_start: 0.7626 (ttpt) cc_final: 0.7005 (mttp) REVERT: I 150 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7434 (pt) REVERT: I 267 TRP cc_start: 0.7617 (m100) cc_final: 0.7357 (m100) REVERT: I 340 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6619 (mtp-110) REVERT: J 213 PHE cc_start: 0.7786 (t80) cc_final: 0.7552 (t80) REVERT: K 81 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6482 (ttm) REVERT: K 213 PHE cc_start: 0.7745 (t80) cc_final: 0.7531 (t80) REVERT: K 334 LYS cc_start: 0.8073 (mptt) cc_final: 0.7825 (mptt) REVERT: L 150 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7281 (pt) REVERT: L 267 TRP cc_start: 0.7640 (m100) cc_final: 0.7331 (m100) REVERT: L 331 ARG cc_start: 0.7767 (mtp85) cc_final: 0.7404 (mtm-85) REVERT: L 333 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7790 (mmpt) REVERT: L 340 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6569 (mtp-110) outliers start: 123 outliers final: 62 residues processed: 540 average time/residue: 1.4150 time to fit residues: 859.7187 Evaluate side-chains 501 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 427 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 422 THR Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 137 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 283 SER Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 190 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 229 optimal weight: 20.0000 chunk 64 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 51 HIS B 70 ASN B 106 ASN C 105 GLN D 38 ASN E 105 GLN F 70 ASN F 106 ASN G 105 GLN I 85 GLN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21428 Z= 0.214 Angle : 0.613 7.673 29133 Z= 0.293 Chirality : 0.043 0.170 3543 Planarity : 0.003 0.034 3542 Dihedral : 9.383 129.654 2915 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.24 % Allowed : 18.81 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.17), residues: 2663 helix: 2.29 (0.12), residues: 1649 sheet: 0.92 (0.31), residues: 273 loop : -1.15 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP I 181 HIS 0.003 0.001 HIS H 110 PHE 0.041 0.001 PHE L 94 TYR 0.011 0.001 TYR I 270 ARG 0.010 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 442 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8006 (m-30) cc_final: 0.7447 (m-30) REVERT: B 23 LYS cc_start: 0.7913 (mtpp) cc_final: 0.7595 (mtmp) REVERT: B 59 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6903 (mt-10) REVERT: B 60 GLU cc_start: 0.7482 (tp30) cc_final: 0.7115 (tp30) REVERT: B 108 TYR cc_start: 0.7001 (m-80) cc_final: 0.6517 (m-80) REVERT: B 127 ASP cc_start: 0.7964 (m-30) cc_final: 0.7618 (m-30) REVERT: C 16 ARG cc_start: 0.8134 (mtm-85) cc_final: 0.7886 (mtp180) REVERT: C 59 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7219 (mt-10) REVERT: C 111 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7742 (mtpt) REVERT: D 126 LYS cc_start: 0.7476 (ttpt) cc_final: 0.6967 (mmtp) REVERT: E 72 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7315 (tp30) REVERT: E 127 ASP cc_start: 0.8011 (m-30) cc_final: 0.7474 (m-30) REVERT: F 16 ARG cc_start: 0.8611 (mtm180) cc_final: 0.8404 (mtm-85) REVERT: F 23 LYS cc_start: 0.7912 (mtpp) cc_final: 0.7580 (mtmp) REVERT: F 59 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6598 (mm-30) REVERT: F 60 GLU cc_start: 0.7510 (tp30) cc_final: 0.7133 (tp30) REVERT: F 62 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6698 (mt-10) REVERT: F 108 TYR cc_start: 0.7028 (m-80) cc_final: 0.6526 (m-80) REVERT: G 16 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7873 (mtp180) REVERT: G 27 ARG cc_start: 0.7751 (ttp80) cc_final: 0.7384 (ttp80) REVERT: G 59 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7286 (mt-10) REVERT: G 111 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7726 (mtpt) REVERT: G 139 