Starting phenix.real_space_refine on Sat Dec 16 02:55:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pww_20513/12_2023/6pww_20513_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pww_20513/12_2023/6pww_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_20513/12_2023/6pww_20513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pww_20513/12_2023/6pww_20513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pww_20513/12_2023/6pww_20513_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pww_20513/12_2023/6pww_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 10.18, per 1000 atoms: 0.56 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: 9.45 Conformation dependent library (CDL) restraints added in 2.1 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: 9.66 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: 8.17 Time building geometry restraints manager: 9.99 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.010 Extract box with map and model: 9.620 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 62.000 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.110 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.250 ------------------------------------------------------------------------------- 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 : 1.629 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 outliers start: 16 outliers final: 4 residues processed: 370 average time/residue: 0.3551 time to fit residues: 186.4517 Evaluate side-chains 238 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 234 time to evaluate : 1.533 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1509 time to fit residues: 3.0664 ------------------------------------------------------------------------------- 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: 0.8980 chunk 72 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 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: 0.7818 ------------------------------------------------------------------------------- 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 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** ** 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1740 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= 0.193 Angle : 0.627 12.455 27114 Z= 0.351 Chirality : 0.042 0.271 3080 Planarity : 0.004 0.045 2419 Dihedral : 29.819 174.367 4880 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.23 % Allowed : 4.44 % Favored : 95.33 % 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: 0.69 (0.21), residues: 574 sheet: -2.01 (0.26), residues: 306 loop : -1.89 (0.23), residues: 643 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 0.027 0.002 PHE K 67 TYR 0.026 0.002 TYR H 98 ARG 0.010 0.001 ARG C3821 *********************** 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 327 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 324 time to evaluate : 1.667 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 outliers start: 3 outliers final: 1 residues processed: 325 average time/residue: 0.3377 time to fit residues: 161.5886 Evaluate side-chains 239 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 1.709 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2045 time to fit residues: 2.4911 ------------------------------------------------------------------------------- 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: 0.9990 chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 110 optimal weight: 0.0970 chunk 44 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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** B 310 HIS ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** H 75 HIS ** 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 79 HIS ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19118 Z= 0.234 Angle : 0.630 13.421 27114 Z= 0.353 Chirality : 0.041 0.265 3080 Planarity : 0.004 0.041 2419 Dihedral : 29.605 174.487 4880 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.33 % 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: -1.12 (0.21), residues: 1523 helix: 0.94 (0.22), residues: 556 sheet: -1.87 (0.26), residues: 325 loop : -1.58 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 156 HIS 0.009 0.001 HIS B 310 PHE 0.022 0.001 PHE K 104 TYR 0.041 0.002 TYR H 88 ARG 0.006 0.001 ARG M 32 *********************** 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 301 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 300 time to evaluate : 1.625 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 outliers start: 1 outliers final: 1 residues processed: 300 average time/residue: 0.3137 time to fit residues: 140.5826 Evaluate side-chains 222 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 1.508 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1957 time to fit residues: 2.1744 ------------------------------------------------------------------------------- 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: 5.9990 chunk 121 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 GLN ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 HIS K 125 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 64 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 19118 Z= 0.272 Angle : 0.646 13.129 27114 Z= 0.363 Chirality : 0.041 0.201 3080 Planarity : 0.004 0.046 2419 Dihedral : 29.569 174.920 4880 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 25.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: -1.10 (0.21), residues: 1523 helix: 0.79 (0.21), residues: 559 sheet: -1.72 (0.27), residues: 319 loop : -1.51 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 114 HIS 0.007 0.001 HIS H 75 PHE 0.023 0.002 PHE K 104 TYR 0.028 0.002 TYR H 88 ARG 0.006 0.001 ARG J 76 *********************** 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 282 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.631 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 outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2933 time to fit residues: 126.9306 Evaluate side-chains 219 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.688 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1510 ------------------------------------------------------------------------------- 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: 8.9990 chunk 2 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 57 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** K 125 GLN ** 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** L 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 19118 Z= 0.467 Angle : 0.781 18.691 27114 Z= 0.434 Chirality : 0.046 0.197 3080 Planarity : 0.006 0.055 2419 Dihedral : 29.846 172.535 4880 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 40.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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: -1.74 (0.20), residues: 1523 helix: 0.02 (0.20), residues: 553 sheet: -1.87 (0.27), residues: 311 loop : -1.74 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 156 HIS 0.008 0.002 HIS L 75 PHE 0.027 0.002 PHE H 61 TYR 0.031 0.002 TYR G 54 ARG 0.009 0.001 ARG L 45 *********************** 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 251 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.769 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 outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2984 time to fit residues: 115.4245 Evaluate side-chains 189 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.608 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0014 ------------------------------------------------------------------------------- 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: 40.0000 chunk 101 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19118 Z= 0.252 Angle : 0.668 13.659 27114 Z= 0.373 Chirality : 0.043 0.237 3080 Planarity : 0.004 0.053 2419 Dihedral : 29.851 174.511 4880 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 27.