Starting phenix.real_space_refine on Sat Nov 16 12:38:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7u_36049/11_2024/8j7u_36049.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7u_36049/11_2024/8j7u_36049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7u_36049/11_2024/8j7u_36049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7u_36049/11_2024/8j7u_36049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7u_36049/11_2024/8j7u_36049.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7u_36049/11_2024/8j7u_36049.cif" } resolution = 3.12 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 ------------------------------------------------------------------------------- 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= 0.013 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 45 5.16 5 C 7034 2.51 5 N 1839 2.21 5 O 2083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11003 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2133 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 7, 'TRANS': 263} Chain breaks: 4 Chain: "E" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "D" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "F" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2248 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.97, per 1000 atoms: 0.63 Number of scatterers: 11003 At special positions: 0 Unit cell: (87.468, 113.472, 158.388, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 45 16.00 O 2083 8.00 N 1839 7.00 C 7034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 200 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 240 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 240 " 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 26 sheets defined 32.1% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 removed outlier: 4.027A pdb=" N PHE A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 57 removed outlier: 3.775A pdb=" N PHE A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A 45 " --> pdb=" O PHE A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 88 Processing helix chain 'A' and resid 102 through 132 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 159 removed outlier: 3.761A pdb=" N LEU A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 259 removed outlier: 4.077A pdb=" N GLN A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 294 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.343A pdb=" N ASN A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.633A pdb=" N ALA C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 131 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'D' and resid 125 through 131 Processing helix chain 'D' and resid 187 through 193 removed outlier: 3.724A pdb=" N HIS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'B' and resid 23 through 30 Processing helix chain 'B' and resid 32 through 57 Processing helix chain 'B' and resid 60 through 88 removed outlier: 4.049A pdb=" N LEU B 64 " --> pdb=" O ASN B 60 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 132 removed outlier: 4.469A pdb=" N VAL B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 159 removed outlier: 3.993A pdb=" N LEU B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 259 removed outlier: 4.522A pdb=" N GLN B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 294 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 298 through 303 removed outlier: 4.545A pdb=" N ASN B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 347 through 362 removed outlier: 3.524A pdb=" N ALA B 362 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 329 removed outlier: 5.548A pdb=" N LEU A 321 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE A 341 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLU A 323 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS A 339 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR A 334 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TYR A 368 " --> pdb=" O TYR A 334 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY A 336 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLN A 370 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 338 " --> pdb=" O GLN A 370 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASP A 372 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 340 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.501A pdb=" N GLN E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.575A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR E 107 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.575A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.712A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS E 145 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER E 184 " --> pdb=" O CYS E 145 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.712A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS E 145 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER E 184 " --> pdb=" O CYS E 145 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR E 181 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.747A pdb=" N VAL E 211 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.261A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.261A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AB3, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.641A