Starting phenix.real_space_refine on Sun Jul 21 10:44:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnu_37673/07_2024/8wnu_37673.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnu_37673/07_2024/8wnu_37673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnu_37673/07_2024/8wnu_37673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnu_37673/07_2024/8wnu_37673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnu_37673/07_2024/8wnu_37673.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnu_37673/07_2024/8wnu_37673.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.024 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: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 8864 2.51 5 N 2436 2.21 5 O 2778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "C ASP 18": "OD1" <-> "OD2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 123": "OD1" <-> "OD2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ASP 168": "OD1" <-> "OD2" Residue "C TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "D GLU 7": "OE1" <-> "OE2" Residue "D PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 212": "OD1" <-> "OD2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 37": "OD1" <-> "OD2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ASP 138": "OD1" <-> "OD2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E ASP 174": "OD1" <-> "OD2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 208": "OD1" <-> "OD2" Residue "E ASP 234": "OD1" <-> "OD2" Residue "E GLU 272": "OE1" <-> "OE2" Residue "E ASP 327": "OD1" <-> "OD2" Residue "F ASP 7": "OD1" <-> "OD2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 138": "OD1" <-> "OD2" Residue "F ASP 174": "OD1" <-> "OD2" Residue "F TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F ASP 208": "OD1" <-> "OD2" Residue "F GLU 272": "OE1" <-> "OE2" Residue "F GLU 289": "OE1" <-> "OE2" Residue "F PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 55": "OD1" <-> "OD2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 89": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14152 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1660 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Chain: "B" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1661 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "C" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1660 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Chain: "D" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1661 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "E" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2818 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2818 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "G" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 923 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 923 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.17, per 1000 atoms: 0.58 Number of scatterers: 14152 At special positions: 0 Unit cell: (127.28, 109.22, 132.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 2778 8.00 N 2436 7.00 C 8864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 89 " distance=2.04 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS F 4 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 143 " distance=2.03 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 223 " distance=2.03 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 329 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 312 " distance=2.03 Simple disulfide: pdb=" SG CYS E 313 " - pdb=" SG CYS E 316 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 15 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 143 " distance=2.03 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 223 " distance=2.03 Simple disulfide: pdb=" SG CYS F 280 " - pdb=" SG CYS F 329 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 312 " distance=2.03 Simple disulfide: pdb=" SG CYS F 313 " - pdb=" SG CYS F 316 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E 401 " - " ASN E 207 " Time building additional restraints: 4.71 Conformation dependent library (CDL) restraints added in 2.5 seconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3356 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 31 sheets defined 11.2% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 removed outlier: 4.299A pdb=" N PHE A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'B' and resid 29 through 33 removed outlier: 3.763A pdb=" N SER B 32 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN B 33 " --> pdb=" O VAL B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 33' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.005A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.540A pdb=" N LYS C 127 " --> pdb=" O ASP C 123 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 128' Processing helix chain 'C' and resid 151 through 154 Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 205 through 208 Processing