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: -1.24 (0.21), residues: 1523 helix: 0.59 (0.21), residues: 561 sheet: -1.85 (0.27), residues: 323 loop : -1.46 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 156 HIS 0.012 0.001 HIS H 75 PHE 0.018 0.002 PHE H 61 TYR 0.019 0.002 TYR G 54 ARG 0.006 0.001 ARG J 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 270 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.594 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 outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2851 time to fit residues: 118.4106 Evaluate side-chains 203 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.760 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3292 ------------------------------------------------------------------------------- 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: 0.9980 chunk 98 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19118 Z= 0.247 Angle : 0.657 13.098 27114 Z= 0.366 Chirality : 0.042 0.197 3080 Planarity : 0.004 0.048 2419 Dihedral : 29.687 175.809 4880 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 26.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: -1.06 (0.21), residues: 1523 helix: 0.72 (0.21), residues: 559 sheet: -1.73 (0.27), residues: 320 loop : -1.34 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 156 HIS 0.003 0.001 HIS L 75 PHE 0.024 0.002 PHE H 61 TYR 0.035 0.002 TYR L 98 ARG 0.007 0.001 ARG J 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 269 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.623 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 outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2870 time to fit residues: 118.7755 Evaluate side-chains 212 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.578 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8431 ------------------------------------------------------------------------------- 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: 3.9990 chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** H 75 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 19118 Z= 0.332 Angle : 0.694 15.709 27114 Z= 0.387 Chirality : 0.043 0.187 3080 Planarity : 0.005 0.049 2419 Dihedral : 29.699 175.147 4880 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 31.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -1.11 (0.21), residues: 1523 helix: 0.58 (0.21), residues: 561 sheet: -1.64 (0.28), residues: 307 loop : -1.37 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 156 HIS 0.005 0.001 HIS L 75 PHE 0.026 0.002 PHE K 67 TYR 0.019 0.002 TYR G 54 ARG 0.008 0.001 ARG J 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 259 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.811 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 outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.2908 time to fit residues: 115.9482 Evaluate side-chains 190 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.643 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0301 ------------------------------------------------------------------------------- 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: 3.9990 chunk 159 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 19118 Z= 0.372 Angle : 0.723 15.744 27114 Z= 0.404 Chirality : 0.044 0.188 3080 Planarity : 0.005 0.049 2419 Dihedral : 29.804 174.475 4880 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 34.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % 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: -1.36 (0.20), residues: 1523 helix: 0.24 (0.20), residues: 555 sheet: -1.51 (0.29), residues: 285 loop : -1.54 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 156 HIS 0.005 0.001 HIS L 75 PHE 0.028 0.002 PHE H 61 TYR 0.021 0.002 TYR G 54 ARG 0.009 0.001 ARG J 76 *********************** 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 256 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.607 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 outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.2915 time to fit residues: 115.0982 Evaluate side-chains 188 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.525 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9804 ------------------------------------------------------------------------------- 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: 0.0970 chunk 80 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** 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: 0.8492 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19118 Z= 0.212 Angle : 0.679 11.768 27114 Z= 0.377 Chirality : 0.043 0.179 3080 Planarity : 0.004 0.082 2419 Dihedral : 29.739 177.060 4880 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -1.08 (0.21), residues: 1523 helix: 0.53 (0.21), residues: 557 sheet: -1.60 (0.28), residues: 309 loop : -1.28 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 156 HIS 0.020 0.001 HIS B 128 PHE 0.021 0.002 PHE K 67 TYR 0.018 0.001 TYR H 98 ARG 0.020 0.001 ARG B 154 ********************** 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 268 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.722 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 outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.3077 time to fit residues: 125.8006 Evaluate side-chains 204 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.734 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1334 ------------------------------------------------------------------------------- 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: 2.9990 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 141 optimal weight: 0.5980 chunk 59 optimal weight: 30.0000 chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** H 75 HIS ** 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** N 60 ASN N 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.042027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.028696 restraints weight = 169865.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.030073 restraints weight = 82871.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.030985 restraints weight = 49619.565| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19118 Z= 0.215 Angle : 0.670 14.018 27114 Z= 0.374 Chirality : 0.042 0.166 3080 Planarity : 0.004 0.054 2419 Dihedral : 29.536 177.058 4880 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 23.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -1.06 (0.21), residues: 1523 helix: 0.51 (0.21), residues: 557 sheet: -1.60 (0.28), residues: 317 loop : -1.21 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 156 HIS 0.008 0.001 HIS B 128 PHE 0.022 0.001 PHE H 61 TYR 0.019 0.002 TYR L 51 ARG 0.014 0.001 ARG G 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3476.81 seconds wall clock time: 64 minutes 38.18 seconds (3878.18 seconds total)