Starting phenix.real_space_refine on Fri Mar 22 14:04:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pww_20513/03_2024/6pww_20513_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pww_20513/03_2024/6pww_20513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pww_20513/03_2024/6pww_20513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pww_20513/03_2024/6pww_20513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pww_20513/03_2024/6pww_20513_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pww_20513/03_2024/6pww_20513_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15700 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 292 5.49 5 S 52 5.16 5 C 10541 2.51 5 N 3308 2.21 5 O 3980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 22": "OD1" <-> "OD2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A ASP 353": "OD1" <-> "OD2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3891": "OE1" <-> "OE2" Residue "C ARG 3916": "NH1" <-> "NH2" Residue "C ARG 3936": "NH1" <-> "NH2" Residue "C ARG 3965": "NH1" <-> "NH2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G ASP 106": "OD1" <-> "OD2" Residue "H ASP 68": "OD1" <-> "OD2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "J TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 68": "OE1" <-> "OE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K ASP 106": "OD1" <-> "OD2" Residue "M GLU 91": "OE1" <-> "OE2" Residue "L ASP 68": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18174 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2613 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 303, 2339 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 293} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Conformer: "B" Number of residues, atoms: 303, 2339 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 293} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 bond proxies already assigned to first conformer: 2392 Chain: "C" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1228 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 146} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "J" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "O" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "P" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "L" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6089 SG CYS C3957 66.535 36.201 100.003 1.00788.66 S Time building chain proxies: 10.44, per 1000 atoms: 0.57 Number of scatterers: 18174 At special positions: 0 Unit cell: (136.35, 146.45, 123.22, 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) Zn 1 29.99 S 52 16.00 P 292 15.00 O 3980 8.00 N 3308 7.00 C 10541 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.66 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C4002 " pdb="ZN ZN C4002 " - pdb=" SG CYS C3957 " 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2902 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 17 sheets defined 34.3% alpha, 18.3% beta 150 base pairs and 233 stacking pairs defined. Time for finding SS restraints: 10.02 Creating SS restraints... Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'C' and resid 3816 through 3826 Processing helix chain 'C' and resid 3865 through 3878 removed outlier: 4.112A pdb=" N ASP C3869 " --> pdb=" O SER C3865 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS C3870 " --> pdb=" O ILE C3866 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C3878 " --> pdb=" O TYR C3874 " (cutoff:3.500A) Processing helix chain 'C' and resid 3901 through 3904 Processing helix chain 'G' and resid 45 through 56 Processing helix chain 'G' and resid 64 through 78 removed outlier: 3.768A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 113 Processing helix chain 'G' and resid 121 through 130 Processing helix chain 'H' and resid 25 through 28 Processing helix chain 'H' and resid 31 through 41 Processing helix chain 'H' and resid 48 through 75 removed outlier: 4.471A pdb=" N GLU H 52 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE H 66 " --> pdb=" O GLU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 92 Processing helix chain 'I' and resid 17 through 20 No H-bonds generated for 'chain 'I' and resid 17 through 20' Processing helix chain 'I' and resid 27 through 37 Processing helix chain 'I' and resid 45 through 73 removed outlier: 4.422A pdb=" N VAL I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU I 65 " --> pdb=" O GLU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 89 Processing helix chain 'I' and resid 91 through 96 Processing helix chain 'J' and resid 35 through 45 Processing helix chain 'J' and resid 53 through 80 Processing helix chain 'J' and resid 88 through 98 Processing helix chain 'J' and resid 102 through 119 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 64 through 78 removed outlier: 3.768A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 113 Processing helix chain 'K' and resid 121 through 130 Processing helix chain 'M' and resid 17 through 21 Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 45 through 72 removed outlier: 4.554A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 89 Processing helix chain 'M' and resid 91 through 97 Processing helix chain 'N' and resid 35 through 45 Processing helix chain 'N' and resid 53 through 80 Processing helix chain 'N' and resid 88 through 98 Processing helix chain 'N' and resid 101 through 120 Processing helix chain 'L' and resid 25 through 28 Processing helix chain 'L' and resid 31 through 41 Processing helix chain 'L' and resid 48 through 75 removed outlier: 4.470A pdb=" N GLU L 52 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE L 66 " --> pdb=" O GLU L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 92 Processing sheet with id= A, first strand: chain 'A' and resid 30 through 32 removed outlier: 5.113A pdb=" N ASP A 52 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ILE A 58 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 69 through 74 removed outlier: 6.511A pdb=" N ALA A 84 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 72 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A 82 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TRP A 74 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS A 80 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 102 " --> pdb=" O GLN A 92 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ASP A 94 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N CYS A 100 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 142 through 144 Processing sheet with id= D, first strand: chain 'A' and resid 156 through 159 removed outlier: 6.237A pdb=" N LYS A 179 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A 185 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 243 through 246 removed outlier: 4.320A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 217 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 256 through 259 removed outlier: 4.007A pdb=" N LYS A 256 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLU A 280 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 286 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 317 through 321 Processing sheet with id= H, first strand: chain 'B' and resid 48 through 53 removed outlier: 6.749A pdb=" N SER B 63 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL B 51 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA B 61 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE B 53 " --> pdb=" O TRP B 59 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TRP B 59 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLY B 73 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N PHE B 79 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 90 through 95 removed outlier: 6.985A pdb=" N ALA B 105 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL B 93 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 103 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TRP B 95 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU B 101 " --> pdb=" O TRP B 95 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 115 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS B 121 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 132 through 137 removed outlier: 6.781A pdb=" N GLY B 147 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N CYS B 135 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 145 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE B 137 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 143 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP B 157 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS B 163 " --> pdb=" O ASP B 157 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.633A pdb=" N SER B 189 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL B 177 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 187 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE B 179 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 185 " --> pdb=" O PHE B 179 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP B 199 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N CYS B 205 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 217 through 222 removed outlier: 6.672A pdb=" N ALA B 232 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B 220 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 230 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N PHE B 222 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR B 228 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP B 242 " --> pdb=" O CYS B 248 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N CYS B 248 " --> pdb=" O ASP B 242 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 264 through 267 removed outlier: 5.922A pdb=" N ASN B 287 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B 293 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 36 through 42 removed outlier: 6.674A pdb=" N LEU B 329 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 40 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE B 327 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR B 326 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 3831 through 3835 Processing sheet with id= P, first strand: chain 'C' and resid 3861 through 3864 Processing sheet with id= Q, first strand: chain 'C' and resid 3913 through 3920 removed outlier: 6.099A pdb=" N ALA C3930 " --> pdb=" O MET C3854 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET C3854 " --> pdb=" O ALA C3930 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 385 hydrogen bonds 754 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 233 stacking parallelities Total time for adding SS restraints: 7.97 Time building geometry restraints manager: 11.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4146 1.33 - 1.45: 5136 1.45 - 1.57: 9181 1.57 - 1.69: 582 1.69 - 1.81: 73 Bond restraints: 19118 Sorted by residual: bond pdb=" C2 SAH C4001 " pdb=" N3 SAH C4001 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.70e+00 bond pdb=" C8 SAH C4001 " pdb=" N7 SAH C4001 " ideal model delta sigma weight residual 1.299 1.349 -0.050 2.00e-02 2.50e+03 6.33e+00 bond pdb=" C2 SAH C4001 " pdb=" N1 SAH C4001 " ideal model delta sigma weight residual 1.330 1.380 -0.050 2.00e-02 2.50e+03 6.15e+00 bond pdb=" C6 SAH C4001 " pdb=" N1 SAH C4001 " ideal model delta sigma weight residual 1.338 1.378 -0.040 2.00e-02 2.50e+03 4.03e+00 bond pdb=" C3' DT P 15 " pdb=" O3' DT P 15 " ideal model delta sigma weight residual 1.422 1.470 -0.048 3.00e-02 1.11e+03 2.55e+00 ... (remaining 19113 not shown) Histogram of bond angle deviations from ideal: 91.53 - 100.02: 55 100.02 - 108.51: 3429 108.51 - 117.01: 11776 117.01 - 125.50: 10754 125.50 - 133.99: 1100 Bond angle restraints: 27114 Sorted by residual: angle pdb=" N VAL B 268 " pdb=" CA VAL B 268 " pdb=" C VAL B 268 " ideal model delta sigma weight residual 113.53 109.22 4.31 9.80e-01 1.04e+00 1.93e+01 angle pdb=" N GLY J 101 " pdb=" CA GLY J 101 " pdb=" C GLY J 101 " ideal model delta sigma weight residual 110.77 117.75 -6.98 1.93e+00 2.68e-01 1.31e+01 angle pdb=" CG SAH C4001 " pdb=" SD SAH C4001 " pdb=" C5' SAH C4001 " ideal model delta sigma weight residual 101.77 91.53 10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" O SAH C4001 " pdb=" C SAH C4001 " pdb=" OXT SAH C4001 " ideal model delta sigma weight residual 126.79 116.93 9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C2 SAH C4001 " pdb=" N3 SAH C4001 " pdb=" C4 SAH C4001 " ideal model delta sigma weight residual 111.67 120.27 -8.60 3.00e+00 1.11e-01 8.23e+00 ... (remaining 27109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.23: 9068 34.23 - 68.46: 1574 68.46 - 102.69: 41 102.69 - 136.92: 3 136.92 - 171.14: 2 Dihedral angle restraints: 10688 sinusoidal: 6195 harmonic: 4493 Sorted by residual: dihedral pdb=" CA ASN A 328 " pdb=" C ASN A 328 " pdb=" N TRP A 329 " pdb=" CA TRP A 329 " ideal model delta harmonic sigma weight residual 180.00 159.07 20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA SER A 196 " pdb=" C SER A 196 " pdb=" N ASN A 197 " pdb=" CA ASN A 197 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ASN L 64 " pdb=" C ASN L 64 " pdb=" N VAL L 65 " pdb=" CA VAL L 65 " ideal model delta harmonic sigma weight residual 180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 10685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2190 0.038 - 0.076: 680 0.076 - 0.114: 174 0.114 - 0.152: 35 0.152 - 0.190: 1 Chirality restraints: 3080 Sorted by residual: chirality pdb=" CB ILE A 278 " pdb=" CA ILE A 278 " pdb=" CG1 ILE A 278 " pdb=" CG2 ILE A 278 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" C3' SAH C4001 " pdb=" C2' SAH C4001 " pdb=" C4' SAH C4001 " pdb=" O3' SAH C4001 " both_signs ideal model delta sigma weight residual False -2.71 -2.56 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE A 204 " pdb=" N ILE A 204 " pdb=" C ILE A 204 " pdb=" CB ILE A 204 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 3077 not shown) Planarity restraints: 2419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC O 54 " -0.000 2.00e-02 2.50e+03 1.43e-02 4.62e+00 pdb=" N1 DC O 54 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DC O 54 " 0.037 2.00e-02 2.50e+03 pdb=" O2 DC O 54 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DC O 54 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DC O 54 " 0.006 2.00e-02 2.50e+03 pdb=" N4 DC O 54 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DC O 54 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC O 54 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC O 110 " -0.011 2.00e-02 2.50e+03 1.30e-02 3.81e+00 pdb=" N1 DC O 110 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DC O 110 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DC O 110 " 0.024 2.00e-02 2.50e+03 pdb=" N3 DC O 110 " -0.012 2.00e-02 2.50e+03 pdb=" C4 DC O 110 " -0.014 2.00e-02 2.50e+03 pdb=" N4 DC O 110 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC O 110 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DC O 110 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 126 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO A 127 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 127 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 127 " -0.026 5.00e-02 4.00e+02 ... (remaining 2416 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 296 2.58 - 3.16: 15930 3.16 - 3.74: 36915 3.74 - 4.32: 46682 4.32 - 4.90: 67198 Nonbonded interactions: 167021 Sorted by model distance: nonbonded pdb=" N2 DG O 83 " pdb=" O2 DC P 65 " model vdw 1.996 2.496 nonbonded pdb=" OG1 THR A 217 " pdb=" OD1 ASP A 219 " model vdw 2.152 2.440 nonbonded pdb=" N CYS C3909 " pdb="ZN ZN C4002 " model vdw 2.172 2.310 nonbonded pdb=" O ILE C3905 " pdb=" OH TYR C3944 " model vdw 2.175 2.440 nonbonded pdb=" O PHE B 263 " pdb=" OG1 THR B 307 " model vdw 2.184 2.440 ... (remaining 167016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = (chain 