pdb=" N ASN C 141 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 137 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 149 through 153 removed outlier: 3.512A pdb=" N PHE C 213 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS C 198 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS C 211 " --> pdb=" O CYS C 198 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C 200 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS C 202 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER C 207 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.818A pdb=" N MET D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TYR D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 14 removed outlier: 3.811A pdb=" N THR D 101 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AB9, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.800A pdb=" N VAL D 137 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR D 177 " --> pdb=" O ASN D 142 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 157 through 158 removed outlier: 3.584A pdb=" N ASN D 149 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE D 209 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N HIS D 202 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER D 207 " --> pdb=" O HIS D 202 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC3, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.682A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER F 40 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU F 45 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.959A pdb=" N TYR F 107 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.586A pdb=" N SER F 184 " --> pdb=" O CYS F 145 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY F 149 " --> pdb=" O TYR F 180 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.586A pdb=" N SER F 184 " --> pdb=" O CYS F 145 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY F 149 " --> pdb=" O TYR F 180 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 156 through 159 removed outlier: 3.781A pdb=" N LYS F 213 " --> pdb=" O CYS F 200 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL F 211 " --> pdb=" O VAL F 202 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 318 through 329 removed outlier: 5.557A pdb=" N LEU B 321 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE B 341 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLU B 323 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS B 339 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR B 334 " --> pdb=" O VAL B 364 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.05 Time building geometry restraints manager: 3.19 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: 3053 1.33 - 1.45: 2113 1.45 - 1.57: 6031 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 11262 Sorted by residual: bond pdb=" N ASP C 74 " pdb=" CA ASP C 74 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.33e-02 5.65e+03 8.50e+00 bond pdb=" N VAL B 51 " pdb=" CA VAL B 51 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.17e+00 bond pdb=" CA SER F 40 " pdb=" CB SER F 40 " ideal model delta sigma weight residual 1.536 1.496 0.040 1.46e-02 4.69e+03 7.58e+00 bond pdb=" N VAL F 147 " pdb=" CA VAL F 147 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.43e+00 bond pdb=" N LYS F 148 " pdb=" CA LYS F 148 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.21e-02 6.83e+03 7.14e+00 ... (remaining 11257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 15086 2.72 - 5.45: 198 5.45 - 8.17: 37 8.17 - 10.90: 4 10.90 - 13.62: 5 Bond angle restraints: 15330 Sorted by residual: angle pdb=" CB MET D 179 " pdb=" CG MET D 179 " pdb=" SD MET D 179 " ideal model delta sigma weight residual 112.70 124.54 -11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CA GLU B 128 " pdb=" CB GLU B 128 " pdb=" CG GLU B 128 " ideal model delta sigma weight residual 114.10 121.92 -7.82 2.00e+00 2.50e-01 1.53e+01 angle pdb=" CA LEU D 129 " pdb=" CB LEU D 129 " pdb=" CG LEU D 129 " ideal model delta sigma weight residual 116.30 129.92 -13.62 3.50e+00 8.16e-02 1.52e+01 angle pdb=" CB MET A 258 " pdb=" CG MET A 258 " pdb=" SD MET A 258 " ideal model delta sigma weight residual 112.70 124.15 -11.45 3.00e+00 1.11e-01 1.46e+01 angle pdb=" C ARG C 72 " pdb=" CA ARG C 72 " pdb=" CB ARG C 72 " ideal model delta sigma weight residual 116.54 112.18 4.36 1.15e+00 7.56e-01 1.44e+01 ... (remaining 15325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5938 17.72 - 35.44: 524 35.44 - 53.16: 154 53.16 - 70.88: 31 70.88 - 88.60: 10 Dihedral angle restraints: 6657 sinusoidal: 2530 harmonic: 4127 Sorted by residual: dihedral pdb=" CB CYS E 145 " pdb=" SG CYS E 145 " pdb=" SG CYS E 200 " pdb=" CB CYS E 200 " ideal model delta sinusoidal sigma weight residual 93.00 154.17 -61.17 1 1.00e+01 1.00e-02 4.97e+01 dihedral pdb=" CB CYS F 145 " pdb=" SG CYS F 145 " pdb=" SG CYS F 200 " pdb=" CB CYS F 200 " ideal model delta sinusoidal sigma weight residual 93.00 147.65 -54.65 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 198 " pdb=" CB CYS D 198 " ideal model delta