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: H 126 LYS cc_start: 0.7514 (ttpt) cc_final: 0.7020 (mmtp) REVERT: I 150 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7482 (pt) REVERT: I 267 TRP cc_start: 0.7589 (m100) cc_final: 0.7320 (m100) REVERT: I 340 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6656 (mtp-110) REVERT: J 196 LEU cc_start: 0.8057 (mt) cc_final: 0.7151 (tp) REVERT: J 243 MET cc_start: 0.7691 (ttp) cc_final: 0.7431 (ttt) REVERT: J 344 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7680 (mmtm) REVERT: K 196 LEU cc_start: 0.8119 (mt) cc_final: 0.7174 (tp) REVERT: K 334 LYS cc_start: 0.8046 (mptt) cc_final: 0.7814 (mptt) REVERT: K 344 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7673 (mmtm) REVERT: L 150 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7329 (pt) REVERT: L 186 MET cc_start: 0.7846 (mtp) cc_final: 0.7488 (mtm) REVERT: L 243 MET cc_start: 0.7732 (ttt) cc_final: 0.7502 (ttp) REVERT: L 267 TRP cc_start: 0.7620 (m100) cc_final: 0.7345 (m100) REVERT: L 331 ARG cc_start: 0.7725 (mtp85) cc_final: 0.7387 (mtp180) REVERT: L 333 LYS cc_start: 0.8136 (mmtm) cc_final: 0.7804 (mmpt) REVERT: L 340 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6593 (mtp-110) outliers start: 95 outliers final: 51 residues processed: 502 average time/residue: 1.4473 time to fit residues: 817.1712 Evaluate side-chains 485 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 423 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 344 LYS Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 344 LYS Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 283 SER Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 395 MET Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 255 optimal weight: 0.6980 chunk 212 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 70 ASN B 106 ASN C 83 GLN C 105 GLN D 38 ASN E 81 ASN E 105 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 38 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21428 Z= 0.241 Angle : 0.618 6.910 29133 Z= 0.296 Chirality : 0.043 0.166 3543 Planarity : 0.003 0.034 3542 Dihedral : 9.377 132.457 2915 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.50 % Allowed : 19.22 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.16), residues: 2663 helix: 2.31 (0.12), residues: 1642 sheet: 0.80 (0.32), residues: 273 loop : -1.17 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP L 181 HIS 0.003 0.001 HIS F 30 PHE 0.031 0.002 PHE K 202 TYR 0.012 0.001 TYR I 270 ARG 0.008 0.001 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 433 time to evaluate : 2.374 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7825 (t0) cc_final: 0.7579 (p0) REVERT: A 127 ASP cc_start: 0.8020 (m-30) cc_final: 0.7470 (m-30) REVERT: B 23 LYS cc_start: 0.7896 (mtpp) cc_final: 0.7562 (mtmp) REVERT: B 39 GLU cc_start: 0.6790 (mp0) cc_final: 0.6097 (mp0) REVERT: B 59 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6761 (pt0) REVERT: B 60 GLU cc_start: 0.7520 (tp30) cc_final: 0.7152 (tp30) REVERT: B 108 TYR cc_start: 0.6995 (m-80) cc_final: 0.6531 (m-80) REVERT: B 127 ASP cc_start: 0.7966 (m-30) cc_final: 0.7623 (m-30) REVERT: C 16 ARG cc_start: 0.8137 (mtm-85) cc_final: 0.7896 (mtp180) REVERT: C 27 ARG cc_start: 0.7727 (ttp80) cc_final: 0.7290 (ttp80) REVERT: C 59 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: C 111 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7735 (mtpt) REVERT: C 139 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.4931 (mp0) REVERT: D 126 LYS cc_start: 0.7466 (ttpt) cc_final: 0.6945 (mmtp) REVERT: E 72 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7334 (tp30) REVERT: E 81 ASN cc_start: 0.8648 (p0) cc_final: 0.8242 (p0) REVERT: E 127 ASP cc_start: 0.8020 (m-30) cc_final: 0.7480 (m-30) REVERT: F 16 ARG cc_start: 0.8621 (mtm180) cc_final: 0.8415 (mtm-85) REVERT: F 23 LYS cc_start: 0.7908 (mtpp) cc_final: 0.7628 (mtpt) REVERT: F 39 GLU cc_start: 0.6803 (mp0) cc_final: 0.6109 (mp0) REVERT: F 59 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6642 (mm-30) REVERT: F 60 GLU cc_start: 0.7491 (tp30) cc_final: 0.7084 (tp30) REVERT: F 62 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6682 (mt-10) REVERT: F 108 TYR cc_start: 0.7029 (m-80) cc_final: 0.6538 (m-80) REVERT: G 16 ARG cc_start: 0.8143 (mtm-85) cc_final: 0.7800 (mtp180) REVERT: G 27 ARG cc_start: 0.7590 (ttp80) cc_final: 0.7306 (ttp80) REVERT: G 59 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7299 (mt-10) REVERT: G 111 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7739 (mtpt) REVERT: G 139 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: H 126 LYS cc_start: 0.7523 (ttpt) cc_final: 0.6970 (mttp) REVERT: I 150 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7460 (pt) REVERT: I 162 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6884 (mm) REVERT: I 267 TRP cc_start: 0.7614 (m100) cc_final: 0.7362 (m100) REVERT: I 340 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6724 (mtp-110) REVERT: J 196 LEU cc_start: 0.8057 (mt) cc_final: 0.7247 (tp) REVERT: J 344 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7681 (mmtm) REVERT: K 196 LEU cc_start: 0.8075 (mt) cc_final: 0.7196 (tp) REVERT: K 213 PHE cc_start: 0.7733 (t80) cc_final: 0.7527 (t80) REVERT: K 334 LYS cc_start: 0.8064 (mptt) cc_final: 0.7837 (mptt) REVERT: K 344 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7651 (mmtm) REVERT: L 150 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7329 (pt) REVERT: L 162 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6646 (mm) REVERT: L 243 MET cc_start: 0.7801 (ttt) cc_final: 0.7496 (ttp) REVERT: L 267 TRP cc_start: 0.7611 (m100) cc_final: 0.7343 (m100) REVERT: L 331 ARG cc_start: 0.7764 (mtp85) cc_final: 0.7352 (mtm-85) REVERT: L 333 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7802 (mmtt) REVERT: L 340 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6654 (mtp-110) outliers start: 101 outliers final: 59 residues processed: 498 average time/residue: 1.4091 time to fit residues: 790.0472 Evaluate side-chains 494 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 421 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 344 LYS Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 137 SER Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 344 LYS Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 283 SER Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 142 optimal weight: 0.1980 chunk 254 optimal weight: 0.7980 chunk 159 optimal weight: 0.0970 chunk 155 optimal weight: 0.0970 chunk 117 optimal weight: 7.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 70 ASN C 83 GLN C 105 GLN D 38 ASN E 105 GLN F 70 ASN G 105 GLN H 38 ASN J 218 ASN J 434 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21428 Z= 0.148 Angle : 0.578 7.086 29133 Z= 0.273 Chirality : 0.041 0.159 3543 Planarity : 0.003 0.033 3542 Dihedral : 8.837 125.798 2915 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.03 % Allowed : 20.95 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.17), residues: 2663 helix: 2.54 (0.12), residues: 1654 sheet: 0.92 (0.32), residues: 270 loop : -1.01 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 181 HIS 0.002 0.000 HIS D 110 PHE 0.027 0.001 PHE K 202 TYR 0.013 0.001 TYR I 270 ARG 0.008 0.001 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 443 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7914 (m-30) cc_final: 0.7343 (m-30) REVERT: B 16 ARG cc_start: 0.8640 (mtm180) cc_final: 0.8417 (mtm-85) REVERT: B 23 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7655 (mtmm) REVERT: B 39 GLU cc_start: 0.6751 (mp0) cc_final: 0.6159 (mp0) REVERT: B 60 GLU cc_start: 0.7416 (tp30) cc_final: 0.7064 (tp30) REVERT: B 62 