helix chain 'E' and resid 24 through 32 removed outlier: 3.615A pdb=" N ALA E 27 " --> pdb=" O ASP E 24 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG E 29 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP E 30 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG E 31 " --> pdb=" O TRP E 28 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR E 32 " --> pdb=" O ARG E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 52 removed outlier: 3.628A pdb=" N LEU E 42 " --> pdb=" O SER E 38 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 44 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU E 52 " --> pdb=" O GLN E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 72 Processing helix chain 'E' and resid 73 through 82 removed outlier: 3.902A pdb=" N GLU E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 124 removed outlier: 4.182A pdb=" N TYR E 122 " --> pdb=" O GLY E 119 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL E 124 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 180 through 183 removed outlier: 4.283A pdb=" N VAL E 183 " --> pdb=" O ASP E 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 180 through 183' Processing helix chain 'E' and resid 226 through 230 removed outlier: 3.683A pdb=" N HIS E 229 " --> pdb=" O PRO E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'F' and resid 38 through 53 removed outlier: 4.295A pdb=" N ALA F 44 " --> pdb=" O ARG F 40 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA F 45 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 72 Processing helix chain 'F' and resid 72 through 83 removed outlier: 4.044A pdb=" N ASN F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 146 No H-bonds generated for 'chain 'F' and resid 144 through 146' Processing helix chain 'F' and resid 244 through 248 Processing helix chain 'G' and resid 27 through 31 removed outlier: 3.816A pdb=" N ARG G 30 " --> pdb=" O THR G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'H' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.620A pdb=" N SER A 8 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 23 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 20 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A 66 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 14 removed outlier: 3.781A pdb=" N GLU A 106 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 14 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 48 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 119 removed outlier: 3.654A pdb=" N PHE A 119 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL A 134 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR A 174 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 155 removed outlier: 3.836A pdb=" N VAL A 151 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 8 removed outlier: 3.920A pdb=" N GLN B 4 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 6 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 22 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.023A pdb=" N GLY B 11 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 92 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET B 35 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL B 51 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP B 37 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 126 removed outlier: 5.557A pdb=" N LEU B 145 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N SER B 184 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYS B 147 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU B 182 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR B 149 " --> pdb=" O TYR B 180 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER B 181 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA B 172 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER B 183 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS B 168 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 154 through 158 removed outlier: 4.096A pdb=" N TYR B 198 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 5 through 8 removed outlier: 3.592A pdb=" N SER C 8 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C 23 " --> pdb=" O SER C 8 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 14 removed outlier: 3.581A pdb=" N LEU C 12 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU C 106 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR C 50 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 130 through 140 removed outlier: 6.039A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 148 through 149 Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 8 removed outlier: 3.695A pdb=" N VAL D 6 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER D 8 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER D 22 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 19 " --> pdb=" O MET D 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.495A pdb=" N GLY D 11 