'I' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'M' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'J' selection = (chain 'N' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.010 Extract box with map and model: 9.640 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 64.780 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 0.059 19118 Z= 0.228 Angle : 0.640 13.783 27114 Z= 0.374 Chirality : 0.040 0.190 3080 Planarity : 0.003 0.046 2419 Dihedral : 25.779 171.144 7786 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.22 % Allowed : 5.81 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.19), residues: 1523 helix: -0.53 (0.20), residues: 568 sheet: -2.40 (0.26), residues: 300 loop : -2.44 (0.21), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 329 HIS 0.004 0.001 HIS L 75 PHE 0.009 0.001 PHE N 62 TYR 0.009 0.001 TYR A 225 ARG 0.003 0.000 ARG G 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 368 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9370 (ttp) cc_final: 0.9040 (tmm) REVERT: A 242 MET cc_start: 0.9407 (ttm) cc_final: 0.9120 (ttp) REVERT: A 265 TYR cc_start: 0.9251 (m-80) cc_final: 0.8999 (m-80) REVERT: A 267 VAL cc_start: 0.9771 (p) cc_final: 0.9540 (m) REVERT: A 277 TYR cc_start: 0.9215 (m-10) cc_final: 0.8729 (m-80) REVERT: B 241 TRP cc_start: 0.7611 (m100) cc_final: 0.7352 (m-10) REVERT: C 3969 ASN cc_start: 0.6113 (m-40) cc_final: 0.5890 (m110) REVERT: G 50 GLU cc_start: 0.9590 (tp30) cc_final: 0.9277 (tp30) REVERT: G 58 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8504 (m) REVERT: G 60 LEU cc_start: 0.8578 (mm) cc_final: 0.7971 (mm) REVERT: G 62 ILE cc_start: 0.9673 (mt) cc_final: 0.9435 (mm) REVERT: G 70 LEU cc_start: 0.9731 (tp) cc_final: 0.9133 (tp) REVERT: G 73 GLU cc_start: 0.8870 (tt0) cc_final: 0.8664 (tt0) REVERT: G 77 ASP cc_start: 0.9152 (m-30) cc_final: 0.8830 (m-30) REVERT: G 97 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8501 (mt-10) REVERT: G 109 LEU cc_start: 0.9824 (OUTLIER) cc_final: 0.9607 (tt) REVERT: G 112 ILE cc_start: 0.9723 (OUTLIER) cc_final: 0.9463 (mt) REVERT: G 133 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7562 (mt-10) REVERT: H 25 ASN cc_start: 0.8331 (m-40) cc_final: 0.7386 (t0) REVERT: H 72 TYR cc_start: 0.9359 (m-80) cc_final: 0.9074 (m-10) REVERT: H 88 TYR cc_start: 0.9404 (m-10) cc_final: 0.8932 (m-80) REVERT: H 98 TYR cc_start: 0.8792 (m-10) cc_final: 0.8386 (m-80) REVERT: I 41 GLU cc_start: 0.9319 (tt0) cc_final: 0.8816 (tm-30) REVERT: I 56 GLU cc_start: 0.9375 (tt0) cc_final: 0.8825 (mt-10) REVERT: I 63 LEU cc_start: 0.9552 (pp) cc_final: 0.9306 (pp) REVERT: I 64 GLU cc_start: 0.9633 (tt0) cc_final: 0.9333 (mm-30) REVERT: I 83 LEU cc_start: 0.9677 (mp) cc_final: 0.9310 (mp) REVERT: I 91 GLU cc_start: 0.9547 (tm-30) cc_final: 0.9326 (tm-30) REVERT: I 95 LYS cc_start: 0.9646 (tptt) cc_final: 0.9380 (tppt) REVERT: J 59 MET cc_start: 0.9856 (mmm) cc_final: 0.9482 (mmm) REVERT: J 62 PHE cc_start: 0.9715 (t80) cc_final: 0.9454 (t80) REVERT: J 65 ASP cc_start: 0.9168 (t70) cc_final: 0.8610 (t0) REVERT: J 68 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8983 (tm-30) REVERT: J 76 ARG cc_start: 0.9434 (ttm110) cc_final: 0.9031 (ttm110) REVERT: J 92 GLN cc_start: 0.9254 (mt0) cc_final: 0.8921 (mp10) REVERT: J 102 GLU cc_start: 0.9267 (tp30) cc_final: 0.8962 (tm-30) REVERT: J 103 LEU cc_start: 0.9619 (mt) cc_final: 0.9286 (mt) REVERT: K 41 TYR cc_start: 0.9041 (m-80) cc_final: 0.8612 (m-80) REVERT: K 50 GLU cc_start: 0.9060 (tp30) cc_final: 0.8670 (tp30) REVERT: K 61 LEU cc_start: 0.9489 (mm) cc_final: 0.9148 (mp) REVERT: K 65 LEU cc_start: 0.9768 (mm) cc_final: 0.9502 (mm) REVERT: K 73 GLU cc_start: 0.8731 (tt0) cc_final: 0.8433 (pt0) REVERT: K 82 LEU cc_start: 0.9417 (mt) cc_final: 0.9202 (mt) REVERT: K 97 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8478 (mt-10) REVERT: K 106 ASP cc_start: 0.8629 (p0) cc_final: 0.8351 (p0) REVERT: K 119 ILE cc_start: 0.8920 (pt) cc_final: 0.8697 (tp) REVERT: K 123 ASP cc_start: 0.8800 (t70) cc_final: 0.8142 (t70) REVERT: M 36 LYS cc_start: 0.9235 (mttm) cc_final: 0.8822 (mtmm) REVERT: M 56 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9166 (mt-10) REVERT: M 90 ASP cc_start: 0.9615 (t0) cc_final: 0.9381 (t70) REVERT: M 94 ASN cc_start: 0.9552 (t0) cc_final: 0.9299 (t0) REVERT: M 112 GLN cc_start: 0.9417 (mm-40) cc_final: 0.8360 (tm-30) REVERT: N 30 ARG cc_start: 0.8536 (mtt90) cc_final: 0.8176 (mtt180) REVERT: N 59 MET cc_start: 0.9824 (mmm) cc_final: 0.9501 (tpt) REVERT: N 65 ASP cc_start: 0.9252 (t0) cc_final: 0.8837 (t0) REVERT: N 83 ARG cc_start: 0.9383 (mmp-170) cc_final: 0.8951 (mmp80) REVERT: N 92 GLN cc_start: 0.9482 (tt0) cc_final: 0.9222 (pp30) REVERT: N 96 ARG cc_start: 0.9537 (mtp180) cc_final: 0.9234 (tpp80) REVERT: N 98 LEU cc_start: 0.9038 (mt) cc_final: 0.8700 (mt) REVERT: N 110 GLU cc_start: 0.9372 (mm-30) cc_final: 0.8939 (mm-30) REVERT: L 74 GLU cc_start: 0.9393 (tm-30) cc_final: 0.9120 (tm-30) REVERT: L 91 LYS cc_start: 0.9687 (tttt) cc_final: 0.9354 (mtpt) REVERT: L 97 LEU cc_start: 0.9703 (tp) cc_final: 0.9022 (tp) REVERT: L 98 TYR cc_start: 0.8973 (m-10) cc_final: 0.8364 (m-80) outliers start: 16 outliers final: 4 residues processed: 370 average time/residue: 0.3478 time to fit residues: 182.4480 Evaluate side-chains 264 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 257 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 5.9990 chunk 134 optimal weight: 0.0170 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 91 optimal weight: 0.2980 chunk 72 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 53 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 0.0970 chunk 161 optimal weight: 4.9990 overall best weight: 1.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS A 250 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS B 265 ASN B 289 GLN B 323 ASN ** C3906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS G 68 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN H 64 ASN ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN J 106 HIS ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 HIS M 104 GLN ** N 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN L 25 ASN L 64 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19118 Z= 0.213 Angle : 0.617 13.894 27114 Z= 0.347 Chirality : 0.041 0.254 3080 Planarity : 0.004 0.044 2419 Dihedral : 29.840 174.085 4880 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1523 helix: 0.76 (0.22), residues: 572 sheet: -2.06 (0.26), residues: 314 loop : -1.92 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 156 HIS 0.009 0.001 HIS H 75 PHE 0.025 0.002 PHE K 67 TYR 0.012 0.001 TYR C3874 ARG 0.007 0.001 ARG K 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 325 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9342 (ttp) cc_final: 0.9021 (tmm) REVERT: A 242 MET cc_start: 0.9412 (ttm) cc_final: 0.9113 (ttp) REVERT: A 265 TYR cc_start: 0.9257 (m-80) cc_final: 0.9028 (m-80) REVERT: G 50 GLU cc_start: 0.9580 (tp30) cc_final: 0.9280 (tp30) REVERT: G 60 LEU cc_start: 0.8618 (mm) cc_final: 0.8356 (mm) REVERT: G 61 LEU cc_start: 0.9228 (mm) cc_final: 0.8997 (mm) REVERT: G 62 ILE cc_start: 0.9731 (mt) cc_final: 0.9527 (mm) REVERT: G 68 GLN cc_start: 0.9793 (tt0) cc_final: 0.9342 (tm-30) REVERT: G 70 LEU cc_start: 0.9632 (tp) cc_final: 0.8952 (tp) REVERT: G 84 PHE cc_start: 0.9291 (m-80) cc_final: 0.8827 (m-10) REVERT: G 90 MET cc_start: 0.9647 (mmp) cc_final: 0.9340 (mmm) REVERT: G 97 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8552 (mt-10) REVERT: G 109 LEU cc_start: 0.9819 (tt) cc_final: 0.9607 (pp) REVERT: G 120 MET cc_start: 0.9288 (mtt) cc_final: 0.8834 (mtt) REVERT: G 125 GLN cc_start: 0.9713 (mt0) cc_final: 0.9435 (mm-40) REVERT: G 130 ILE cc_start: 0.9712 (mm) cc_final: 0.9456 (mm) REVERT: H 25 ASN cc_start: 0.7791 (m-40) cc_final: 0.7179 (t0) REVERT: H 26 ILE cc_start: 0.9665 (tt) cc_final: 0.9447 (tt) REVERT: H 72 TYR cc_start: 0.9320 (m-80) cc_final: 0.9001 (m-80) REVERT: H 74 GLU cc_start: 0.9603 (tm-30) cc_final: 0.9372 (tm-30) REVERT: H 88 TYR cc_start: 0.9417 (m-10) cc_final: 0.8993 (m-80) REVERT: I 41 GLU cc_start: 0.9303 (tt0) cc_final: 0.8652 (tp30) REVERT: I 56 GLU cc_start: 0.9367 (tt0) cc_final: 0.8777 (mt-10) REVERT: I 83 LEU cc_start: 0.9678 (mp) cc_final: 0.9338 (mp) REVERT: I 91 GLU cc_start: 0.9497 (tm-30) cc_final: 0.9220 (tm-30) REVERT: I 95 LYS cc_start: 0.9638 (tptt) cc_final: 0.9376 (tppt) REVERT: J 30 ARG cc_start: 0.7848 (ptp-110) cc_final: 0.7235 (mtm-85) REVERT: J 59 MET cc_start: 0.9846 (mmm) cc_final: 0.9571 (mmp) REVERT: J 62 PHE cc_start: 0.9684 (t80) cc_final: 0.9425 (t80) REVERT: J 65 ASP cc_start: 0.9242 (t70) cc_final: 0.8924 (t0) REVERT: J 76 ARG cc_start: 0.9512 (ttm110) cc_final: 0.9210 (ttm110) REVERT: J 91 ILE cc_start: 0.9842 (mp) cc_final: 0.9515 (tt) REVERT: J 92 GLN cc_start: 0.9176 (mt0) cc_final: 0.8878 (mp10) REVERT: J 102 GLU cc_start: 0.9225 (tp30) cc_final: 0.8933 (tm-30) REVERT: J 103 LEU cc_start: 0.9622 (mt) cc_final: 0.9230 (mt) REVERT: K 41 TYR cc_start: 0.9016 (m-80) cc_final: 0.8469 (m-80) REVERT: K 50 GLU cc_start: 0.9158 (tp30) cc_final: 0.8610 (tp30) REVERT: K 61 LEU cc_start: 0.9451 (mm) cc_final: 0.9093 (mp) REVERT: K 62 ILE cc_start: 0.9646 (mm) cc_final: 0.9430 (mm) REVERT: K 80 THR cc_start: 0.9575 (p) cc_final: 0.9226 (p) REVERT: K 120 MET cc_start: 0.8541 (mtp) cc_final: 0.8262 (mtp) REVERT: K 123 ASP cc_start: 0.8393 (t70) cc_final: 0.8001 (t70) REVERT: K 124 ILE cc_start: 0.9826 (mp) cc_final: 0.9563 (mp) REVERT: K 125 GLN cc_start: 0.9493 (mt0) cc_final: 0.9105 (mm110) REVERT: M 38 ASN cc_start: 0.9462 (m110) cc_final: 0.9085 (p0) REVERT: M 56 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9177 (mt-10) REVERT: M 64 GLU cc_start: 0.9238 (pp20) cc_final: 0.9024 (pp20) REVERT: M 94 ASN cc_start: 0.9529 (t0) cc_final: 0.9285 (t0) REVERT: M 112 GLN cc_start: 0.9433 (mm-40) cc_final: 0.9196 (mm110) REVERT: N 30 ARG cc_start: 0.8367 (mtt90) cc_final: 0.8067 (mtt180) REVERT: N 64 ASN cc_start: 0.9774 (m-40) cc_final: 0.9574 (m-40) REVERT: N 65 ASP cc_start: 0.9306 (t0) cc_final: 0.8919 (t0) REVERT: N 92 GLN cc_start: 0.9456 (tt0) cc_final: 0.9204 (pp30) REVERT: N 96 ARG cc_start: 0.9518 (mtp180) cc_final: 0.9218 (tpp80) REVERT: N 105 LYS cc_start: 0.9693 (mttt) cc_final: 0.9356 (mmmt) REVERT: N 110 GLU cc_start: 0.9371 (mm-30) cc_final: 0.8911 (mm-30) REVERT: L 24 ASP cc_start: 0.8453 (t0) cc_final: 0.8210 (t0) REVERT: L 30 THR cc_start: 0.9174 (p) cc_final: 0.8930 (t) REVERT: L 45 ARG cc_start: 0.9252 (ttt-90) cc_final: 0.8915 (ttm170) REVERT: L 51 TYR cc_start: 0.9125 (m-10) cc_final: 0.8851 (m-80) REVERT: L 53 GLU cc_start: 0.9572 (tt0) cc_final: 0.9163 (tt0) REVERT: L 67 ARG cc_start: 0.9176 (ttp-110) cc_final: 0.8874 (ttp80) REVERT: L 74 GLU cc_start: 0.9391 (tm-30) cc_final: 0.9101 (tm-30) REVERT: L 82 THR cc_start: 0.9265 (m) cc_final: 0.9055 (p) REVERT: L 84 MET cc_start: 0.9531 (mmm) cc_final: 0.9094 (mmt) REVERT: L 91 LYS cc_start: 0.9711 (tttt) cc_final: 0.9322 (mtpt) REVERT: L 97 LEU cc_start: 0.9577 (tp) cc_final: 0.9308 (tp) REVERT: L 98 TYR cc_start: 0.8920 (m-10) cc_final: 0.8224 (m-80) outliers start: 1 outliers final: 0 residues processed: 326 average time/residue: 0.3382 time to fit residues: 163.3960 Evaluate side-chains 257 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN I 68 ASN ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 19118 Z= 0.353 Angle : 0.680 17.281 27114 Z= 0.380 Chirality : 0.042 0.212 3080 Planarity : 0.005 0.047 2419 Dihedral : 29.800 172.878 4880 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 30.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1523 helix: 0.74 (0.22), residues: 558 sheet: -1.98 (0.27), residues: 308 loop : -1.72 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 156 HIS 0.006 0.001 HIS B 310 PHE 0.017 0.002 PHE K 104 TYR 0.014 0.002 TYR G 99 ARG 0.013 0.001 ARG G 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9376 (ttp) cc_final: 0.8986 (tmm) REVERT: A 242 MET cc_start: 0.9365 (ttm) cc_final: 0.9087 (ttp) REVERT: A 265 TYR cc_start: 0.9332 (m-80) cc_final: 0.9001 (m-80) REVERT: A 277 TYR cc_start: 0.9108 (m-80) cc_final: 0.8590 (m-80) REVERT: B 241 TRP cc_start: 0.8310 (m-10) cc_final: 0.7803 (m100) REVERT: C 3884 MET cc_start: 0.2182 (ppp) cc_final: 0.1547 (ttm) REVERT: G 50 GLU cc_start: 0.9573 (tp30) cc_final: 0.9277 (tp30) REVERT: G 60 LEU cc_start: 0.8501 (mm) cc_final: 0.8131 (mm) REVERT: G 70 LEU cc_start: 0.9537 (tp) cc_final: 0.8861 (tp) REVERT: G 84 PHE cc_start: 0.9310 (m-80) cc_final: 0.8862 (m-80) REVERT: G 90 MET cc_start: 0.9660 (mmp) cc_final: 0.9301 (mmm) REVERT: G 97 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8649 (mt-10) REVERT: H 72 TYR cc_start: 0.9373 (m-80) cc_final: 0.9053 (m-80) REVERT: H 88 TYR cc_start: 0.9433 (m-10) cc_final: 0.9080 (m-80) REVERT: I 41 GLU cc_start: 0.9327 (tt0) cc_final: 0.8714 (tp30) REVERT: I 56 GLU cc_start: 0.9437 (tt0) cc_final: 0.8778 (mt-10) REVERT: I 64 GLU cc_start: 0.9629 (tt0) cc_final: 0.9065 (tp30) REVERT: I 83 LEU cc_start: 0.9699 (mp) cc_final: 0.9497 (mt) REVERT: I 91 GLU cc_start: 0.9519 (tm-30) cc_final: 0.9275 (tm-30) REVERT: I 95 LYS cc_start: 0.9655 (tptt) cc_final: 0.9410 (tppt) REVERT: I 112 GLN cc_start: 0.9293 (mp10) cc_final: 0.9060 (mp10) REVERT: J 59 MET cc_start: 0.9859 (mmm) cc_final: 0.9566 (mmm) REVERT: J 65 ASP cc_start: 0.9257 (t70) cc_final: 0.8925 (t0) REVERT: J 76 ARG cc_start: 0.9481 (ttm110) cc_final: 0.9106 (ttm110) REVERT: J 91 ILE cc_start: 0.9809 (mp) cc_final: 0.9537 (tt) REVERT: J 96 ARG cc_start: 0.9451 (mtp180) cc_final: 0.9219 (mmm-85) REVERT: K 50 GLU cc_start: 0.9186 (tp30) cc_final: 0.8676 (tp30) REVERT: K 61 LEU cc_start: 0.9456 (mm) cc_final: 0.9089 (mp) REVERT: K 62 ILE cc_start: 0.9635 (mm) cc_final: 0.9158 (mm) REVERT: K 80 THR cc_start: 0.9607 (p) cc_final: 0.9148 (t) REVERT: K 81 ASP cc_start: 0.8899 (m-30) cc_final: 0.8686 (m-30) REVERT: K 90 MET cc_start: 0.9635 (mmp) cc_final: 0.9390 (mmm) REVERT: K 93 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8210 (tm-30) REVERT: K 115 LYS cc_start: 0.9763 (mmmt) cc_final: 0.9487 (mmmm) REVERT: K 120 MET cc_start: 0.8761 (mtp) cc_final: 0.8314 (mtp) REVERT: K 123 ASP cc_start: 0.8451 (t70) cc_final: 0.8116 (t70) REVERT: K 125 GLN cc_start: 0.9557 (mt0) cc_final: 0.9195 (mm110) REVERT: M 56 GLU cc_start: 0.9404 (mt-10) cc_final: 0.9161 (mt-10) REVERT: M 90 ASP cc_start: 0.9623 (t0) cc_final: 0.9411 (t70) REVERT: M 92 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8366 (mt-10) REVERT: M 94 ASN cc_start: 0.9607 (t0) cc_final: 0.9384 (t0) REVERT: M 112 GLN cc_start: 0.9463 (mm-40) cc_final: 0.9189 (mm110) REVERT: N 30 ARG cc_start: 0.8410 (mtt90) cc_final: 0.7932 (mtt180) REVERT: N 65 ASP cc_start: 0.9238 (t0) cc_final: 0.8915 (t0) REVERT: N 92 GLN cc_start: 0.9515 (tt0) cc_final: 0.9263 (pp30) REVERT: N 96 ARG cc_start: 0.9547 (mtp180) cc_final: 0.9266 (tpp80) REVERT: N 103 LEU cc_start: 0.9849 (mt) cc_final: 0.9480 (mt) REVERT: N 110 GLU cc_start: 0.9375 (mm-30) cc_final: 0.8973 (mm-30) REVERT: L 30 THR cc_start: 0.9165 (p) cc_final: 0.8938 (t) REVERT: L 53 GLU cc_start: 0.9677 (tt0) cc_final: 0.9287 (tt0) REVERT: L 60 VAL cc_start: 0.9793 (t) cc_final: 0.9535 (t) REVERT: L 74 GLU cc_start: 0.9378 (tm-30) cc_final: 0.9112 (tm-30) REVERT: L 84 MET cc_start: 0.9501 (mmm) cc_final: 0.9177 (mmt) REVERT: L 91 LYS cc_start: 0.9738 (tttt) cc_final: 0.9370 (mtpt) REVERT: L 93 GLN cc_start: 0.9655 (tm-30) cc_final: 0.9431 (tm-30) REVERT: L 97 LEU cc_start: 0.9519 (tp) cc_final: 0.8823 (tp) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3020 time to fit residues: 134.4155 Evaluate side-chains 238 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS ** C3906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN I 68 ASN I 104 GLN ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 19118 Z= 0.315 Angle : 0.665 16.123 27114 Z= 0.372 Chirality : 0.042 0.195 3080 Planarity : 0.004 0.040 2419 Dihedral : 29.844 173.657 4880 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 28.