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7044 (mp0) REVERT: B 108 TYR cc_start: 0.6886 (m-80) cc_final: 0.6425 (m-80) REVERT: B 127 ASP cc_start: 0.7983 (m-30) cc_final: 0.7635 (m-30) REVERT: C 16 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7766 (mtp180) REVERT: C 27 ARG cc_start: 0.7696 (ttp80) cc_final: 0.7335 (ttp80) REVERT: C 59 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7274 (mt-10) REVERT: C 111 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7656 (mtpt) REVERT: D 125 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8161 (tp30) REVERT: D 126 LYS cc_start: 0.7437 (ttpt) cc_final: 0.7003 (mmtp) REVERT: E 81 ASN cc_start: 0.8503 (p0) cc_final: 0.8176 (p0) REVERT: E 127 ASP cc_start: 0.7913 (m-30) cc_final: 0.7374 (m-30) REVERT: F 23 LYS cc_start: 0.7892 (mtpp) cc_final: 0.7615 (mtpt) REVERT: F 39 GLU cc_start: 0.6741 (mp0) cc_final: 0.6105 (mp0) REVERT: F 60 GLU cc_start: 0.7396 (tp30) cc_final: 0.7051 (tp30) REVERT: F 108 TYR cc_start: 0.6950 (m-80) cc_final: 0.6473 (m-80) REVERT: G 16 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7722 (mtp180) REVERT: G 59 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7186 (mt-10) REVERT: G 111 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7651 (mtpt) REVERT: H 126 LYS cc_start: 0.7388 (ttpt) cc_final: 0.7046 (mttp) REVERT: I 150 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7424 (pt) REVERT: I 267 TRP cc_start: 0.7551 (m100) cc_final: 0.7299 (m100) REVERT: I 340 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6863 (mtm-85) REVERT: J 243 MET cc_start: 0.7605 (ttp) cc_final: 0.7381 (ttt) REVERT: J 344 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7664 (mmtm) REVERT: K 243 MET cc_start: 0.7631 (ttp) cc_final: 0.7402 (ttt) REVERT: K 334 LYS cc_start: 0.8070 (mptt) cc_final: 0.7851 (mptt) REVERT: K 344 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7639 (mmtm) REVERT: L 191 ASP cc_start: 0.7437 (m-30) cc_final: 0.7192 (m-30) REVERT: L 267 TRP cc_start: 0.7537 (m100) cc_final: 0.7279 (m100) REVERT: L 331 ARG cc_start: 0.7693 (mtp85) cc_final: 0.7314 (mtp180) REVERT: L 333 LYS cc_start: 0.8121 (mmtm) cc_final: 0.7773 (mmtt) outliers start: 68 outliers final: 41 residues processed: 484 average time/residue: 1.2309 time to fit residues: 670.3043 Evaluate side-chains 459 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 410 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 218 ASN Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 344 LYS Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 137 SER Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 344 LYS Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 410 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 6.9990 chunk 101 optimal weight: 0.1980 chunk 151 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 chunk 125 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 70 ASN C 105 GLN D 38 ASN E 105 GLN F 70 ASN G 70 ASN G 83 GLN G 105 GLN H 38 ASN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21428 Z= 0.255 Angle : 0.634 8.938 29133 Z= 0.303 Chirality : 0.043 0.169 3543 Planarity : 0.003 0.035 3542 Dihedral : 9.135 126.477 2915 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.50 % Allowed : 20.60 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.17), residues: 2663 helix: 2.40 (0.12), residues: 1639 sheet: 0.78 (0.32), residues: 273 loop : -1.11 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 181 HIS 0.004 0.001 HIS B 30 PHE 0.055 0.002 PHE I 94 TYR 0.015 0.001 TYR I 270 ARG 0.009 0.001 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 424 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8629 (p0) cc_final: 0.8262 (p0) REVERT: A 127 ASP cc_start: 0.8025 (m-30) cc_final: 0.7472 (m-30) REVERT: B 23 LYS cc_start: 0.7915 (mtpp) cc_final: 0.7677 (mtmm) REVERT: B 60 GLU cc_start: 0.7420 (tp30) cc_final: 0.7070 (tp30) REVERT: B 108 TYR cc_start: 0.6936 (m-80) cc_final: 0.6482 (m-80) REVERT: B 127 ASP cc_start: 0.8015 (m-30) cc_final: 0.7687 (m-30) REVERT: C 16 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7746 (mtp180) REVERT: C 27 ARG cc_start: 0.7608 (ttp80) cc_final: 0.7269 (ttp80) REVERT: C 59 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: C 111 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7730 (mtpt) REVERT: C 139 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.4936 (mp0) REVERT: D 126 LYS cc_start: 0.7465 (ttpt) cc_final: 0.6987 (mmtp) REVERT: E 81 ASN cc_start: 0.8590 (p0) cc_final: 0.8254 (p0) REVERT: E 127 ASP cc_start: 0.8019 (m-30) cc_final: 0.7467 (m-30) REVERT: F 23 LYS cc_start: 0.7916 (mtpp) cc_final: 0.7678 (mtmm) REVERT: F 59 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6616 (pt0) REVERT: F 60 GLU cc_start: 0.7455 (tp30) cc_final: 0.7092 (tp30) REVERT: F 62 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.5880 (mt-10) REVERT: F 108 TYR cc_start: 0.7008 (m-80) cc_final: 0.6539 (m-80) REVERT: F 115 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7194 (mppt) REVERT: G 16 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7794 (mtp180) REVERT: G 27 ARG cc_start: 0.7589 (ttp80) cc_final: 0.7340 (ttp80) REVERT: G 111 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7717 (mtpt) REVERT: G 139 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.5047 (mp0) REVERT: H 83 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7443 (mt0) REVERT: H 126 LYS cc_start: 0.7484 (ttpt) cc_final: 0.6994 (mmtp) REVERT: I 94 PHE cc_start: 0.6521 (t80) cc_final: 0.6317 (t80) REVERT: I 150 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7413 (pt) REVERT: I 267 TRP cc_start: 0.7647 (m100) cc_final: 0.7394 (m100) REVERT: I 340 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6789 (mtp-110) REVERT: J 344 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7663 (mmtm) REVERT: K 334 LYS cc_start: 0.8085 (mptt) cc_final: 0.7864 (mptt) REVERT: K 344 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7680 (mmtm) REVERT: L 98 ILE cc_start: 0.8162 (mm) cc_final: 0.7940 (mp) REVERT: L 191 ASP cc_start: 0.7525 (m-30) cc_final: 0.7256 (m-30) REVERT: L 267 TRP cc_start: 0.7660 (m100) cc_final: 0.7405 (m100) REVERT: L 314 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7149 (pt) REVERT: L 331 ARG cc_start: 0.7767 (mtp85) cc_final: 0.7375 (mtp180) REVERT: L 333 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7794 (mmtt) REVERT: L 340 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6762 (mtp-110) outliers start: 101 outliers final: 55 residues processed: 485 average time/residue: 1.4072 time to fit residues: 768.1189 Evaluate side-chains 478 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 409 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 269 SER Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 344 LYS Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 137 SER Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 344 LYS Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 301 MET Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 237 optimal weight: 8.9990 chunk 142 optimal weight: 0.0970 chunk 103 optimal weight: 0.5980 chunk 186 optimal weight: 0.0030 chunk 72 optimal weight: 0.7980 chunk 214 optimal weight: 0.6980 chunk 224 optimal weight: 6.9990 chunk 236 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 70 ASN C 105 GLN D 38 ASN E 105 GLN F 70 ASN G 105 GLN H 38 ASN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 434 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 21428 Z= 0.167 Angle : 0.603 8.800 29133 Z= 0.285 Chirality : 0.042 0.172 3543 Planarity : 0.004 0.089 3542 Dihedral : 8.707 117.727 2915 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.17 % Allowed : 22.07 