sinusoidal sigma weight residual 93.00 56.56 36.44 1 1.00e+01 1.00e-02 1.88e+01 ... (remaining 6654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1577 0.083 - 0.167: 178 0.167 - 0.250: 7 0.250 - 0.333: 0 0.333 - 0.416: 1 Chirality restraints: 1763 Sorted by residual: chirality pdb=" CG LEU F 129 " pdb=" CB LEU F 129 " pdb=" CD1 LEU F 129 " pdb=" CD2 LEU F 129 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CB ILE B 122 " pdb=" CA ILE B 122 " pdb=" CG1 ILE B 122 " pdb=" CG2 ILE B 122 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB THR B 245 " pdb=" CA THR B 245 " pdb=" OG1 THR B 245 " pdb=" CG2 THR B 245 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1760 not shown) Planarity restraints: 1938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 17 " 0.389 9.50e-02 1.11e+02 1.75e-01 1.87e+01 pdb=" NE ARG D 17 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG D 17 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 17 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 17 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 167 " 0.019 2.00e-02 2.50e+03 1.66e-02 6.90e+00 pdb=" CG TRP C 167 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C 167 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 167 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 167 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 167 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 167 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 167 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 167 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 167 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 159 " -0.012 2.00e-02 2.50e+03 1.53e-02 5.87e+00 pdb=" CG TRP E 159 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP E 159 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP E 159 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 159 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 159 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 159 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 159 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 159 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP E 159 " -0.001 2.00e-02 2.50e+03 ... (remaining 1935 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 109 2.57 - 3.15: 8684 3.15 - 3.73: 17704 3.73 - 4.32: 24673 4.32 - 4.90: 40978 Nonbonded interactions: 92148 Sorted by model distance: nonbonded pdb=" OD2 ASP B 74 " pdb="ZN ZN B 501 " model vdw 1.982 2.230 nonbonded pdb=" OD1 ASP A 74 " pdb="ZN ZN A 501 " model vdw 1.985 2.230 nonbonded pdb=" OD2 ASP A 74 " pdb="ZN ZN A 501 " model vdw 1.990 2.230 nonbonded pdb=" OD1 ASP B 244 " pdb="ZN ZN B 501 " model vdw 1.995 2.230 nonbonded pdb=" OD2 ASP B 244 " pdb="ZN ZN B 501 " model vdw 2.004 2.230 ... (remaining 92143 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 22 through 57 or resid 70 through 132 or resid 136 through \ 376 or resid 501)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.670 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 0.061 11262 Z= 0.265 Angle : 0.833 13.623 15330 Z= 0.464 Chirality : 0.049 0.416 1763 Planarity : 0.007 0.175 1938 Dihedral : 15.326 88.599 3969 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.88 % Allowed : 19.74 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 0.27 (0.22), residues: 1399 helix: 0.71 (0.26), residues: 395 sheet: 0.90 (0.24), residues: 450 loop : -0.76 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 167 HIS 0.023 0.002 HIS C 202 PHE 0.035 0.002 PHE A 120 TYR 0.014 0.001 TYR E 180 ARG 0.012 0.001 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 40 SER cc_start: 0.6503 (OUTLIER) cc_final: 0.6087 (p) REVERT: E 75 LYS cc_start: 0.8889 (ptpp) cc_final: 0.8571 (ptmm) REVERT: C 32 TYR cc_start: 0.6870 (m-80) cc_final: 0.6592 (m-80) REVERT: C 203 LYS cc_start: 0.8743 (tmmm) cc_final: 0.8494 (pttt) REVERT: D 46 GLN cc_start: 0.7845 (mp10) cc_final: 0.7498 (pm20) REVERT: D 59 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7196 (tp30) REVERT: B 36 ARG cc_start: 0.7383 (ptp-110) cc_final: 0.6909 (ptp-110) REVERT: B 52 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7559 (pt0) REVERT: B 73 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6311 (t80) outliers start: 23 outliers final: 13 residues processed: 200 average time/residue: 0.3133 time to fit residues: 82.6643 Evaluate side-chains 180 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 322 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 108 optimal weight: 30.0000 chunk 42 optimal weight: 50.0000 chunk 66 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 126 optimal weight: 30.0000 overall best weight: 9.