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1523 helix: 0.84 (0.22), residues: 557 sheet: -1.90 (0.27), residues: 301 loop : -1.65 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 114 HIS 0.011 0.001 HIS H 75 PHE 0.018 0.002 PHE K 104 TYR 0.018 0.002 TYR L 51 ARG 0.005 0.001 ARG C3903 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9400 (ttp) cc_final: 0.8986 (tmm) REVERT: A 242 MET cc_start: 0.9382 (ttm) cc_final: 0.9094 (mtm) REVERT: A 265 TYR cc_start: 0.9337 (m-80) cc_final: 0.9079 (m-80) REVERT: A 277 TYR cc_start: 0.8921 (m-80) cc_final: 0.8330 (m-80) REVERT: B 241 TRP cc_start: 0.8459 (m-10) cc_final: 0.7845 (m100) REVERT: G 50 GLU cc_start: 0.9569 (tp30) cc_final: 0.9261 (tp30) REVERT: G 60 LEU cc_start: 0.8410 (mm) cc_final: 0.8145 (mm) REVERT: G 61 LEU cc_start: 0.9356 (mm) cc_final: 0.8918 (mm) REVERT: G 70 LEU cc_start: 0.9649 (tp) cc_final: 0.9378 (tp) REVERT: G 84 PHE cc_start: 0.9314 (m-80) cc_final: 0.8846 (m-10) REVERT: G 90 MET cc_start: 0.9680 (mmp) cc_final: 0.9339 (mmm) REVERT: G 97 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8736 (mt-10) REVERT: G 120 MET cc_start: 0.9359 (mtm) cc_final: 0.9122 (mtt) REVERT: H 72 TYR cc_start: 0.9360 (m-80) cc_final: 0.9033 (m-10) REVERT: H 88 TYR cc_start: 0.9397 (m-10) cc_final: 0.9056 (m-80) REVERT: I 41 GLU cc_start: 0.9323 (tt0) cc_final: 0.8665 (tp30) REVERT: I 56 GLU cc_start: 0.9400 (tt0) cc_final: 0.8788 (mt-10) REVERT: I 64 GLU cc_start: 0.9595 (tt0) cc_final: 0.9371 (mp0) REVERT: I 83 LEU cc_start: 0.9700 (mp) cc_final: 0.9481 (mt) REVERT: I 91 GLU cc_start: 0.9503 (tm-30) cc_final: 0.9285 (tm-30) REVERT: I 95 LYS cc_start: 0.9623 (tptt) cc_final: 0.9363 (tppt) REVERT: I 101 THR cc_start: 0.8679 (p) cc_final: 0.8340 (p) REVERT: J 59 MET cc_start: 0.9836 (mmm) cc_final: 0.9591 (mmm) REVERT: J 73 GLU cc_start: 0.9669 (tp30) cc_final: 0.9447 (tp30) REVERT: J 76 ARG cc_start: 0.9395 (ttm110) cc_final: 0.9156 (ttm110) REVERT: J 96 ARG cc_start: 0.9458 (mtp180) cc_final: 0.9248 (mmm-85) REVERT: J 102 GLU cc_start: 0.9237 (tp30) cc_final: 0.8968 (tp30) REVERT: J 103 LEU cc_start: 0.9562 (mt) cc_final: 0.9321 (mt) REVERT: K 41 TYR cc_start: 0.9214 (m-80) cc_final: 0.8678 (m-80) REVERT: K 50 GLU cc_start: 0.9165 (tp30) cc_final: 0.8636 (tp30) REVERT: K 61 LEU cc_start: 0.9379 (mm) cc_final: 0.9020 (mp) REVERT: K 62 ILE cc_start: 0.9645 (mm) cc_final: 0.9252 (mm) REVERT: K 80 THR cc_start: 0.9597 (p) cc_final: 0.9104 (t) REVERT: K 81 ASP cc_start: 0.8932 (m-30) cc_final: 0.8677 (m-30) REVERT: K 90 MET cc_start: 0.9636 (mmp) cc_final: 0.9406 (mmm) REVERT: K 94 GLU cc_start: 0.9270 (tm-30) cc_final: 0.8873 (tm-30) REVERT: K 97 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8625 (mt-10) REVERT: K 115 LYS cc_start: 0.9793 (mmmt) cc_final: 0.9502 (mmmm) REVERT: K 120 MET cc_start: 0.8692 (mtp) cc_final: 0.8207 (mtp) REVERT: K 123 ASP cc_start: 0.8424 (t70) cc_final: 0.7822 (t70) REVERT: K 125 GLN cc_start: 0.9616 (mt0) cc_final: 0.9228 (mm110) REVERT: M 56 GLU cc_start: 0.9401 (mt-10) cc_final: 0.9165 (mt-10) REVERT: M 90 ASP cc_start: 0.9645 (t0) cc_final: 0.9409 (t70) REVERT: M 92 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8329 (mt-10) REVERT: M 94 ASN cc_start: 0.9594 (t0) cc_final: 0.9351 (t0) REVERT: M 112 GLN cc_start: 0.9459 (mm-40) cc_final: 0.9189 (mm110) REVERT: N 30 ARG cc_start: 0.8409 (mtt90) cc_final: 0.8067 (mtt180) REVERT: N 56 MET cc_start: 0.9637 (mmp) cc_final: 0.9383 (mmm) REVERT: N 65 ASP cc_start: 0.9280 (t0) cc_final: 0.8995 (t0) REVERT: N 92 GLN cc_start: 0.9512 (tt0) cc_final: 0.9292 (pp30) REVERT: N 96 ARG cc_start: 0.9553 (mtp180) cc_final: 0.9324 (tpp80) REVERT: N 103 LEU cc_start: 0.9818 (mt) cc_final: 0.9556 (mp) REVERT: N 110 GLU cc_start: 0.9393 (mm-30) cc_final: 0.8963 (mm-30) REVERT: L 30 THR cc_start: 0.9280 (p) cc_final: 0.8999 (t) REVERT: L 43 VAL cc_start: 0.9250 (t) cc_final: 0.9022 (m) REVERT: L 51 TYR cc_start: 0.9273 (m-80) cc_final: 0.8913 (m-80) REVERT: L 53 GLU cc_start: 0.9410 (tt0) cc_final: 0.9070 (tt0) REVERT: L 63 GLU cc_start: 0.9380 (mt-10) cc_final: 0.9177 (mt-10) REVERT: L 68 ASP cc_start: 0.9644 (m-30) cc_final: 0.9302 (t0) REVERT: L 74 GLU cc_start: 0.9394 (tm-30) cc_final: 0.9151 (tm-30) REVERT: L 84 MET cc_start: 0.9495 (mmm) cc_final: 0.9146 (mmt) REVERT: L 93 GLN cc_start: 0.9673 (tm-30) cc_final: 0.9469 (tm-30) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2997 time to fit residues: 132.1695 Evaluate side-chains 237 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 70 optimal weight: 0.0030 chunk 146 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN I 68 ASN ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 19118 Z= 0.382 Angle : 0.704 17.663 27114 Z= 0.395 Chirality : 0.044 0.190 3080 Planarity : 0.005 0.041 2419 Dihedral : 29.890 173.147 4880 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 32.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.21), residues: 1523 helix: 0.51 (0.21), residues: 546 sheet: -1.76 (0.28), residues: 294 loop : -1.75 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 156 HIS 0.007 0.001 HIS A 291 PHE 0.021 0.002 PHE K 104 TYR 0.022 0.002 TYR H 51 ARG 0.005 0.001 ARG N 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9434 (ttp) cc_final: 0.8980 (tmm) REVERT: A 242 MET cc_start: 0.9360 (ttm) cc_final: 0.9069 (mtm) REVERT: A 265 TYR cc_start: 0.9382 (m-80) cc_final: 0.8983 (m-80) REVERT: A 277 TYR cc_start: 0.8927 (m-80) cc_final: 0.8419 (m-80) REVERT: B 241 TRP cc_start: 0.8465 (m-10) cc_final: 0.7884 (m100) REVERT: G 50 GLU cc_start: 0.9569 (tp30) cc_final: 0.9284 (tp30) REVERT: G 60 LEU cc_start: 0.8306 (mm) cc_final: 0.8073 (mm) REVERT: G 61 LEU cc_start: 0.9369 (mm) cc_final: 0.8876 (mm) REVERT: G 70 LEU cc_start: 0.9592 (tp) cc_final: 0.9318 (tp) REVERT: G 84 PHE cc_start: 0.9302 (m-80) cc_final: 0.8825 (m-10) REVERT: G 90 MET cc_start: 0.9673 (mmp) cc_final: 0.9326 (mmm) REVERT: G 97 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8716 (mt-10) REVERT: G 120 MET cc_start: 0.9460 (mtm) cc_final: 0.9131 (mtt) REVERT: G 125 GLN cc_start: 0.9771 (mt0) cc_final: 0.9433 (mm-40) REVERT: H 34 ILE cc_start: 0.9834 (mt) cc_final: 0.9528 (tt) REVERT: H 72 TYR cc_start: 0.9408 (m-80) cc_final: 0.9014 (m-80) REVERT: H 74 GLU cc_start: 0.9579 (tm-30) cc_final: 0.9356 (tm-30) REVERT: H 88 TYR cc_start: 0.9401 (m-10) cc_final: 0.9087 (m-80) REVERT: I 41 GLU cc_start: 0.9344 (tt0) cc_final: 0.8677 (tp30) REVERT: I 56 GLU cc_start: 0.9453 (tt0) cc_final: 0.9001 (mt-10) REVERT: I 64 GLU cc_start: 0.9606 (tt0) cc_final: 0.9371 (mp0) REVERT: I 83 LEU cc_start: 0.9693 (mp) cc_final: 0.9481 (mt) REVERT: I 95 LYS cc_start: 0.9627 (tptt) cc_final: 0.9375 (tppt) REVERT: J 59 MET cc_start: 0.9842 (mmm) cc_final: 0.9611 (mmm) REVERT: J 96 ARG cc_start: 0.9519 (mtp180) cc_final: 0.9266 (mmm-85) REVERT: J 102 GLU cc_start: 0.9220 (tp30) cc_final: 0.8977 (tp30) REVERT: J 103 LEU cc_start: 0.9569 (mt) cc_final: 0.9304 (mt) REVERT: K 41 TYR cc_start: 0.9239 (m-80) cc_final: 0.8983 (m-80) REVERT: K 50 GLU cc_start: 0.9144 (tp30) cc_final: 0.8617 (tp30) REVERT: K 59 GLU cc_start: 0.9312 (pm20) cc_final: 0.9079 (pm20) REVERT: K 61 LEU cc_start: 0.9279 (mm) cc_final: 0.8838 (mp) REVERT: K 80 THR cc_start: 0.9576 (p) cc_final: 0.9211 (t) REVERT: K 81 ASP cc_start: 0.8995 (m-30) cc_final: 0.8788 (m-30) REVERT: K 90 MET cc_start: 0.9673 (mmp) cc_final: 0.9448 (mmm) REVERT: K 94 GLU cc_start: 0.9303 (tm-30) cc_final: 0.8981 (tm-30) REVERT: K 115 LYS cc_start: 0.9783 (mmmt) cc_final: 0.9473 (mmmm) REVERT: K 120 MET cc_start: 0.8699 (mtp) cc_final: 0.8447 (mtp) REVERT: K 123 ASP cc_start: 0.8385 (t70) cc_final: 0.7894 (t70) REVERT: K 125 GLN cc_start: 0.9642 (mt0) cc_final: 0.9268 (mm110) REVERT: M 56 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9179 (mt-10) REVERT: M 90 ASP cc_start: 0.9646 (t0) cc_final: 0.9413 (t70) REVERT: M 112 GLN cc_start: 0.9443 (mm-40) cc_final: 0.9155 (mm110) REVERT: N 30 ARG cc_start: 0.8433 (mtt90) cc_final: 0.7953 (mtt180) REVERT: N 56 MET cc_start: 0.9615 (mmp) cc_final: 0.9352 (mmm) REVERT: N 92 GLN cc_start: 0.9550 (tt0) cc_final: 0.9292 (pp30) REVERT: N 96 ARG cc_start: 0.9573 (mtp180) cc_final: 0.9344 (tpp80) REVERT: N 103 LEU cc_start: 0.9829 (mt) cc_final: 0.9602 (mp) REVERT: N 110 GLU cc_start: 0.9363 (mm-30) cc_final: 0.8966 (mm-30) REVERT: L 53 GLU cc_start: 0.9452 (tt0) cc_final: 0.9041 (tt0) REVERT: L 63 GLU cc_start: 0.9405 (mt-10) cc_final: 0.9186 (mt-10) REVERT: L 74 GLU cc_start: 0.9440 (tm-30) cc_final: 0.9210 (tm-30) REVERT: L 84 MET cc_start: 0.9485 (mmm) cc_final: 0.9035 (mmt) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.3005 time to fit residues: 127.5426 Evaluate side-chains 226 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 50.0000 chunk 172 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 56 optimal weight: 30.0000 chunk 90 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN I 104 GLN ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 19118 Z= 0.318 Angle : 0.674 15.539 27114 Z= 0.378 Chirality : 0.043 0.223 3080 Planarity : 0.004 0.050 2419 Dihedral : 29.901 174.106 4880 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 29.