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.17), residues: 2663 helix: 2.60 (0.12), residues: 1640 sheet: 0.73 (0.32), residues: 275 loop : -1.10 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP L 181 HIS 0.002 0.000 HIS D 110 PHE 0.058 0.001 PHE I 94 TYR 0.022 0.001 TYR I 270 ARG 0.015 0.001 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 415 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7913 (m-30) cc_final: 0.7365 (m-30) REVERT: B 16 ARG cc_start: 0.8664 (mtm180) cc_final: 0.8435 (mtm-85) REVERT: B 23 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7620 (mtpt) REVERT: B 60 GLU cc_start: 0.7256 (tp30) cc_final: 0.6959 (tp30) REVERT: B 108 TYR cc_start: 0.6913 (m-80) cc_final: 0.6465 (m-80) REVERT: B 114 GLU cc_start: 0.7502 (tt0) cc_final: 0.7289 (mt-10) REVERT: B 127 ASP cc_start: 0.7994 (m-30) cc_final: 0.7656 (m-30) REVERT: C 16 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7696 (mtp180) REVERT: C 111 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7297 (mmpt) REVERT: D 126 LYS cc_start: 0.7415 (ttpt) cc_final: 0.7010 (mmtp) REVERT: E 81 ASN cc_start: 0.8336 (p0) cc_final: 0.8120 (p0) REVERT: E 127 ASP cc_start: 0.7921 (m-30) cc_final: 0.7382 (m-30) REVERT: F 23 LYS cc_start: 0.7873 (mtpp) cc_final: 0.7611 (mtpt) REVERT: F 60 GLU cc_start: 0.7308 (tp30) cc_final: 0.6991 (tp30) REVERT: F 62 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7063 (mp0) REVERT: F 108 TYR cc_start: 0.6978 (m-10) cc_final: 0.6522 (m-80) REVERT: F 114 GLU cc_start: 0.7494 (tt0) cc_final: 0.7275 (mt-10) REVERT: G 16 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7713 (mtp180) REVERT: G 111 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7626 (mtpt) REVERT: H 126 LYS cc_start: 0.7446 (ttpt) cc_final: 0.7095 (mttp) REVERT: I 150 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7368 (pt) REVERT: J 243 MET cc_start: 0.7592 (ttp) cc_final: 0.7363 (ttt) REVERT: J 344 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7659 (mmtm) REVERT: K 243 MET cc_start: 0.7603 (ttp) cc_final: 0.7395 (ttt) REVERT: K 334 LYS cc_start: 0.8045 (mptt) cc_final: 0.7832 (mptt) REVERT: K 344 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7648 (mmtm) REVERT: L 191 ASP cc_start: 0.7322 (m-30) cc_final: 0.7084 (m-30) REVERT: L 267 TRP cc_start: 0.7531 (m100) cc_final: 0.7291 (m100) REVERT: L 331 ARG cc_start: 0.7730 (mtp85) cc_final: 0.7364 (mtp180) REVERT: L 333 LYS cc_start: 0.8173 (mmtm) cc_final: 0.7845 (mmtt) outliers start: 71 outliers final: 44 residues processed: 461 average time/residue: 1.3895 time to fit residues: 728.4703 Evaluate side-chains 458 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 409 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 269 SER Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 344 LYS Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 344 LYS Chi-restraints excluded: chain L residue 189 VAL Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 301 MET Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 410 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.0050 chunk 153 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 263 optimal weight: 0.0980 chunk 242 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 38 ASN E 105 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 38 ASN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 71 GLN ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21428 Z= 0.217 Angle : 0.631 9.210 29133 Z= 0.300 Chirality : 0.043 0.270 3543 Planarity : 0.004 0.075 3542 Dihedral : 8.833 114.374 2915 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.72 % Allowed : 22.69 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.17), residues: 2663 helix: 2.48 (0.12), residues: 1639 sheet: 0.68 (0.32), residues: 275 loop : -1.05 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP K 267 HIS 