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 325 HIS A 357 ASN A 366 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 HIS ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN D 41 GLN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 138 HIS B 307 GLN B 325 HIS B 366 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.137 11262 Z= 0.879 Angle : 0.897 14.930 15330 Z= 0.458 Chirality : 0.055 0.235 1763 Planarity : 0.006 0.058 1938 Dihedral : 7.154 59.587 1550 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.89 % Allowed : 17.78 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 0.17 (0.22), residues: 1399 helix: 0.72 (0.25), residues: 398 sheet: 0.77 (0.23), residues: 466 loop : -0.89 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP F 52 HIS 0.009 0.002 HIS C 202 PHE 0.038 0.004 PHE C 36 TYR 0.024 0.003 TYR C 32 ARG 0.010 0.001 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 174 time to evaluate : 1.317 Fit side-chains REVERT: A 233 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7481 (mp) REVERT: E 75 LYS cc_start: 0.8936 (ptpp) cc_final: 0.8464 (ptmm) REVERT: E 110 GLN cc_start: 0.7767 (pm20) cc_final: 0.7529 (pm20) REVERT: E 148 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9128 (mmmm) REVERT: C 167 TRP cc_start: 0.8524 (m-90) cc_final: 0.7912 (m-90) REVERT: C 171 ASP cc_start: 0.7844 (m-30) cc_final: 0.7426 (m-30) REVERT: C 193 HIS cc_start: 0.6781 (OUTLIER) cc_final: 0.6412 (t-90) REVERT: C 203 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8521 (pttt) REVERT: D 179 MET cc_start: 0.7153 (tmm) cc_final: 0.6056 (tmm) REVERT: F 72 ASP cc_start: 0.7596 (t0) cc_final: 0.7310 (t0) REVERT: F 193 TRP cc_start: 0.8572 (t60) cc_final: 0.8355 (t60) REVERT: B 33 LYS cc_start: 0.8366 (tppt) cc_final: 0.8092 (tppt) REVERT: B 36 ARG cc_start: 0.7641 (ptp-110) cc_final: 0.6678 (ptp-110) REVERT: B 45 ASN cc_start: 0.9029 (m-40) cc_final: 0.8821 (p0) REVERT: B 48 PHE cc_start: 0.8965 (t80) cc_final: 0.8292 (t80) REVERT: B 52 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7398 (pt0) REVERT: B 72 PHE cc_start: 0.8950 (m-10) cc_final: 0.8742 (m-10) REVERT: B 73 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6150 (t80) REVERT: B 89 LYS cc_start: 0.8924 (mtmm) cc_final: 0.8661 (mtmm) outliers start: 60 outliers final: 35 residues processed: 210 average time/residue: 0.2951 time to fit residues: 82.8955 Evaluate side-chains 201 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 332 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 0.0020 chunk 105 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 112 optimal weight: 40.0000 chunk 125 optimal weight: 20.0000 chunk 43 optimal weight: 50.0000 chunk 101 optimal weight: 9.9990 overall best weight: 5.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 366 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS B 307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 11262 Z= 0.500 Angle : 0.727 11.488 15330 Z= 0.372 Chirality : 0.047 0.158 1763 Planarity : 0.005 0.056 1938 Dihedral : 6.511 59.633 1533 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.89 % Allowed : 17.62 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 0.41 (0.22), residues: 1399 helix: 1.16 (0.25), residues: 399 sheet: 0.75 (0.23), residues: 466 loop : -0.80 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 52 HIS 0.007 0.001 HIS B 240 PHE 0.031 0.003 PHE C 36 TYR 0.018 0.002 TYR C 32 ARG 0.005 0.001 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 164 time to evaluate : 1.348 Fit side-chains REVERT: A 233 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7429 (mp) REVERT: E 51 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7594 (tp) REVERT: E 72 ASP cc_start: 0.8040 (t0) cc_final: 0.7781 (t0) REVERT: E 86 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7393 (mm-40) REVERT: E 110 GLN cc_start: 0.7755 (pm20) cc_final: 0.7522 (pm20) REVERT: C 112 ARG cc_start: 0.5828 (ttp-110) cc_final: 0.5288 (ttp80) REVERT: C 167 TRP cc_start: 0.8475 (m-90) cc_final: 0.7829 (m-90) REVERT: C 203 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8443 (pttt) REVERT: D 179 MET cc_start: 0.7334 (tmm) cc_final: 0.6025 (tmm) REVERT: F 43 LYS cc_start: 0.7754 (mtmm) cc_final: 0.7535 (pttp) REVERT: F 51 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.7175 (tp) REVERT: F 72 ASP cc_start: 0.7593 (t0) cc_final: 0.7227 (t0) REVERT: F 193 TRP cc_start: 0.8520 (t60) cc_final: 0.8191 (t60) REVERT: B 36 ARG cc_start: 0.7637 (ptp-110) cc_final: 0.7000 (ptp-110) REVERT: B 45 ASN cc_start: 0.8933 (m-40) cc_final: 0.8723 (p0) REVERT: B 52 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7444 (pt0) REVERT: B 72 PHE cc_start: 0.8934 (m-10) cc_final: 0.8652 (m-10) REVERT: B 73 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.5992 (t80) REVERT: B 104 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7389 (pt0) REVERT: B 287 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.4613 (ttm170) REVERT: B 332 ASP cc_start: 0.8233 (t70) cc_final: 0.7563 (t0) outliers start: 60 outliers final: 35 residues processed: 200 average time/residue: 0.3095 time to fit residues: 81.7973 Evaluate side-chains 201 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 371 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 60 optimal weight: 30.0000 chunk 84 optimal weight: 40.0000 chunk 126 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 66 optimal weight: 50.0000 chunk 120 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 366 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11262 Z= 0.366 Angle : 0.673 9.957 15330 Z= 0.343 Chirality : 0.046 0.210 1763 Planarity : 0.005 0.053 1938 Dihedral : 6.305 59.695 1533 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.57 % Allowed : 19.00 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 0.60 (0.22), residues: 1399 helix: 1.46 (0.26), residues: 401 sheet: 0.85 (0.23), residues: 456 loop : -0.78 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 167 HIS 0.006 0.001 HIS B 240 PHE 0.026 0.002 PHE B 69 TYR 0.015 0.002 TYR C 32 ARG 0.006 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 164 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8552 (pmtt) cc_final: 0.8210 (pmtt) REVERT: A 233 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7505 (mp) REVERT: E 51 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7581 (tp) REVERT: E 72 ASP cc_start: 0.7987 (t0) cc_final: 0.7581 (t0) REVERT: E 75 LYS cc_start: 0.8845 (ptpp) cc_final: 0.8576 (ptpp) REVERT: E 86 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7235 (mm110) REVERT: E 88 ASP cc_start: 0.8615 (p0) cc_final: 0.8413 (p0) REVERT: C 24 ARG cc_start: 0.6857 (ttp-110) cc_final: 0.6575 (ttp-110) REVERT: C 112 ARG cc_start: 0.5843 (ttp-110) cc_final: 0.5422 (ttp80) REVERT: C 171 ASP cc_start: 0.7816 (m-30) cc_final: 0.7583 (m-30) REVERT: C 193 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7565 (t-90) REVERT: C 203 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8397 (pttt) REVERT: D 72 ARG cc_start: 0.7365 (mmp80) cc_final: 0.7135 (mmp80) REVERT: D 179 MET cc_start: 0.7329 (tmm) cc_final: 0.6109 (tmm) REVERT: F 51 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7136 (tp) REVERT: F 72 ASP cc_start: 0.7600 (t0) cc_final: 0.7039 (t0) REVERT: F 193 TRP cc_start: 0.8518 (t60) cc_final: 0.8177 (t60) REVERT: B 36 ARG cc_start: 0.7537 (ptp-110) cc_final: 0.6698 (ptp-110) REVERT: B 48 PHE cc_start: 0.8992 (t80) cc_final: 0.8762 (t80) REVERT: B 52 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7375 (pt0) REVERT: B 71 MET cc_start: 0.8826 (ppp) cc_final: 0.8614 (ppp) REVERT: B 72 PHE cc_start: 0.8940 (m-10) cc_final: 0.8664 (m-10) REVERT: B 73 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.5887 (t80) REVERT: B 104 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: B 332 ASP cc_start: 0.8224 (t70) cc_final: 0.7537 (t0) outliers start: 56 outliers final: 36 residues processed: 199 average time/residue: 0.2971 time to fit residues: 78.8908 Evaluate side-chains 203 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 328 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 40.0000 chunk 76 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 114 optimal weight: 50.0000 chunk 92 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 0.0170 chunk 120 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 366 GLN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11262 Z= 0.407 Angle : 0.678 10.102 15330 Z= 0.347 Chirality : 0.046 0.230 1763 Planarity : 0.005 0.053 1938 Dihedral : 6.171 59.540 1533 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.06 % Allowed : 18.76 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 0.58 (0.22), residues: 1399 helix: 1.47 (0.26), residues: 399 sheet: 0.82 (0.23), residues: 460 loop : -0.80 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 52 HIS 0.005 0.001 HIS B 240 PHE 0.027 0.002 PHE C 36 TYR 0.016 0.002 TYR C 32 ARG 0.005 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 164 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7586 (mp) REVERT: E 51 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7591 (tp) REVERT: E 72 ASP cc_start: 0.7988 (t0) cc_final: 0.7644 (t0) REVERT: E 148 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9156 (mmmm) REVERT: C 24 ARG cc_start: 0.6848 (ttp-110) cc_final: 0.6563 (ttp-110) REVERT: C 171 ASP cc_start: 0.7842 (m-30) cc_final: 0.7541 (m-30) REVERT: C 193 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.7138 (t70) REVERT: C 203 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8363 (pttt) REVERT: D 83 GLU cc_start: 0.6839 (mp0) cc_final: 0.5805 (mp0) REVERT: D 179 MET cc_start: 0.7349 (tmm) cc_final: 0.7141 (tpp) REVERT: F 51 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.7156 (tp) REVERT: F 72 ASP cc_start: 0.7521 (t0) cc_final: 0.7161 (t0) REVERT: F 193 TRP cc_start: 0.8561 (t60) cc_final: 0.8208 (t60) REVERT: B 36 ARG cc_start: 0.7559 (ptp-110) cc_final: 0.6777 (ptp-110) REVERT: B 48 PHE cc_start: 0.9019 (t80) cc_final: 0.8782 (t80) REVERT: B 52 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7493 (pt0) REVERT: B 72 PHE cc_start: 0.8936 (m-10) cc_final: 0.8650 (m-10) REVERT: B 73 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.5964 (t80) REVERT: B 104 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7342 (pt0) REVERT: B 332 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7524 (t0) outliers start: 62 outliers final: 39 residues processed: 201 average time/residue: 0.3002 time to fit residues: 80.3695 Evaluate side-chains 208 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 159 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 332 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 111 optimal weight: 40.0000 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 chunk 70 optimal weight: 7.9990 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 303 ASN A 310 GLN A 366 GLN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 