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET D 35 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL D 51 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP D 37 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 124 through 126 removed outlier: 3.866A pdb=" N PHE D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU D 145 " --> pdb=" O PHE D 126 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU D 145 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER D 184 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS D 147 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU D 182 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR D 149 " --> pdb=" O TYR D 180 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 124 through 126 removed outlier: 3.866A pdb=" N PHE D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU D 145 " --> pdb=" O PHE D 126 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU D 145 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER D 184 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS D 147 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU D 182 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR D 149 " --> pdb=" O TYR D 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 155 through 158 removed outlier: 3.596A pdb=" N TYR D 198 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS D 200 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 213 " --> pdb=" O CYS D 200 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AC1, first strand: chain 'E' and resid 20 through 22 removed outlier: 3.681A pdb=" N ARG F 14 " --> pdb=" O SER F 5 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.638A pdb=" N HIS E 35 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N VAL E 171 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS E 170 " --> pdb=" O LEU E 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 87 through 88 removed outlier: 5.962A pdb=" N THR E 87 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL E 135 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE E 57 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N GLY E 56 " --> pdb=" O ALA E 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 328 through 331 removed outlier: 3.743A pdb=" N PHE E 323 " --> pdb=" O TRP E 330 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU E 212 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU E 205 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG E 214 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR F 186 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA F 187 " --> pdb=" O ALA F 194 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLU F 205 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU F 212 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N LYS F 213 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N PHE F 277 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.400A pdb=" N TRP F 168 " --> pdb=" O GLU F 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 56 through 57 removed outlier: 7.629A pdb=" N GLY F 56 " --> pdb=" O ALA F 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 87 through 90 removed outlier: 6.916A pdb=" N THR F 87 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL F 135 " --> pdb=" O THR F 87 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL F 89 " --> pdb=" O VAL F 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 284 through 287 removed outlier: 7.238A pdb=" N LYS F 284 " --> pdb=" O TRP F 311 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N CYS F 313 " --> pdb=" O LYS F 284 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR F 286 " --> pdb=" O CYS F 313 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.554A pdb=" N ALA G 22 " --> pdb=" O GLN G 4 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.745A pdb=" N VAL G 11 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG G 37 " --> pdb=" O PHE G 46 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE G 46 " --> pdb=" O ARG G 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 2 through 6 removed outlier: 3.613A pdb=" N LEU H 17 " --> pdb=" O MET H 82 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.822A pdb=" N VAL H 11 " --> pdb=" O THR H 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.095A pdb=" N PHE H 46 " --> pdb=" O ARG H 37 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ARG H 37 " --> pdb=" O PHE H 46 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER H 34 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA H 96 " --> pdb=" O SER H 34 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 867 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: 3.83 Time building geometry restraints manager: 5.