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1523 helix: 0.63 (0.21), residues: 552 sheet: -1.82 (0.27), residues: 306 loop : -1.59 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 156 HIS 0.010 0.001 HIS H 75 PHE 0.025 0.002 PHE K 104 TYR 0.021 0.002 TYR H 51 ARG 0.005 0.001 ARG N 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9429 (ttp) cc_final: 0.8976 (tmm) REVERT: A 224 VAL cc_start: 0.9913 (t) cc_final: 0.9694 (t) REVERT: A 242 MET cc_start: 0.9360 (ttm) cc_final: 0.9052 (mtp) REVERT: A 265 TYR cc_start: 0.9349 (m-80) cc_final: 0.9122 (m-80) REVERT: A 277 TYR cc_start: 0.8945 (m-80) cc_final: 0.8286 (m-80) REVERT: B 241 TRP cc_start: 0.8487 (m-10) cc_final: 0.7796 (m-10) REVERT: G 50 GLU cc_start: 0.9497 (tp30) cc_final: 0.9212 (tp30) REVERT: G 61 LEU cc_start: 0.9323 (mm) cc_final: 0.8852 (mm) REVERT: G 70 LEU cc_start: 0.9648 (tp) cc_final: 0.9363 (tp) REVERT: G 84 PHE cc_start: 0.9323 (m-80) cc_final: 0.8914 (m-10) REVERT: G 90 MET cc_start: 0.9660 (mmp) cc_final: 0.9315 (mmm) REVERT: G 97 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8678 (mt-10) REVERT: G 120 MET cc_start: 0.9422 (mtm) cc_final: 0.8942 (mtt) REVERT: G 125 GLN cc_start: 0.9762 (mt0) cc_final: 0.9438 (mm-40) REVERT: H 34 ILE cc_start: 0.9825 (mt) cc_final: 0.9488 (tt) REVERT: H 72 TYR cc_start: 0.9359 (m-80) cc_final: 0.9040 (m-10) REVERT: H 88 TYR cc_start: 0.9378 (m-10) cc_final: 0.9037 (m-80) REVERT: H 93 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8949 (tm-30) REVERT: I 41 GLU cc_start: 0.9341 (tt0) cc_final: 0.8672 (tp30) REVERT: I 56 GLU cc_start: 0.9486 (tt0) cc_final: 0.9058 (mt-10) REVERT: I 64 GLU cc_start: 0.9609 (tt0) cc_final: 0.9352 (pt0) REVERT: I 83 LEU cc_start: 0.9689 (mp) cc_final: 0.9458 (mt) REVERT: I 95 LYS cc_start: 0.9607 (tptt) cc_final: 0.9349 (tppt) REVERT: I 112 GLN cc_start: 0.9397 (mp10) cc_final: 0.9192 (mp10) REVERT: J 59 MET cc_start: 0.9837 (mmm) cc_final: 0.9594 (mmm) REVERT: J 65 ASP cc_start: 0.9077 (t70) cc_final: 0.8789 (t0) REVERT: J 96 ARG cc_start: 0.9495 (mtp180) cc_final: 0.9247 (mmm-85) REVERT: J 102 GLU cc_start: 0.9197 (tp30) cc_final: 0.8968 (tp30) REVERT: J 103 LEU cc_start: 0.9572 (mt) cc_final: 0.9329 (mt) REVERT: K 41 TYR cc_start: 0.9316 (m-80) cc_final: 0.8555 (m-80) REVERT: K 50 GLU cc_start: 0.9172 (tp30) cc_final: 0.8635 (tp30) REVERT: K 59 GLU cc_start: 0.9279 (pm20) cc_final: 0.9014 (pm20) REVERT: K 61 LEU cc_start: 0.9186 (mm) cc_final: 0.8820 (mp) REVERT: K 80 THR cc_start: 0.9573 (p) cc_final: 0.9141 (t) REVERT: K 81 ASP cc_start: 0.9025 (m-30) cc_final: 0.8817 (m-30) REVERT: K 90 MET cc_start: 0.9671 (mmp) cc_final: 0.9455 (mmm) REVERT: K 94 GLU cc_start: 0.9314 (tm-30) cc_final: 0.8947 (tm-30) REVERT: K 115 LYS cc_start: 0.9795 (mmmt) cc_final: 0.9513 (mmmm) REVERT: K 120 MET cc_start: 0.8672 (mtp) cc_final: 0.8442 (mtp) REVERT: K 123 ASP cc_start: 0.8541 (t70) cc_final: 0.7906 (t70) REVERT: M 90 ASP cc_start: 0.9634 (t0) cc_final: 0.9272 (t70) REVERT: M 94 ASN cc_start: 0.9629 (t0) cc_final: 0.9422 (m-40) REVERT: M 112 GLN cc_start: 0.9459 (mm-40) cc_final: 0.9197 (mm110) REVERT: N 30 ARG cc_start: 0.8402 (mtt90) cc_final: 0.7923 (mtt180) REVERT: N 39 TYR cc_start: 0.9163 (t80) cc_final: 0.8960 (t80) REVERT: N 56 MET cc_start: 0.9612 (mmp) cc_final: 0.9339 (mmm) REVERT: N 92 GLN cc_start: 0.9522 (tt0) cc_final: 0.9291 (pp30) REVERT: N 96 ARG cc_start: 0.9557 (mtp180) cc_final: 0.9335 (tpp80) REVERT: N 110 GLU cc_start: 0.9390 (mm-30) cc_final: 0.8967 (mm-30) REVERT: L 49 LEU cc_start: 0.9589 (mm) cc_final: 0.9035 (mm) REVERT: L 53 GLU cc_start: 0.9439 (tt0) cc_final: 0.9210 (mt-10) REVERT: L 63 GLU cc_start: 0.9429 (mt-10) cc_final: 0.9221 (mt-10) REVERT: L 74 GLU cc_start: 0.9443 (tm-30) cc_final: 0.9221 (tm-30) REVERT: L 84 MET cc_start: 0.9494 (mmm) cc_final: 0.9050 (mmt) REVERT: L 91 LYS cc_start: 0.9586 (tttt) cc_final: 0.9376 (mtpt) REVERT: L 93 GLN cc_start: 0.9610 (tm-30) cc_final: 0.9370 (tm-30) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.3046 time to fit residues: 131.3233 Evaluate side-chains 232 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 19118 Z= 0.301 Angle : 0.669 14.846 27114 Z= 0.375 Chirality : 0.042 0.206 3080 Planarity : 0.004 0.044 2419 Dihedral : 29.871 174.739 4880 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 28.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1523 helix: 0.77 (0.21), residues: 546 sheet: -1.63 (0.28), residues: 294 loop : -1.59 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 156 HIS 0.004 0.001 HIS L 75 PHE 0.020 0.001 PHE G 67 TYR 0.016 0.001 TYR G 54 ARG 0.007 0.000 ARG N 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9413 (ttp) cc_final: 0.8977 (tmm) REVERT: A 265 TYR cc_start: 0.9347 (m-80) cc_final: 0.9103 (m-80) REVERT: A 273 GLN cc_start: 0.7974 (pp30) cc_final: 0.7435 (pp30) REVERT: A 277 TYR cc_start: 0.8949 (m-80) cc_final: 0.8142 (m-80) REVERT: B 241 TRP cc_start: 0.8517 (m-10) cc_final: 0.7886 (m-10) REVERT: G 50 GLU cc_start: 0.9509 (tp30) cc_final: 0.9232 (tp30) REVERT: G 61 LEU cc_start: 0.9323 (mm) cc_final: 0.8843 (mm) REVERT: G 70 LEU cc_start: 0.9658 (tp) cc_final: 0.9369 (tp) REVERT: G 84 PHE cc_start: 0.9354 (m-80) cc_final: 0.8959 (m-10) REVERT: G 90 MET cc_start: 0.9645 (mmp) cc_final: 0.9333 (mmm) REVERT: G 120 MET cc_start: 0.9288 (mtm) cc_final: 0.9027 (mtt) REVERT: H 72 TYR cc_start: 0.9420 (m-80) cc_final: 0.8977 (m-80) REVERT: H 88 TYR cc_start: 0.9359 (m-10) cc_final: 0.9006 (m-80) REVERT: H 93 GLN cc_start: 0.9184 (tm-30) cc_final: 0.8938 (tm-30) REVERT: I 41 GLU cc_start: 0.9319 (tt0) cc_final: 0.8747 (tm-30) REVERT: I 56 GLU cc_start: 0.9458 (tt0) cc_final: 0.8981 (mt-10) REVERT: I 64 GLU cc_start: 0.9596 (tt0) cc_final: 0.9345 (pt0) REVERT: I 83 LEU cc_start: 0.9687 (mp) cc_final: 0.9447 (mt) REVERT: I 95 LYS cc_start: 0.9600 (tptt) cc_final: 0.9336 (tppt) REVERT: I 112 GLN cc_start: 0.9431 (mp10) cc_final: 0.9186 (mp10) REVERT: J 59 MET cc_start: 0.9839 (mmm) cc_final: 0.9583 (mmm) REVERT: J 65 ASP cc_start: 0.9080 (t70) cc_final: 0.8785 (t0) REVERT: J 77 LEU cc_start: 0.9846 (tp) cc_final: 0.9614 (tt) REVERT: J 92 GLN cc_start: 0.9546 (pt0) cc_final: 0.9306 (pp30) REVERT: J 96 ARG cc_start: 0.9472 (mtp180) cc_final: 0.9205 (mmm-85) REVERT: J 102 GLU cc_start: 0.9181 (tp30) cc_final: 0.8967 (tp30) REVERT: J 103 LEU cc_start: 0.9577 (mt) cc_final: 0.9337 (mt) REVERT: K 41 TYR cc_start: 0.9317 (m-80) cc_final: 0.8554 (m-80) REVERT: K 50 GLU cc_start: 0.9153 (tp30) cc_final: 0.8201 (tp30) REVERT: K 54 TYR cc_start: 0.9220 (m-10) cc_final: 0.8070 (m-10) REVERT: K 59 GLU cc_start: 0.9319 (pm20) cc_final: 0.9064 (pm20) REVERT: K 61 LEU cc_start: 0.9051 (mm) cc_final: 0.8532 (mp) REVERT: K 80 THR cc_start: 0.9567 (p) cc_final: 0.9154 (t) REVERT: K 81 ASP cc_start: 0.9035 (m-30) cc_final: 0.8834 (m-30) REVERT: K 94 GLU cc_start: 0.9301 (tm-30) cc_final: 0.8948 (tm-30) REVERT: K 115 LYS cc_start: 0.9804 (mmmt) cc_final: 0.9509 (mmmm) REVERT: K 120 MET cc_start: 0.8671 (mtp) cc_final: 0.8436 (mtp) REVERT: K 123 ASP cc_start: 0.8540 (t70) cc_final: 0.7901 (t70) REVERT: M 90 ASP cc_start: 0.9651 (t0) cc_final: 0.9174 (t70) REVERT: M 94 ASN cc_start: 0.9626 (t0) cc_final: 0.9399 (m-40) REVERT: M 112 GLN cc_start: 0.9465 (mm-40) cc_final: 0.9192 (mm110) REVERT: N 30 ARG cc_start: 0.8354 (mtt90) cc_final: 0.7876 (mtt180) REVERT: N 56 MET cc_start: 0.9599 (mmp) cc_final: 0.9337 (mmm) REVERT: N 65 ASP cc_start: 0.9409 (t70) cc_final: 0.9198 (t0) REVERT: N 92 GLN cc_start: 0.9515 (tt0) cc_final: 0.9301 (pp30) REVERT: N 96 ARG cc_start: 0.9551 (mtp180) cc_final: 0.9317 (tpp80) REVERT: N 110 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8944 (mm-30) REVERT: L 43 VAL cc_start: 0.9004 (t) cc_final: 0.8695 (t) REVERT: L 49 LEU cc_start: 0.9600 (mm) cc_final: 0.9040 (mm) REVERT: L 53 GLU cc_start: 0.9372 (tt0) cc_final: 0.9122 (mt-10) REVERT: L 63 GLU cc_start: 0.9446 (mt-10) cc_final: 0.9229 (mt-10) REVERT: L 74 GLU cc_start: 0.9448 (tm-30) cc_final: 0.9224 (tm-30) REVERT: L 84 MET cc_start: 0.9487 (mmm) cc_final: 0.9152 (mmt) REVERT: L 91 LYS cc_start: 0.9581 (tttt) cc_final: 0.9370 (mtpt) REVERT: L 93 GLN cc_start: 0.9658 (tm-30) cc_final: 0.9408 (tm-30) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.3009 time to fit residues: 129.9525 Evaluate side-chains 233 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 51 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 109 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19118 Z= 0.235 Angle : 0.650 14.759 27114 Z= 0.362 Chirality : 0.042 0.242 3080 Planarity : 0.004 0.046 2419 Dihedral : 29.775 176.139 4880 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 24.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1523 helix: 0.81 (0.21), residues: 556 sheet: -1.63 (0.28), residues: 298 loop : -1.40 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 156 HIS 0.004 0.001 HIS H 75 PHE 0.019 0.001 PHE N 62 TYR 0.033 0.001 TYR I 50 ARG 0.007 0.000 ARG N 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9397 (ttp) cc_final: 0.8964 (tmm) REVERT: A 242 MET cc_start: 0.9246 (ttm) cc_final: 0.8968 (ttp) REVERT: A 265 TYR cc_start: 0.9347 (m-80) cc_final: 0.9120 (m-80) REVERT: A 273 GLN cc_start: 0.7869 (pp30) cc_final: 0.7411 (pp30) REVERT: A 277 TYR cc_start: 0.8910 (m-80) cc_final: 0.8096 (m-80) REVERT: B 241 TRP cc_start: 0.8535 (m-10) cc_final: 0.7866 (m-10) REVERT: G 50 GLU cc_start: 0.9493 (tp30) cc_final: 0.9215 (tp30) REVERT: G 61 LEU cc_start: 0.9329 (mm) cc_final: 0.8841 (mm) REVERT: G 70 LEU cc_start: 0.9689 (tp) cc_final: 0.9428 (tp) REVERT: G 73 GLU cc_start: 0.9148 (tt0) cc_final: 0.8758 (mt-10) REVERT: G 84 PHE cc_start: 0.9359 (m-80) cc_final: 0.8917 (m-10) REVERT: G 90 MET cc_start: 0.9621 (mmp) cc_final: 0.9272 (mmm) REVERT: G 120 MET cc_start: 0.9373 (mtm) cc_final: 0.9014 (mtt) REVERT: G 125 GLN cc_start: 0.9741 (mt0) cc_final: 0.9430 (mm-40) REVERT: H 22 LEU cc_start: 0.9080 (mm) cc_final: 0.8734 (mm) REVERT: H 34 ILE cc_start: 0.9833 (mt) cc_final: 0.9483 (tt) REVERT: H 72 TYR cc_start: 0.9427 (m-80) cc_final: 0.9002 (m-80) REVERT: H 88 TYR cc_start: 0.9341 (m-10) cc_final: 0.8976 (m-80) REVERT: H 93 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8897 (tm-30) REVERT: I 41 GLU cc_start: 0.9304 (tt0) cc_final: 0.8712 (tm-30) REVERT: I 56 GLU cc_start: 0.9425 (tt0) cc_final: 0.8938 (mt-10) REVERT: I 64 GLU cc_start: 0.9589 (tt0) cc_final: 0.9311 (pt0) REVERT: I 83 LEU cc_start: 0.9700 (mp) cc_final: 0.9242 (mt) REVERT: I 95 LYS cc_start: 0.9573 (tptt) cc_final: 0.9306 (tppt) REVERT: I 112 GLN cc_start: 0.9555 (mp10) cc_final: 0.9342 (mp10) REVERT: J 30 ARG cc_start: 0.7846 (ptp-110) cc_final: 0.7105 (mtm-85) REVERT: J 59 MET cc_start: 0.9844 (mmm) cc_final: 0.9573 (mmp) REVERT: J 65 ASP cc_start: 0.9067 (t70) cc_final: 0.8758 (t0) REVERT: J 77 LEU cc_start: 0.9837 (tp) cc_final: 0.9592 (tt) REVERT: J 92 GLN cc_start: 0.9604 (pt0) cc_final: 0.9323 (pp30) REVERT: J 97 LEU cc_start: 0.9695 (mm) cc_final: 0.9440 (mm) REVERT: J 102 GLU cc_start: 0.9162 (tp30) cc_final: 0.8961 (tp30) REVERT: J 103 LEU cc_start: 0.9584 (mt) cc_final: 0.9359 (mt) REVERT: K 41 TYR cc_start: 0.9331 (m-80) cc_final: 0.8558 (m-80) REVERT: K 50 GLU cc_start: 0.9173 (tp30) cc_final: 0.8287 (tp30) REVERT: K 54 TYR cc_start: 0.9185 (m-10) cc_final: 0.8098 (m-10) REVERT: K 59 GLU cc_start: 0.9367 (pm20) cc_final: 0.9096 (pm20) REVERT: K 71 VAL cc_start: 0.9726 (t) cc_final: 0.9516 (t) REVERT: K 80 THR cc_start: 0.9555 (p) cc_final: 0.9173 (t) REVERT: K 81 ASP cc_start: 0.9015 (m-30) cc_final: 0.8766 (m-30) REVERT: K 94 GLU cc_start: 0.9315 (tm-30) cc_final: 0.8891 (tm-30) REVERT: K 110 CYS cc_start: 0.9407 (t) cc_final: 0.9197 (t) REVERT: K 115 LYS cc_start: 0.9810 (mmmt) cc_final: 0.9496 (mmmm) REVERT: K 120 MET cc_start: 0.8632 (mtp) cc_final: 0.8378 (mtp) REVERT: K 123 ASP cc_start: 0.8495 (t70) cc_final: 0.7864 (t70) REVERT: K 125 GLN cc_start: 0.9590 (mm-40) cc_final: 0.9161 (mm110) REVERT: M 90 ASP cc_start: 0.9638 (t0) cc_final: 0.9162 (t70) REVERT: M 92 GLU cc_start: 0.9254 (tt0) cc_final: 0.8975 (tt0) REVERT: M 94 ASN cc_start: 0.9637 (t0) cc_final: 0.9428 (m-40) REVERT: M 112 GLN cc_start: 0.9461 (mm-40) cc_final: 0.8594 (tm-30) REVERT: N 30 ARG cc_start: 0.8222 (mtt90) cc_final: 0.8003 (mtt180) REVERT: N 39 TYR cc_start: 0.9158 (t80) cc_final: 0.8957 (t80) REVERT: N 56 MET cc_start: 0.9611 (mmp) cc_final: 0.9360 (mmt) REVERT: N 65 ASP cc_start: 0.9335 (t70) cc_final: 0.9092 (t0) REVERT: N 92 GLN cc_start: 0.9484 (tt0) cc_final: 0.9268 (pp30) REVERT: N 96 ARG cc_start: 0.9536 (mtp180) cc_final: 0.9309 (tpp80) REVERT: N 102 GLU cc_start: 0.9477 (pm20) cc_final: 0.8798 (tp30) REVERT: N 103 LEU cc_start: 0.9860 (mt) cc_final: 0.9571 (mt) REVERT: N 110 GLU cc_start: 0.9387 (mm-30) cc_final: 0.8913 (mm-30) REVERT: L 51 TYR cc_start: 0.8922 (m-80) cc_final: 0.8681 (m-80) REVERT: L 63 GLU cc_start: 0.9464 (mt-10) cc_final: 0.9233 (tp30) REVERT: L 74 GLU cc_start: 0.9404 (tm-30) cc_final: 0.9164 (tm-30) REVERT: L 84 MET cc_start: 0.9504 (mmm) cc_final: 0.9118 (mmt) REVERT: L 91 LYS cc_start: 0.9543 (tttt) cc_final: 0.9312 (mtpt) REVERT: L 93 GLN cc_start: 0.9683 (tm-30) cc_final: 0.9468 (tm-30) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.2862 time to fit residues: 124.0908 Evaluate side-chains 229 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 19118 Z= 0.396 Angle : 0.722 16.947 27114 Z= 0.404 Chirality : 0.044 0.220 3080 Planarity : 0.005 0.043 2419 Dihedral : 29.826 174.698 4880 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 34.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.21), residues: 1523 helix: 0.30 (0.21), residues: 558 sheet: -1.67 (0.28), residues: 300 loop : -1.50 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 156 HIS 0.009 0.001 HIS B 128 PHE 0.025 0.002 PHE G 67 TYR 0.032 0.002 TYR I 50 ARG 0.016 0.001 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9414 (ttp) cc_final: 0.8940 (tmm) REVERT: A 242 MET cc_start: 0.9193 (ttm) cc_final: 0.8765 (mtm) REVERT: A 265 TYR cc_start: 0.9371 (m-80) cc_final: 0.9114 (m-80) REVERT: A 273 GLN cc_start: 0.7945 (pp30) cc_final: 0.7568 (pp30) REVERT: A 277 TYR cc_start: 0.8909 (m-80) cc_final: 0.8152 (m-80) REVERT: B 241 TRP cc_start: 0.8598 (m-10) cc_final: 0.7948 (m-10) REVERT: C 3948 ILE cc_start: 0.3934 (mm) cc_final: 0.3721 (mm) REVERT: G 50 GLU cc_start: 0.9513 (tp30) cc_final: 0.9247 (tp30) REVERT: G 61 LEU cc_start: 0.9467 (mm) cc_final: 0.9162 (mm) REVERT: G 65 LEU cc_start: 0.9783 (mm) cc_final: 0.9481 (mm) REVERT: G 70 LEU cc_start: 0.9648 (tp) cc_final: 0.9368 (tp) REVERT: G 84 PHE cc_start: 0.9369 (m-80) cc_final: 0.8918 (m-10) REVERT: G 90 MET cc_start: 0.9636 (mmp) cc_final: 0.9328 (mmm) REVERT: G 120 MET cc_start: 0.9432 (mtm) cc_final: 0.8918 (mtt) REVERT: H 34 ILE cc_start: 0.9853 (mt) cc_final: 