0.003 0.001 HIS H 110 PHE 0.062 0.002 PHE I 94 TYR 0.016 0.001 TYR L 270 ARG 0.015 0.001 ARG E 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 420 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8011 (m-30) cc_final: 0.7450 (m-30) REVERT: B 23 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7674 (mtmm) REVERT: B 60 GLU cc_start: 0.7225 (tp30) cc_final: 0.6929 (tp30) REVERT: B 108 TYR cc_start: 0.6940 (m-80) cc_final: 0.6482 (m-80) REVERT: B 114 GLU cc_start: 0.7484 (tt0) cc_final: 0.7169 (mt-10) REVERT: B 127 ASP cc_start: 0.7996 (m-30) cc_final: 0.7669 (m-30) REVERT: C 16 ARG cc_start: 0.8077 (mtm-85) cc_final: 0.7746 (mtp180) REVERT: C 111 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7701 (mtpt) REVERT: D 83 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7414 (mt0) REVERT: D 126 LYS cc_start: 0.7507 (ttpt) cc_final: 0.7031 (mttp) REVERT: E 81 ASN cc_start: 0.8380 (p0) cc_final: 0.8148 (p0) REVERT: E 127 ASP cc_start: 0.7985 (m-30) cc_final: 0.7428 (m-30) REVERT: F 23 LYS cc_start: 0.7884 (mtpp) cc_final: 0.7619 (mtpt) REVERT: F 60 GLU cc_start: 0.7271 (tp30) cc_final: 0.6895 (tp30) REVERT: F 108 TYR cc_start: 0.6965 (m-10) cc_final: 0.6493 (m-80) REVERT: F 114 GLU cc_start: 0.7483 (tt0) cc_final: 0.7191 (mt-10) REVERT: G 16 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7779 (mtp180) REVERT: G 27 ARG cc_start: 0.7613 (ttp80) cc_final: 0.7396 (ttp80) REVERT: G 111 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7667 (mtpt) REVERT: H 126 LYS cc_start: 0.7469 (ttpt) cc_final: 0.7020 (mmtp) REVERT: I 150 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7357 (pt) REVERT: J 243 MET cc_start: 0.7687 (ttp) cc_final: 0.7392 (ttt) REVERT: J 344 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7653 (mmtm) REVERT: K 243 MET cc_start: 0.7714 (ttp) cc_final: 0.7429 (ttt) REVERT: K 334 LYS cc_start: 0.8056 (mptt) cc_final: 0.7842 (mptt) REVERT: K 344 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7652 (mmtm) REVERT: L 191 ASP cc_start: 0.7379 (m-30) cc_final: 0.7145 (m-30) REVERT: L 267 TRP cc_start: 0.7635 (m100) cc_final: 0.7366 (m100) REVERT: L 331 ARG cc_start: 0.7756 (mtp85) cc_final: 0.7378 (mtp180) REVERT: L 333 LYS cc_start: 0.8191 (mmtm) cc_final: 0.7858 (mmtt) outliers start: 61 outliers final: 42 residues processed: 459 average time/residue: 1.3888 time to fit residues: 718.2865 Evaluate side-chains 458 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 410 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 344 LYS Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 344 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 189 VAL Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 193 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 87 optimal weight: 0.0030 chunk 215 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 38 ASN D 134 GLN E 105 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 38 ASN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.196650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144232 restraints weight = 23809.156| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.36 r_work: 0.3638 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21428 Z= 0.208 Angle : 0.634 8.557 29133 Z= 0.302 Chirality : 0.043 0.290 3543 Planarity : 0.004 0.092 3542 Dihedral : 8.753 112.946 2915 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.85 % Allowed : 22.78 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.17), residues: 2663 helix: 2.51 (0.12), residues: 1631 sheet: 0.67 (0.32), residues: 275 loop : -1.09 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP J 267 HIS 0.003 0.001 HIS F 51 PHE 0.036 0.001 PHE I 94 TYR 0.017 0.001 TYR L 270 ARG 0.015 0.001 ARG E 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11046.16 seconds wall clock time: 198 minutes 8.88 seconds (11888.88 seconds total)