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4569 1.34 - 1.46: 3475 1.46 - 1.58: 6344 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 14488 Sorted by residual: bond pdb=" N LYS D 133 " pdb=" CA LYS D 133 " ideal model delta sigma weight residual 1.460 1.514 -0.054 2.20e-02 2.07e+03 6.04e+00 bond pdb=" C SER D 132 " pdb=" N LYS D 133 " ideal model delta sigma weight residual 1.341 1.379 -0.038 2.13e-02 2.20e+03 3.11e+00 bond pdb=" N ASP E 1 " pdb=" CA ASP E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" CA LYS B 133 " pdb=" C LYS B 133 " ideal model delta sigma weight residual 1.524 1.546 -0.022 1.47e-02 4.63e+03 2.14e+00 ... (remaining 14483 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.21: 504 107.21 - 113.94: 7975 113.94 - 120.66: 5271 120.66 - 127.39: 5707 127.39 - 134.12: 209 Bond angle restraints: 19666 Sorted by residual: angle pdb=" N LYS D 133 " pdb=" CA LYS D 133 " pdb=" C LYS D 133 " ideal model delta sigma weight residual 108.53 119.80 -11.27 2.07e+00 2.33e-01 2.96e+01 angle pdb=" N GLY H 105 " pdb=" CA GLY H 105 " pdb=" C GLY H 105 " ideal model delta sigma weight residual 113.18 124.87 -11.69 2.37e+00 1.78e-01 2.43e+01 angle pdb=" C SER C 209 " pdb=" N PHE C 210 " pdb=" CA PHE C 210 " ideal model delta sigma weight residual 121.54 129.52 -7.98 1.91e+00 2.74e-01 1.75e+01 angle pdb=" C SER A 209 " pdb=" N PHE A 210 " pdb=" CA PHE A 210 " ideal model delta sigma weight residual 122.19 131.57 -9.38 2.30e+00 1.89e-01 1.66e+01 angle pdb=" N SER H 104 " pdb=" CA SER H 104 " pdb=" C SER H 104 " ideal model delta sigma weight residual 110.80 119.37 -8.57 2.13e+00 2.20e-01 1.62e+01 ... (remaining 19661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 7686 17.57 - 35.13: 773 35.13 - 52.70: 186 52.70 - 70.26: 35 70.26 - 87.83: 12 Dihedral angle restraints: 8692 sinusoidal: 3448 harmonic: 5244 Sorted by residual: dihedral pdb=" CA PRO D 130 " pdb=" C PRO D 130 " pdb=" N SER D 131 " pdb=" CA SER D 131 " ideal model delta harmonic sigma weight residual 180.00 -143.98 -36.02 0 5.00e+00 4.00e-02 5.19e+01 dihedral pdb=" CA PRO E 320 " pdb=" C PRO E 320 " pdb=" N LEU E 321 " pdb=" CA LEU E 321 " ideal model delta harmonic sigma weight residual 180.00 147.14 32.86 0 5.00e+00 4.00e-02 4.32e+01 dihedral pdb=" CB CYS F 313 " pdb=" SG CYS F 313 " pdb=" SG CYS F 316 " pdb=" CB CYS F 316 " ideal model delta sinusoidal sigma weight residual -86.00 -137.40 51.40 1 1.00e+01 1.00e-02 3.61e+01 ... (remaining 8689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1924 0.066 - 0.133: 210 0.133 - 0.199: 8 0.199 - 0.266: 0 0.266 - 0.332: 1 Chirality restraints: 2143 Sorted by residual: chirality pdb=" CA LYS D 133 " pdb=" N LYS D 133 " pdb=" C LYS D 133 " pdb=" CB LYS D 133 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA PRO D 130 " pdb=" N PRO D 130 " pdb=" C PRO D 130 " pdb=" CB PRO D 130 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CA SER H 104 " pdb=" N SER H 104 " pdb=" C SER H 104 " pdb=" CB SER H 104 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 2140 not shown) Planarity restraints: 2529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 318 " -0.044 5.00e-02 4.00e+02 6.83e-02 7.46e+00 pdb=" N PRO E 319 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 319 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 319 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 129 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO B 130 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 130 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 130 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 152 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO D 153 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 153 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 153 " -0.025 5.00e-02 4.00e+02 ... (remaining 2526 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 162 2.55 - 3.14: 11411 3.14 - 3.72: 20696 3.72 - 4.31: 27386 4.31 - 4.90: 46783 Nonbonded interactions: 106438 Sorted by model distance: nonbonded pdb=" OG SER E 5 " pdb=" OH TYR F 22 " model vdw 1.960 2.440 nonbonded pdb=" OD1 ASP C 171 " pdb=" OG1 THR C 173 " model vdw 2.004 2.440 nonbonded pdb=" OD2 ASP D 221 " pdb=" OG1 THR D 223 " model vdw 2.075 2.440 nonbonded pdb=" OG SER H 16 " pdb=" O MET H 82 " model vdw 2.078 2.440 nonbonded pdb=" OD1 ASP A 171 " pdb=" OG1 THR A 173 " model vdw 2.126 2.440 ... (remaining 106433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 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: 0.540 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 36.840 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 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 : 0.003 0.054 14488 Z= 0.160 Angle : 0.579 11.687 19666 Z= 0.311 Chirality : 0.042 0.332 2143 Planarity : 0.004 0.068 2528 Dihedral : 15.008 87.828 5270 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.00 % Favored : 91.78 % Rotamer: Outliers : 0.13 % Allowed : 13.53 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.20), residues: 1800 helix: 0.25 (0.57), residues: 75 sheet: 0.47 (0.26), residues: 440 loop : -1.31 (0.18), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 210 HIS 0.005 