0.9552 (tt) REVERT: H 72 TYR cc_start: 0.9469 (m-80) cc_final: 0.9138 (m-10) REVERT: H 88 TYR cc_start: 0.9405 (m-10) cc_final: 0.9051 (m-80) REVERT: H 93 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8898 (tm-30) REVERT: I 41 GLU cc_start: 0.9334 (tt0) cc_final: 0.8674 (tp30) REVERT: I 64 GLU cc_start: 0.9585 (tt0) cc_final: 0.9317 (pt0) REVERT: I 83 LEU cc_start: 0.9711 (mp) cc_final: 0.9367 (mt) REVERT: I 95 LYS cc_start: 0.9602 (tptt) cc_final: 0.9356 (tppt) REVERT: I 112 GLN cc_start: 0.9523 (mp10) cc_final: 0.9302 (mp10) REVERT: J 59 MET cc_start: 0.9860 (mmm) cc_final: 0.9599 (mmm) REVERT: J 77 LEU cc_start: 0.9783 (tp) cc_final: 0.9569 (tp) REVERT: J 92 GLN cc_start: 0.9637 (pt0) cc_final: 0.9381 (pp30) REVERT: J 103 LEU cc_start: 0.9494 (mt) cc_final: 0.9263 (mt) REVERT: K 41 TYR cc_start: 0.9306 (m-80) cc_final: 0.8531 (m-80) REVERT: K 50 GLU cc_start: 0.9177 (tp30) cc_final: 0.8643 (tp30) REVERT: K 59 GLU cc_start: 0.9350 (pm20) cc_final: 0.9034 (pm20) REVERT: K 80 THR cc_start: 0.9587 (p) cc_final: 0.9168 (t) REVERT: K 81 ASP cc_start: 0.9041 (m-30) cc_final: 0.8622 (m-30) REVERT: K 90 MET cc_start: 0.9698 (mmp) cc_final: 0.9478 (mmm) REVERT: K 94 GLU cc_start: 0.9339 (tm-30) cc_final: 0.9030 (tm-30) REVERT: K 115 LYS cc_start: 0.9793 (mmmt) cc_final: 0.9479 (mmmm) REVERT: K 120 MET cc_start: 0.8728 (mtp) cc_final: 0.8366 (mtp) REVERT: K 123 ASP cc_start: 0.8572 (t70) cc_final: 0.7834 (t70) REVERT: M 90 ASP cc_start: 0.9637 (t0) cc_final: 0.9039 (t0) REVERT: M 94 ASN cc_start: 0.9658 (t0) cc_final: 0.9407 (m-40) REVERT: M 112 GLN cc_start: 0.9457 (mm-40) cc_final: 0.9189 (mm110) REVERT: N 39 TYR cc_start: 0.9201 (t80) cc_final: 0.8951 (t80) REVERT: N 56 MET cc_start: 0.9599 (mmp) cc_final: 0.9354 (mmm) REVERT: N 65 ASP cc_start: 0.9352 (t70) cc_final: 0.9109 (t0) REVERT: N 92 GLN cc_start: 0.9539 (tt0) cc_final: 0.9295 (pp30) REVERT: N 96 ARG cc_start: 0.9564 (mtp180) cc_final: 0.9335 (tpp80) REVERT: N 102 GLU cc_start: 0.9480 (pm20) cc_final: 0.8866 (tp30) REVERT: N 110 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9017 (mm-30) REVERT: L 49 LEU cc_start: 0.9563 (mm) cc_final: 0.9104 (mm) REVERT: L 53 GLU cc_start: 0.9585 (tt0) cc_final: 0.9220 (mt-10) REVERT: L 74 GLU cc_start: 0.9470 (tm-30) cc_final: 0.9263 (tm-30) REVERT: L 84 MET cc_start: 0.9479 (mmm) cc_final: 0.9008 (mmt) REVERT: L 85 ASP cc_start: 0.9454 (m-30) cc_final: 0.8504 (t70) REVERT: L 93 GLN cc_start: 0.9676 (tm-30) cc_final: 0.9392 (tm-30) REVERT: L 97 LEU cc_start: 0.9165 (tp) cc_final: 0.8028 (tp) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2924 time to fit residues: 117.0094 Evaluate side-chains 213 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19118 Z= 0.198 Angle : 0.652 12.475 27114 Z= 0.362 Chirality : 0.043 0.192 3080 Planarity : 0.004 0.049 2419 Dihedral : 29.763 177.112 4880 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.21), residues: 1523 helix: 0.72 (0.22), residues: 559 sheet: -1.55 (0.28), residues: 300 loop : -1.24 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 156 HIS 0.007 0.001 HIS B 128 PHE 0.022 0.001 PHE G 67 TYR 0.024 0.001 TYR I 50 ARG 0.008 0.000 ARG N 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9372 (ttp) cc_final: 0.8889 (tmm) REVERT: A 242 MET cc_start: 0.9278 (ttm) cc_final: 0.8998 (ttp) REVERT: A 265 TYR cc_start: 0.9330 (m-80) cc_final: 0.9111 (m-80) REVERT: A 277 TYR cc_start: 0.8852 (m-80) cc_final: 0.8391 (m-10) REVERT: B 241 TRP cc_start: 0.8539 (m-10) cc_final: 0.7799 (m-10) REVERT: G 50 GLU cc_start: 0.9485 (tp30) cc_final: 0.9168 (tp30) REVERT: G 60 LEU cc_start: 0.9008 (mt) cc_final: 0.8289 (mm) REVERT: G 84 PHE cc_start: 0.9368 (m-80) cc_final: 0.8973 (m-10) REVERT: G 90 MET cc_start: 0.9611 (mmp) cc_final: 0.9300 (mmm) REVERT: G 97 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8174 (mt-10) REVERT: G 120 MET cc_start: 0.9213 (mtm) cc_final: 0.8897 (mtt) REVERT: H 34 ILE cc_start: 0.9821 (mt) cc_final: 0.9368 (tt) REVERT: H 53 GLU cc_start: 0.9783 (mm-30) cc_final: 0.9505 (tt0) REVERT: H 72 TYR cc_start: 0.9460 (m-80) cc_final: 0.9202 (m-80) REVERT: H 88 TYR cc_start: 0.9334 (m-10) cc_final: 0.8931 (m-80) REVERT: H 93 GLN cc_start: 0.9192 (tm-30) cc_final: 0.8886 (tm-30) REVERT: I 41 GLU cc_start: 0.9332 (tt0) cc_final: 0.8801 (tm-30) REVERT: I 56 GLU cc_start: 0.9459 (tt0) cc_final: 0.8960 (mt-10) REVERT: I 64 GLU cc_start: 0.9576 (tt0) cc_final: 0.9327 (pt0) REVERT: I 83 LEU cc_start: 0.9692 (mp) cc_final: 0.9153 (mp) REVERT: I 92 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8939 (mt-10) REVERT: I 95 LYS cc_start: 0.9548 (tptt) cc_final: 0.9269 (tppt) REVERT: I 112 GLN cc_start: 0.9501 (mp10) cc_final: 0.9287 (mp10) REVERT: J 59 MET cc_start: 0.9839 (mmm) cc_final: 0.9533 (mmp) REVERT: J 92 GLN cc_start: 0.9614 (pt0) cc_final: 0.9363 (pp30) REVERT: K 41 TYR cc_start: 0.9318 (m-80) cc_final: 0.8585 (m-80) REVERT: K 50 GLU cc_start: 0.9153 (tp30) cc_final: 0.8297 (tp30) REVERT: K 54 TYR cc_start: 0.9186 (m-10) cc_final: 0.8165 (m-10) REVERT: K 56 LYS cc_start: 0.9702 (mmmm) cc_final: 0.9321 (ptpp) REVERT: K 59 GLU cc_start: 0.9405 (pm20) cc_final: 0.9156 (pm20) REVERT: K 80 THR cc_start: 0.9536 (p) cc_final: 0.9094 (t) REVERT: K 81 ASP cc_start: 0.8998 (m-30) cc_final: 0.8725 (m-30) REVERT: K 90 MET cc_start: 0.9664 (mmp) cc_final: 0.9447 (mmm) REVERT: K 94 GLU cc_start: 0.9318 (tm-30) cc_final: 0.9111 (tm-30) REVERT: K 110 CYS cc_start: 0.9439 (t) cc_final: 0.9233 (t) REVERT: K 115 LYS cc_start: 0.9815 (mmmt) cc_final: 0.9502 (mmmm) REVERT: K 120 MET cc_start: 0.8500 (mtp) cc_final: 0.7913 (mtp) REVERT: K 123 ASP cc_start: 0.8395 (t70) cc_final: 0.7737 (t70) REVERT: K 125 GLN cc_start: 0.9575 (mm110) cc_final: 0.9194 (mm110) REVERT: M 38 ASN cc_start: 0.9336 (m110) cc_final: 0.8814 (t0) REVERT: M 90 ASP cc_start: 0.9609 (t0) cc_final: 0.9102 (t70) REVERT: M 94 ASN cc_start: 0.9641 (t0) cc_final: 0.9426 (m-40) REVERT: M 112 GLN cc_start: 0.9469 (mm-40) cc_final: 0.8579 (tm-30) REVERT: N 39 TYR cc_start: 0.9113 (t80) cc_final: 0.8896 (t80) REVERT: N 65 ASP cc_start: 0.9341 (t70) cc_final: 0.9093 (t0) REVERT: N 92 GLN cc_start: 0.9460 (tt0) cc_final: 0.9246 (pp30) REVERT: N 96 ARG cc_start: 0.9531 (mtp180) cc_final: 0.9278 (tpp80) REVERT: N 110 GLU cc_start: 0.9380 (mm-30) cc_final: 0.8901 (mm-30) REVERT: L 30 THR cc_start: 0.8936 (p) cc_final: 0.8648 (t) REVERT: L 51 TYR cc_start: 0.8842 (m-80) cc_final: 0.8581 (m-80) REVERT: L 53 GLU cc_start: 0.9549 (tt0) cc_final: 0.9221 (tt0) REVERT: L 63 GLU cc_start: 0.9509 (tp30) cc_final: 0.9189 (tp30) REVERT: L 74 GLU cc_start: 0.9388 (tm-30) cc_final: 0.9082 (tm-30) REVERT: L 84 MET cc_start: 0.9498 (mmm) cc_final: 0.9097 (mmt) REVERT: L 97 LEU cc_start: 0.9437 (tp) cc_final: 0.8263 (tp) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.2929 time to fit residues: 122.2698 Evaluate side-chains 239 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 59 optimal weight: 30.0000 chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS N 60 ASN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.040508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.027216 restraints weight = 174206.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.028529 restraints weight = 85245.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.029390 restraints weight = 50996.728| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 19118 Z= 0.310 Angle : 0.677 15.702 27114 Z= 0.378 Chirality : 0.042 0.191 3080 Planarity : 0.004 0.046 2419 Dihedral : 29.679 175.791 4880 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 28.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1523 helix: 0.64 (0.22), residues: 555 sheet: -1.58 (0.29), residues: 301 loop : -1.31 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 156 HIS 0.009 0.001 HIS B 128 PHE 0.024 0.002 PHE G 67 TYR 0.030 0.002 TYR I 50 ARG 0.007 0.001 ARG B 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3437.57 seconds wall clock time: 63 minutes 31.50 seconds (3811.50 seconds total)