11262 Z= 0.483 Angle : 0.704 10.823 15330 Z= 0.360 Chirality : 0.047 0.235 1763 Planarity : 0.005 0.053 1938 Dihedral : 6.241 59.682 1533 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 6.04 % Allowed : 19.09 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 0.54 (0.22), residues: 1399 helix: 1.44 (0.26), residues: 399 sheet: 0.72 (0.23), residues: 460 loop : -0.74 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 167 HIS 0.008 0.001 HIS B 240 PHE 0.030 0.002 PHE C 36 TYR 0.021 0.002 TYR F 180 ARG 0.006 0.001 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 162 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 HIS cc_start: 0.8766 (OUTLIER) cc_final: 0.8322 (p90) REVERT: E 51 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7611 (tp) REVERT: E 72 ASP cc_start: 0.7880 (t0) cc_final: 0.7567 (t0) REVERT: E 148 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9171 (mmmm) REVERT: C 112 ARG cc_start: 0.5889 (ttp-110) cc_final: 0.5408 (ttp80) REVERT: C 159 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6992 (ptm-80) REVERT: C 171 ASP cc_start: 0.7823 (m-30) cc_final: 0.7508 (m-30) REVERT: C 203 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8372 (pttt) REVERT: D 18 ARG cc_start: 0.7939 (tmm-80) cc_final: 0.7621 (ttp80) REVERT: D 83 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.5845 (mp0) REVERT: D 172 SER cc_start: 0.8607 (m) cc_final: 0.8144 (t) REVERT: D 179 MET cc_start: 0.7339 (tmm) cc_final: 0.7113 (tpp) REVERT: F 51 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.7158 (tp) REVERT: F 72 ASP cc_start: 0.7515 (t0) cc_final: 0.7079 (t70) REVERT: F 193 TRP cc_start: 0.8581 (t60) cc_final: 0.8213 (t60) REVERT: B 48 PHE cc_start: 0.9040 (t80) cc_final: 0.8788 (t80) REVERT: B 52 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7358 (pt0) REVERT: B 71 MET cc_start: 0.8852 (ppp) cc_final: 0.8570 (ppp) REVERT: B 72 PHE cc_start: 0.8947 (m-10) cc_final: 0.8644 (m-10) REVERT: B 73 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.5938 (t80) REVERT: B 258 MET cc_start: 0.5908 (mmm) cc_final: 0.5307 (ppp) REVERT: B 287 ARG cc_start: 0.6364 (OUTLIER) cc_final: 0.4623 (ttm170) REVERT: B 332 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7542 (t0) outliers start: 74 outliers final: 48 residues processed: 210 average time/residue: 0.3091 time to fit residues: 86.8730 Evaluate side-chains 222 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 163 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 371 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 61 optimal weight: 50.0000 chunk 82 optimal weight: 0.1980 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 366 GLN E 160 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11262 Z= 0.345 Angle : 0.664 9.725 15330 Z= 0.339 Chirality : 0.046 0.246 1763 Planarity : 0.005 0.052 1938 Dihedral : 6.020 59.759 1533 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.38 % Allowed : 19.58 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 0.66 (0.22), residues: 1399 helix: 1.61 (0.26), residues: 399 sheet: 0.78 (0.23), residues: 460 loop : -0.72 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 167 HIS 0.007 0.001 HIS B 240 PHE 0.025 0.002 PHE C 36 TYR 0.021 0.002 TYR C 144 ARG 0.008 0.001 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 165 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 HIS cc_start: 0.8748 (OUTLIER) cc_final: 0.8322 (p90) REVERT: E 51 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7593 (tp) REVERT: E 72 ASP cc_start: 0.7839 (t0) cc_final: 0.7519 (t0) REVERT: E 75 LYS cc_start: 0.8731 (ptpp) cc_final: 0.8423 (ptpp) REVERT: E 148 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9162 (mmmm) REVERT: C 24 ARG cc_start: 0.6836 (ttp-110) cc_final: 0.6557 (ttp-110) REVERT: C 112 ARG cc_start: 0.5853 (ttp-110) cc_final: 0.5464 (ttp80) REVERT: C 159 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6970 (ptm-80) REVERT: C 171 ASP cc_start: 0.7817 (m-30) cc_final: 0.7391 (m-30) REVERT: C 203 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8370 (pttt) REVERT: D 18 ARG cc_start: 0.7895 (tmm-80) cc_final: 0.7631 (ttp80) REVERT: D 46 GLN cc_start: 0.7985 (mp10) cc_final: 0.7709 (pm20) REVERT: D 83 GLU cc_start: 0.6871 (mp0) cc_final: 0.5825 (mp0) REVERT: D 172 SER cc_start: 0.8600 (m) cc_final: 0.8134 (t) REVERT: D 215 ARG cc_start: 0.5409 (mmp80) cc_final: 0.5039 (mmp80) REVERT: F 51 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.7127 (tp) REVERT: F 72 ASP cc_start: 0.7490 (t0) cc_final: 0.7061 (t70) REVERT: F 193 TRP cc_start: 0.8561 (t60) cc_final: 0.8254 (t60) REVERT: B 48 PHE cc_start: 0.9042 (t80) cc_final: 0.8793 (t80) REVERT: B 52 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7418 (pt0) REVERT: B 71 MET cc_start: 0.8838 (ppp) cc_final: 0.8593 (ppp) REVERT: B 72 PHE cc_start: 0.8948 (m-10) cc_final: 0.8641 (m-10) REVERT: B 73 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.5913 (t80) REVERT: B 104 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7371 (pt0) REVERT: B 332 ASP cc_start: 0.8227 (t70) cc_final: 0.7550 (t0) REVERT: B 365 ARG cc_start: 0.7724 (mtt180) cc_final: 0.7497 (ttm-80) outliers start: 66 outliers final: 49 residues processed: 