0.001 HIS C 199 PHE 0.020 0.001 PHE A 210 TYR 0.017 0.001 TYR F 22 ARG 0.012 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 261 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 LEU cc_start: 0.8278 (pt) cc_final: 0.7886 (tt) REVERT: F 37 ASP cc_start: 0.6890 (t0) cc_final: 0.6606 (t70) REVERT: F 318 MET cc_start: 0.6461 (tpp) cc_final: 0.5642 (tpp) REVERT: G 30 ARG cc_start: 0.6190 (mtm180) cc_final: 0.5924 (ptt90) REVERT: G 94 TYR cc_start: 0.7920 (m-80) cc_final: 0.7701 (m-80) REVERT: G 112 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7153 (pm20) outliers start: 2 outliers final: 1 residues processed: 262 average time/residue: 0.2689 time to fit residues: 100.5731 Evaluate side-chains 215 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 198 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 105 optimal weight: 0.0770 chunk 163 optimal weight: 6.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 125 GLN A 211 ASN ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN C 161 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 HIS F 82 ASN H 76 ASN H 81 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 14488 Z= 0.395 Angle : 0.831 13.090 19666 Z= 0.442 Chirality : 0.048 0.232 2143 Planarity : 0.007 0.074 2528 Dihedral : 6.283 57.449 2032 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.78 % Favored : 89.94 % Rotamer: Outliers : 4.55 % Allowed : 15.00 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.19), residues: 1800 helix: -1.14 (0.52), residues: 82 sheet: 0.05 (0.23), residues: 511 loop : -1.66 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP H 35 HIS 0.009 0.002 HIS C 199 PHE 0.023 0.003 PHE A 72 TYR 0.030 0.003 TYR F 22 ARG 0.007 0.001 ARG G 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 244 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.5708 (tpp) cc_final: 0.5392 (tpp) REVERT: A 15 SER cc_start: 0.7681 (t) cc_final: 0.7341 (m) REVERT: A 18 ASP cc_start: 0.6723 (t0) cc_final: 0.6515 (t0) REVERT: B 12 LEU cc_start: 0.8342 (pt) cc_final: 0.7865 (tt) REVERT: C 18 ASP cc_start: 0.7492 (t0) cc_final: 0.7029 (t0) REVERT: C 211 ASN cc_start: 0.1169 (OUTLIER) cc_final: 0.0820 (m110) REVERT: F 20 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.6566 (m-80) REVERT: F 50 TRP cc_start: 0.7809 (t60) cc_final: 0.7605 (t-100) REVERT: F 70 SER cc_start: 0.9008 (m) cc_final: 0.8751 (t) REVERT: F 209 THR cc_start: 0.8473 (p) cc_final: 0.8243 (p) REVERT: G 35 TRP cc_start: 0.6510 (t-100) cc_final: 0.6171 (t-100) REVERT: G 94 TYR cc_start: 0.7877 (m-80) cc_final: 0.7635 (m-80) REVERT: G 112 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7064 (pm20) REVERT: H 35 TRP cc_start: 0.6875 (m100) cc_final: 0.6553 (m100) REVERT: H 66 ARG cc_start: 0.8544 (mmp80) cc_final: 0.8268 (mmp80) outliers start: 71 outliers final: 49 residues processed: 295 average time/residue: 0.2611 time to fit residues: 113.4826 Evaluate side-chains 255 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 204 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 162 optimal weight: 0.0870 chunk 55 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14488 Z= 0.210 Angle : 0.669 12.891 19666 Z= 0.349 Chirality : 0.043 0.221 2143 Planarity : 0.005 0.086 2528 Dihedral : 5.488 54.124 2032 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.39 % Favored : 92.39 % Rotamer: Outliers : 4.23 % Allowed : 18.33 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.20), residues: 1800 helix: -0.92 (0.52), residues: 81 sheet: 0.06 (0.24), residues: 486 loop : -1.49 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 210 HIS 0.006 0.001 HIS C 199 PHE 0.021 0.001 PHE A 210 TYR 0.022 0.002 TYR C 141 ARG 0.005 0.000 ARG E 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 230 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.6721 (t0) cc_final: 0.6491 (t0) REVERT: B 5 LEU cc_start: 0.5680 (OUTLIER) cc_final: 0.5398 (mp) REVERT: B 12 LEU cc_start: 0.8350 (pt) cc_final: 0.7829 (tt) REVERT: C 18 ASP cc_start: 0.7150 (t0) cc_final: 0.6935 (t0) REVERT: C 88 TYR cc_start: 0.5756 (OUTLIER) cc_final: 0.3735 (p90) REVERT: D 95 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.5438 (p90) REVERT: E 67 MET cc_start: 0.9087 (tmm) cc_final: 0.8748 (tmm) REVERT: E 349 MET cc_start: 0.5428 (ttt) cc_final: 0.4304 (ptt) REVERT: F 151 ASN cc_start: 0.8165 (t0) cc_final: 0.7931 (t0) REVERT: F 209 THR cc_start: 0.8531 (p) cc_final: 0.8326 (p) REVERT: G 94 TYR cc_start: 0.7936 (m-80) cc_final: 0.7733 (m-80) REVERT: G 112 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7174 (pm20) REVERT: H 19 LEU cc_start: 0.8722 (mm) cc_final: 0.8419 (tt) REVERT: H 36 PHE cc_start: 0.7849 (m-80) cc_final: 0.7540 (t80) REVERT: H 82 MET cc_start: 0.8777 (ptp) cc_final: 0.8117 (tmm) REVERT: H 89 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7295 (t0) outliers start: 66 outliers final: 42 residues processed: 277 average time/residue: 0.2403 time to fit residues: 98.9271 Evaluate side-chains 249 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 203 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN D 175 GLN F 147 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14488 Z= 0.266 Angle : 0.728 21.572 19666 Z= 0.380 Chirality : 0.045 0.225 2143 Planarity : 0.005 0.072 2528 Dihedral : 5.679 55.903 2030 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.17 % Favored : 90.61 % Rotamer: Outliers : 4.87 % Allowed : 19.29 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.19), residues: 1800 helix: -0.84 (0.53), residues: 81 sheet: -0.02 (0.24), residues: 468 loop : -1.62 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 35 HIS 0.005 0.001 HIS C 199 PHE 0.022 0.002 PHE A 210 TYR 0.020 0.002 TYR C 141 ARG 0.005 0.001 ARG F 338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 216 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7058 (t0) cc_final: 0.6776 (t0) REVERT: B 12 LEU cc_start: 0.8390 (pt) cc_final: 0.7937 (tt) REVERT: C 18 ASP cc_start: 0.7431 (t0) cc_final: 0.7222 (t0) REVERT: C 88 TYR cc_start: 0.5648 (OUTLIER) cc_final: 0.3049 (p90) REVERT: D 95 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.5326 (p90) REVERT: E 67 MET cc_start: 0.9087 (tmm) cc_final: 0.8832 (tmm) REVERT: E 349 MET cc_start: 0.5578 (ttt) cc_final: 0.4531 (ptm) REVERT: F 22 TYR cc_start: 0.7424 (m-80) cc_final: 0.7099 (m-80) REVERT: G 112 GLN cc_start: 0.7369 (mm-40) cc_final: 0.7123 (pm20) REVERT: H 36 PHE cc_start: 0.7966 (m-80) cc_final: 0.7608 (t80) outliers start: 76 outliers final: 55 residues processed: 274 average time/residue: 0.2405 time to fit residues: 97.8538 Evaluate side-chains 259 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 202 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 120 optimal weight: 0.0770 chunk 0 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN C 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14488 Z= 0.183 Angle : 0.666 15.791 19666 Z= 0.343 Chirality : 0.043 0.224 2143 Planarity : 0.005 0.067 2528 Dihedral : 5.288 54.386 2030 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.39 % Favored : 92.39 % Rotamer: Outliers : 4.29 % Allowed : 21.15 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.19), residues: 1800 helix: -0.66 (0.54), residues: 81 sheet: 0.14 (0.25), residues: 441 loop : -1.58 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 35 HIS 0.003 0.001 HIS C 199 PHE 0.019 0.001 PHE A 210 TYR 0.024 0.001 TYR C 141 ARG 0.005 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 218 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7085 (t0) cc_final: 0.6798 (t0) REVERT: A 32 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7330 (t) REVERT: B 12 LEU cc_start: 0.8449 (pt) cc_final: 0.8004 (tt) REVERT: B 47 GLU cc_start: 0.7242 (tp30) cc_final: 0.6265 (mt-10) REVERT: C 18 ASP cc_start: 0.7314 (t0) cc_final: 0.7091 (t0) REVERT: C 88 TYR cc_start: 0.5643 (OUTLIER) cc_final: 0.3858 (p90) REVERT: C 90 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8163 (tm130) REVERT: D 95 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.4821 (p90) REVERT: E 349 MET cc_start: 0.5590 (ttt) cc_final: 0.4601 (ptm) REVERT: F 22 TYR cc_start: 0.7090 (m-80) cc_final: 0.6867 (m-80) REVERT: F 26 GLU cc_start: 0.6881 (mp0) cc_final: 0.6164 (pp20) REVERT: G 112 GLN cc_start: 0.7393 (mm-40) cc_final: 0.7114 (pm20) outliers start: 67 outliers final: 47 residues processed: 275 average time/residue: 0.2455 time to fit residues: 99.8610 Evaluate side-chains 256 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 205 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 223 CYS Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 0.0040 chunk 42 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14488 Z= 0.195 Angle : 0.675 15.010 19666 Z= 0.346 Chirality : 0.043 0.220 2143 Planarity : 0.005 0.069 2528 Dihedral : 5.253 54.706 2030 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.61 % Favored : 91.22 % Rotamer: Outliers : 4.23 % Allowed : 21.99 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.19), residues: 1800 helix: -0.63 (0.54), residues: 81 sheet: 0.18 (0.25), residues: 415 loop : -1.55 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 35 HIS 0.003 0.001 HIS B 168 PHE 0.019 0.001 PHE A 210 TYR 0.023 0.001 TYR C 141 ARG 0.005 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 220 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7085 (t0) cc_final: 0.6761 (t0) REVERT: A 32 SER cc_start: 0.7722 (OUTLIER) cc_final: 0.7306 (t) REVERT: B 4 GLN cc_start: 0.6333 (OUTLIER) cc_final: 0.5836 (tm-30) REVERT: B 12 LEU cc_start: 0.8415 (pt) cc_final: 0.7932 (tt) REVERT: B 47 GLU cc_start: 0.7248 (tp30) cc_final: 0.6305 (mt-10) REVERT: C 88 TYR cc_start: 0.5659 (OUTLIER) cc_final: 0.4013 (p90) REVERT: D 95 TYR cc_start: 0.6783 (OUTLIER) cc_final: 0.4814 (p90) REVERT: E 349 MET cc_start: 0.5647 (ttt) cc_final: 0.4703 (ptm) REVERT: F 22 TYR cc_start: 0.7170 (m-80) cc_final: 0.6900 (m-80) REVERT: F 318 MET cc_start: 0.5420 (OUTLIER) cc_final: 0.4696 (tmm) REVERT: G 35 TRP cc_start: 0.6638 (OUTLIER) cc_final: 0.5606 (m-90) REVERT: G 112 GLN cc_start: 0.7300 (mm-40) cc_final: 0.7043 (pm20) REVERT: H 36 PHE cc_start: 0.7869 (m-80) cc_final: 0.7381 (t80) outliers start: 66 outliers final: 52 residues processed: 271 average time/residue: 0.2378 time to fit residues: 96.1590 Evaluate side-chains 270 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 212 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 329 CYS Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 223 CYS Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 318 MET Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 0.0470 chunk 173 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 269 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14488 Z= 0.273 Angle : 0.723 17.127 19666 Z= 0.376 Chirality : 0.044 0.221 2143 Planarity : 0.005 0.068 2528 Dihedral : 5.640 56.067 2030 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.44 % Favored : 90.39 % Rotamer: Outliers : 4.94 % Allowed : 22.05 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.19), residues: 1800 helix: -0.96 (0.52), residues: 81 sheet: 0.06 (0.25), residues: 461 loop : -1.71 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 35 HIS 0.004 0.001 HIS E 195 PHE 0.020 0.002 PHE A 210 TYR 0.023 0.002 TYR C 141 ARG 0.004 0.001 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 217 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7274 (t0) cc_final: 0.6974 (t0) REVERT: A 32 SER cc_start: 0.8062 (OUTLIER) cc_final: 0.7640 (t) REVERT: B 12 LEU cc_start: 0.8429 (pt) cc_final: 0.7955 (tt) REVERT: B 47 GLU cc_start: 0.7489 (tp30) cc_final: 0.6496 (mt-10) REVERT: D 95 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.5263 (p90) REVERT: E 85 GLN cc_start: 0.7325 (tp40) cc_final: 0.7100 (tp40) REVERT: F 318 MET cc_start: 0.5182 (OUTLIER) cc_final: 0.4663 (tmm) REVERT: G 35 TRP cc_start: 0.6745 (OUTLIER) cc_final: 0.5456 (m-90) REVERT: G 112 GLN cc_start: 0.7184 (mm-40) cc_final: 0.6856 (pp30) REVERT: H 36 PHE cc_start: 0.8080 (m-80) cc_final: 0.7485 (t80) outliers start: 77 outliers final: 63 residues processed: 278 average time/residue: 0.2262 time to fit residues: 94.8875 Evaluate side-chains 275 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 208 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 223 CYS Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 318 MET Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 4 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14488 Z= 0.197 Angle : 0.683 13.938 19666 Z= 0.349 Chirality : 0.043 0.221 2143 Planarity : 0.005 0.073 2528 Dihedral : 5.321 54.428 2030 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.11 % Favored : 91.72 % Rotamer: Outliers : 4.49 % Allowed : 22.95 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.19), residues: 1800 helix: -0.93 (0.53), residues: 82 sheet: 0.10 (0.25), residues: 418 loop : -1.60 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 35 HIS 0.003 0.001 HIS B 204 PHE 0.017 0.001 PHE A 210 TYR 0.028 0.001 TYR D 149 ARG 0.005 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 219 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7215 (t0) cc_final: 0.6909 (t0) REVERT: A 32 SER cc_start: 0.7888 (OUTLIER) cc_final: 0.7541 (t) REVERT: B 12 LEU cc_start: 0.8390 (pt) cc_final: 0.7938 (tt) REVERT: B 47 GLU cc_start: 0.7412 (tp30) cc_final: 0.6436 (mt-10) REVERT: C 88 TYR cc_start: 0.5682 (OUTLIER) cc_final: 0.4037 (p90) REVERT: D 4 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6178 (mp10) REVERT: D 95 TYR cc_start: 0.6748 (OUTLIER) cc_final: 0.4766 (p90) REVERT: E 85 GLN cc_start: 0.7267 (tp40) cc_final: 0.7040 (tp40) REVERT: E 349 MET cc_start: 0.5650 (ttt) cc_final: 0.5329 (ptm) REVERT: F 26 GLU cc_start: 0.6823 (mp0) cc_final: 0.6390 (pp20) REVERT: F 318 MET cc_start: 0.5202 (OUTLIER) cc_final: 0.4564 (tmm) REVERT: G 35 TRP cc_start: 0.6655 (OUTLIER) cc_final: 0.5180 (m-90) REVERT: G 112 GLN cc_start: 0.7057 (mm-40) cc_final: 0.6620 (pp30) outliers start: 70 outliers final: 54 residues processed: 272 average time/residue: 0.2423 time to fit residues: 98.7966 Evaluate side-chains 271 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 211 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 223 CYS Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 318 MET Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 chunk 97 optimal weight: 0.1980 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 106 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 156 GLN E 48 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14488 Z= 0.184 Angle : 0.670 13.808 19666 Z= 0.342 Chirality : 0.043 0.212 2143 Planarity : 0.005 0.073 2528 Dihedral : 5.170 54.239 2030 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.50 % Favored : 91.33 % Rotamer: Outliers : 4.04 % Allowed : 23.59 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.19), residues: 