210 average time/residue: 0.2971 time to fit residues: 82.9144 Evaluate side-chains 220 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 328 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.0470 chunk 85 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 105 optimal weight: 30.0000 chunk 121 optimal weight: 10.0000 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 366 GLN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11262 Z= 0.409 Angle : 0.706 12.364 15330 Z= 0.356 Chirality : 0.047 0.251 1763 Planarity : 0.005 0.053 1938 Dihedral : 6.039 59.758 1533 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.55 % Allowed : 19.33 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 0.56 (0.22), residues: 1399 helix: 1.49 (0.26), residues: 399 sheet: 0.75 (0.23), residues: 460 loop : -0.77 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 52 HIS 0.007 0.001 HIS C 193 PHE 0.027 0.002 PHE C 36 TYR 0.017 0.002 TYR C 144 ARG 0.006 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 164 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 HIS cc_start: 0.8753 (OUTLIER) cc_final: 0.8326 (p90) REVERT: E 51 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7610 (tp) REVERT: E 72 ASP cc_start: 0.7838 (t0) cc_final: 0.7492 (t0) REVERT: E 75 LYS cc_start: 0.8720 (ptpp) cc_final: 0.8390 (ptpp) REVERT: E 148 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.9158 (mmmm) REVERT: E 164 LEU cc_start: 0.8859 (pp) cc_final: 0.8629 (pt) REVERT: C 112 ARG cc_start: 0.5960 (ttp-110) cc_final: 0.5568 (ttp80) REVERT: C 159 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6961 (ptm-80) REVERT: C 171 ASP cc_start: 0.7829 (m-30) cc_final: 0.7463 (m-30) REVERT: C 192 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8572 (ppt90) REVERT: C 203 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8452 (pttt) REVERT: D 18 ARG cc_start: 0.7898 (tmm-80) cc_final: 0.7606 (ttp80) REVERT: D 46 GLN cc_start: 0.7992 (mp10) cc_final: 0.7697 (pm20) REVERT: D 83 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.5836 (mp0) REVERT: D 172 SER cc_start: 0.8602 (m) cc_final: 0.8132 (t) REVERT: F 51 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.7146 (tp) REVERT: F 72 ASP cc_start: 0.7503 (t0) cc_final: 0.7056 (t70) REVERT: F 180 TYR cc_start: 0.8416 (m-10) cc_final: 0.8161 (m-10) REVERT: F 193 TRP cc_start: 0.8573 (t60) cc_final: 0.8256 (t60) REVERT: B 48 PHE cc_start: 0.9055 (t80) cc_final: 0.8834 (t80) REVERT: B 52 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: B 71 MET cc_start: 0.8867 (ppp) cc_final: 0.8612 (ppp) REVERT: B 72 PHE cc_start: 0.8966 (m-10) cc_final: 0.8673 (m-10) REVERT: B 73 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.5835 (t80) REVERT: B 258 MET cc_start: 0.5708 (mmm) cc_final: 0.5203 (ppp) REVERT: B 332 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7578 (t0) outliers start: 68 outliers final: 51 residues processed: 209 average time/residue: 0.3069 time to fit residues: 85.4192 Evaluate side-chains 224 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 162 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 371 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 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 303 ASN A 366 GLN E 160 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11262 Z= 0.376 Angle : 0.696 12.748 15330 Z= 0.350 Chirality : 0.046 0.248 1763 Planarity : 0.005 0.052 1938 Dihedral : 5.947 59.899 1533 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.06 % Allowed : 19.74 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 0.60 (0.22), residues: 1399 helix: 1.60 (0.26), residues: 401 sheet: 0.75 (0.23), residues: 460 loop : -0.81 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 52 HIS 0.005 0.001 HIS B 240 PHE 0.026 0.002 PHE B 69 TYR 0.016 0.002 TYR C 144 ARG 0.009 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 163 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 HIS cc_start: 0.8739 (OUTLIER) cc_final: 0.8324 (p90) REVERT: E 51 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7607 (tp) REVERT: E 72 ASP cc_start: 0.7852 (t0) cc_final: 0.7510 (t0) REVERT: E 75 LYS cc_start: 0.8705 (ptpp) cc_final: 0.8365 (ptpp) REVERT: E 148 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9144 (mmmm) REVERT: E 164 LEU cc_start: 0.8837 (pp) cc_final: 0.8583 (pt) REVERT: C 112 ARG cc_start: 0.5971 (ttp-110) cc_final: 0.5567 (ttp80) REVERT: C 159 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6997 (ptm-80) REVERT: C 171 ASP cc_start: 0.7843 (m-30) cc_final: 0.7459 (m-30) REVERT: C 192 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8646 (ppt90) REVERT: D 18 ARG cc_start: 0.7887 (tmm-80) cc_final: 0.7622 (ttp80) REVERT: D 46 GLN cc_start: 0.7976 (mp10) cc_final: 0.7702 (pm20) REVERT: D 83 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.5830 (mp0) REVERT: D 172 SER cc_start: 0.8583 (m) cc_final: 0.8095 (t) REVERT: D 215 ARG cc_start: 0.5379 (mmp80) cc_final: 0.5136 (mmp80) REVERT: F 72 ASP cc_start: 0.7510 (t0) cc_final: 0.7067 (t70) REVERT: F 148 LYS cc_start: 0.9417 (tppt) cc_final: 0.9171 (tptm) REVERT: F 193 TRP cc_start: 0.8590 (t60) cc_final: 0.8267 (t60) REVERT: B 52 GLU cc_start: 0.8007 (pt0) cc_final: 0.7519 (pt0) REVERT: B 71 MET cc_start: 0.8851 (ppp) cc_final: 0.8584 (ppp) REVERT: B 72 PHE cc_start: 0.8976 (m-10) cc_final: 0.8662 (m-10) REVERT: B 73 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.5852 (t80) REVERT: B 258 MET cc_start: 0.5832 (mmm) cc_final: 0.5315 (ppp) REVERT: B 332 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7588 (t0) outliers start: 62 outliers final: 48 residues processed: 205 average time/residue: 0.2954 time to fit residues: 80.8334 Evaluate side-chains 217 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 161 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 371 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 9.9990 chunk 62 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 110 optimal weight: 50.0000 chunk 11 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 67 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 117 optimal weight: 7.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 366 GLN E 160 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11262 Z= 0.336 Angle : 0.708 13.173 15330 Z= 0.353 Chirality : 0.046 0.246 1763 Planarity : 0.005 0.052 1938 Dihedral : 5.803 59.865 1530 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.57 % Allowed : 20.47 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 0.61 (0.22), residues: 1399 helix: 1.59 (0.26), residues: 401 sheet: 0.76 (0.23), residues: 460 loop : -0.80 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 52 HIS 0.005 0.001 HIS B 240 PHE 0.025 0.002 PHE B 69 TYR 0.027 0.002 TYR C 144 ARG 0.009 0.001 ARG C 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 165 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 HIS cc_start: 0.8736 (OUTLIER) cc_final: 0.8324 (p90) REVERT: E 51 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7548 (tp) REVERT: E 72 ASP cc_start: 0.7841 (t0) cc_final: 0.7429 (t0) REVERT: E 75 LYS cc_start: 0.8696 (ptpp) cc_final: 0.8314 (ptpp) REVERT: E 148 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9141 (mmmm) REVERT: C 18 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7894 (ttm-80) REVERT: C 24 ARG cc_start: 0.6816 (ttp-110) cc_final: 0.6514 (ttp-110) REVERT: C 112 ARG cc_start: 0.6019 (ttp-110) cc_final: 0.5689 (ttp80) REVERT: C 159 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7087 (ptm-80) REVERT: C 171 ASP cc_start: 0.7855 (m-30) cc_final: 0.7380 (m-30) REVERT: C 192 ARG cc_start: 0.9073 (mtm110) cc_final: 0.8669 (ppt90) REVERT: D 18 ARG cc_start: 0.7852 (tmm-80) cc_final: 0.7622 (ttp80) REVERT: D 46 GLN cc_start: 0.7980 (mp10) cc_final: 0.7636 (pm20) REVERT: D 83 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.5821 (mp0) REVERT: D 172 SER cc_start: 0.8566 (m) cc_final: 0.8082 (t) REVERT: D 215 ARG cc_start: 0.5445 (mmp80) cc_final: 0.5192 (mmp80) REVERT: F 66 ARG cc_start: 0.7714 (ptt90) cc_final: 0.7104 (ptt90) REVERT: F 72 ASP cc_start: 0.7507 (t0) cc_final: 0.7069 (t70) REVERT: F 148 LYS cc_start: 0.9416 (tppt) cc_final: 0.9172 (tptm) REVERT: F 193 TRP cc_start: 0.8578 (t60) cc_final: 0.8257 (t60) REVERT: B 52 GLU cc_start: 0.8006 (pt0) cc_final: 0.7489 (pt0) REVERT: B 71 MET cc_start: 0.8838 (ppp) cc_final: 0.8579 (ppp) REVERT: B 72 PHE cc_start: 0.8978 (m-10) cc_final: 0.8669 (m-10) REVERT: B 73 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.5514 (t80) REVERT: B 258 MET cc_start: 0.5846 (mmm) cc_final: 0.5293 (ppp) REVERT: B 332 ASP cc_start: 0.8238 (t70) cc_final: 0.7587 (t0) outliers start: 56 outliers final: 46 residues processed: 206 average time/residue: 0.3036 time to fit residues: 82.8878 Evaluate side-chains 216 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 328 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 9.9990 chunk 101 optimal weight: 30.0000 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 110 optimal weight: 50.0000 chunk 46 optimal weight: 40.0000 chunk 113 optimal weight: 8.9990 chunk 13 optimal weight: 30.0000 chunk 20 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 overall best weight: 4.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 366 GLN C 57 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** 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 = 0.4582 r_free = 0.4582 target = 0.230373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.209625 restraints weight = 13565.303| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 1.03 r_work: 0.4243 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.4212 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 11262 Z= 0.469 Angle : 0.743 12.685 15330 Z= 0.370 Chirality : 0.048 0.237 1763 Planarity : 0.005 0.052 1938 Dihedral : 5.937 59.921 1529 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.57 % Allowed : 20.47 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 0.50 (0.22), residues: 1399 helix: 1.48 (0.26), residues: 400 sheet: 0.70 (0.23), residues: 464 loop : -0.86 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 52 HIS 0.005 0.001 HIS A 325 PHE 0.030 0.002 PHE C 36 TYR 0.022 0.002 TYR C 144 ARG 0.009 0.001 ARG C 18 =============================================================================== Job complete usr+sys time: 2598.81 seconds wall clock time: 48 minutes 10.99 seconds (2890.99 seconds total)