1800 helix: -0.75 (0.53), residues: 82 sheet: 0.02 (0.25), residues: 448 loop : -1.52 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 35 HIS 0.002 0.001 HIS B 168 PHE 0.017 0.001 PHE A 210 TYR 0.023 0.001 TYR C 141 ARG 0.003 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 217 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7146 (t0) cc_final: 0.6844 (t0) REVERT: A 21 THR cc_start: 0.7046 (OUTLIER) cc_final: 0.6767 (t) REVERT: A 32 SER cc_start: 0.7882 (OUTLIER) cc_final: 0.7520 (t) REVERT: B 12 LEU cc_start: 0.8406 (pt) cc_final: 0.8079 (tt) REVERT: B 47 GLU cc_start: 0.7431 (tp30) cc_final: 0.6399 (mt-10) REVERT: C 2 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7265 (m-30) REVERT: C 88 TYR cc_start: 0.5549 (OUTLIER) cc_final: 0.3735 (p90) REVERT: D 95 TYR cc_start: 0.6683 (OUTLIER) cc_final: 0.4580 (p90) REVERT: E 85 GLN cc_start: 0.7241 (tp40) cc_final: 0.7005 (tp40) REVERT: E 349 MET cc_start: 0.5812 (ttt) cc_final: 0.5284 (ptm) REVERT: F 26 GLU cc_start: 0.6828 (mp0) cc_final: 0.6470 (pp20) REVERT: F 318 MET cc_start: 0.5213 (OUTLIER) cc_final: 0.4497 (tmm) REVERT: G 34 SER cc_start: 0.7854 (p) cc_final: 0.7254 (m) REVERT: G 35 TRP cc_start: 0.6644 (OUTLIER) cc_final: 0.5104 (m-90) REVERT: G 112 GLN cc_start: 0.7150 (mm-40) cc_final: 0.6523 (pp30) REVERT: H 36 PHE cc_start: 0.7901 (m-80) cc_final: 0.7363 (t80) outliers start: 63 outliers final: 47 residues processed: 266 average time/residue: 0.2360 time to fit residues: 94.0488 Evaluate side-chains 264 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 210 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 223 CYS Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 318 MET Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 118 optimal weight: 0.4980 chunk 179 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 4 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14488 Z= 0.232 Angle : 0.710 15.406 19666 Z= 0.364 Chirality : 0.044 0.212 2143 Planarity : 0.005 0.077 2528 Dihedral : 5.374 53.326 2030 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.39 % Favored : 90.39 % Rotamer: Outliers : 3.78 % Allowed : 23.97 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.19), residues: 1800 helix: -0.71 (0.55), residues: 76 sheet: -0.01 (0.25), residues: 454 loop : -1.52 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 35 HIS 0.004 0.001 HIS E 195 PHE 0.017 0.002 PHE A 210 TYR 0.026 0.002 TYR C 141 ARG 0.004 0.000 ARG C 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 211 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7301 (t0) cc_final: 0.6920 (t0) REVERT: A 21 THR cc_start: 0.7273 (OUTLIER) cc_final: 0.7037 (t) REVERT: A 32 SER cc_start: 0.8081 (OUTLIER) cc_final: 0.7627 (t) REVERT: B 12 LEU cc_start: 0.8489 (pt) cc_final: 0.8176 (tt) REVERT: B 47 GLU cc_start: 0.7502 (tp30) cc_final: 0.6451 (mt-10) REVERT: C 88 TYR cc_start: 0.5635 (OUTLIER) cc_final: 0.3701 (p90) REVERT: D 4 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6319 (mp10) REVERT: D 32 SER cc_start: 0.6704 (p) cc_final: 0.6467 (p) REVERT: D 95 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.4860 (p90) REVERT: E 349 MET cc_start: 0.6098 (ttt) cc_final: 0.5305 (ptm) REVERT: G 34 SER cc_start: 0.7862 (p) cc_final: 0.7242 (m) REVERT: G 35 TRP cc_start: 0.6758 (OUTLIER) cc_final: 0.5088 (m-90) REVERT: G 112 GLN cc_start: 0.7044 (mm-40) cc_final: 0.6403 (pp30) REVERT: H 36 PHE cc_start: 0.7965 (m-80) cc_final: 0.7323 (t80) outliers start: 59 outliers final: 49 residues processed: 261 average time/residue: 0.2432 time to fit residues: 95.0471 Evaluate side-chains 257 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 202 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 223 CYS Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 0.0030 chunk 125 optimal weight: 1.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 4 GLN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.163862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124688 restraints weight = 27801.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.124825 restraints weight = 16828.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.125891 restraints weight = 13638.688| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.196 14488 Z= 0.332 Angle : 0.895 59.193 19666 Z= 0.519 Chirality : 0.045 0.385 2143 Planarity : 0.005 0.076 2528 Dihedral : 5.368 53.247 2030 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.39 % Favored : 90.39 % Rotamer: Outliers : 4.04 % Allowed : 23.78 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.19), residues: 1800 helix: -0.87 (0.53), residues: 82 sheet: 0.00 (0.25), residues: 453 loop : -1.54 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 35 HIS 0.004 0.001 HIS E 195 PHE 0.018 0.002 PHE A 210 TYR 0.024 0.002 TYR C 141 ARG 0.005 0.000 ARG G 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3073.62 seconds wall clock time: 56 minutes 3.36 seconds (3363.36 seconds total)