Starting phenix.real_space_refine on Sat Mar 16 13:30:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnb_14073/03_2024/7qnb_14073_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnb_14073/03_2024/7qnb_14073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnb_14073/03_2024/7qnb_14073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnb_14073/03_2024/7qnb_14073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnb_14073/03_2024/7qnb_14073_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnb_14073/03_2024/7qnb_14073_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 82 5.16 5 C 9639 2.51 5 N 2383 2.21 5 O 2689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14793 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2701 Classifications: {'peptide': 328} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 314} Chain breaks: 1 Chain: "B" Number of atoms: 2714 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 bond proxies already assigned to first conformer: 2775 Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2701 Classifications: {'peptide': 328} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 314} Chain breaks: 1 Chain: "D" Number of atoms: 2721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 bond proxies already assigned to first conformer: 2767 Chain: "E" Number of atoms: 2714 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 bond proxies already assigned to first conformer: 2775 Chain: "N" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" 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: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" 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 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR D 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 66 " occ=0.50 Time building chain proxies: 12.63, per 1000 atoms: 0.85 Number of scatterers: 14793 At special positions: 0 Unit cell: (119.168, 92.288, 128.128, 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 82 16.00 O 2689 8.00 N 2383 7.00 C 9639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS N 409 " - pdb=" SG CYS N 483 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG b 1 " - " NAG b 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 501 " - " ASN A 208 " " NAG C 501 " - " ASN C 208 " " NAG F 1 " - " ASN B 149 " " NAG G 1 " - " ASN D 149 " " NAG H 1 " - " ASN E 149 " " NAG b 1 " - " ASN B 80 " " NAG d 1 " - " ASN D 80 " " NAG e 1 " - " ASN E 80 " Time building additional restraints: 5.90 Conformation dependent library (CDL) restraints added in 4.0 seconds 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 23 sheets defined 34.5% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 28 through 35 Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.532A pdb=" N GLY A 104 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 241 through 256 removed outlier: 3.956A pdb=" N SER A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP A 256 " --> pdb=" O TRP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 283 removed outlier: 3.568A pdb=" N ILE A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 322 removed outlier: 3.503A pdb=" N LEU A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 434 removed outlier: 3.600A pdb=" N ILE A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.542A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.502A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 4.115A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 306 Processing helix chain 'B' and resid 313 through 446 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.533A pdb=" N GLY C 104 " --> pdb=" O ASN C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 241 through 256 removed outlier: 3.955A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 283 removed outlier: 3.568A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 322 removed outlier: 3.504A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 434 removed outlier: 3.600A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.542A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 226 through 241 removed outlier: 4.359A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 271 removed outlier: 4.114A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR D 271 " --> pdb=" O HIS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 306 Processing helix chain 'D' and resid 313 through 446 Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 85 through 90 removed outlier: 3.542A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 226 through 241 removed outlier: 3.501A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 271 removed outlier: 4.114A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR E 271 " --> pdb=" O HIS E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 306 Processing helix chain 'E' and resid 313 through 446 Proline residue: E 432 - end of helix Processing helix chain 'N' and resid 475 through 477 No H-bonds generated for 'chain 'N' and resid 475 through 477' Processing helix chain 'N' and resid 496 through 498 No H-bonds generated for 'chain 'N' and resid 496 through 498' Processing sheet with id= A, first strand: chain 'A' and resid 179 through 183 removed outlier: 6.114A pdb=" N THR A 51 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLN A 182 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE A 53 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 52 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYR A 83 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR A 58 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP A 75 " --> pdb=" O ASN A 60 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE A 62 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR A 73 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG A 138 " --> pdb=" O TRP A 134 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU A 131 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 57 through 59 Processing sheet with id= C, first strand: chain 'A' and resid 111 through 113 removed outlier: 4.644A pdb=" N SER A 171 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 221 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 205 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER A 230 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE A 203 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 116 through 121 removed outlier: 6.931A pdb=" N ASP A 148 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA A 119 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR A 146 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.206A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.929A pdb=" N MET B 49 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.952A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.679A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 179 through 183 removed outlier: 6.115A pdb=" N THR C 51 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLN C 182 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE C 53 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR C 58 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 57 through 59 Processing sheet with id= K, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.644A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 116 through 121 removed outlier: 6.932A pdb=" N ASP C 148 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA C 119 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR C 146 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 164 through 168 removed outlier: 6.206A pdb=" N VAL D 36 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR D 167 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL D 38 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.929A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.952A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.680A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.206A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 49 through 51 removed outlier: 3.929A pdb=" N MET E 49 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.951A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.679A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'N' and resid 2 through 7 removed outlier: 3.557A pdb=" N THR N 465 " --> pdb=" O ASP N 460 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'N' and resid 506 through 508 removed outlier: 3.647A pdb=" N VAL N 508 " --> pdb=" O ALA N 479 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ARG N 425 " --> pdb=" O PHE N 434 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N PHE N 434 " --> pdb=" O ARG N 425 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'N' and resid 484 through 486 removed outlier: 3.922A pdb=" N TYR N 501 " --> pdb=" O ALA N 485 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 6.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4481 1.34 - 1.46: 3821 1.46 - 1.58: 6741 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 15183 Sorted by residual: bond pdb=" CG ABU B 501 " pdb=" CD ABU B 501 " ideal model delta sigma weight residual 1.540 1.500 0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" C1 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.399 1.429 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 MAN G 5 " pdb=" O5 MAN G 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 MAN H 5 " pdb=" O5 MAN H 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 MAN F 5 " pdb=" O5 MAN F 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.05e+00 ... (remaining 15178 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.19: 450 107.19 - 113.89: 8618 113.89 - 120.59: 5936 120.59 - 127.29: 5493 127.29 - 133.99: 165 Bond angle restraints: 20662 Sorted by residual: angle pdb=" CG ABU B 501 " pdb=" CD ABU B 501 " pdb=" OE2 ABU B 501 " ideal model delta sigma weight residual 115.90 123.18 -7.28 3.00e+00 1.11e-01 5.89e+00 angle pdb=" C3 BMA H 3 " pdb=" C2 BMA H 3 " pdb=" O2 BMA H 3 " ideal model delta sigma weight residual 112.95 106.61 6.34 3.00e+00 1.11e-01 4.47e+00 angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.69 6.26 3.00e+00 1.11e-01 4.35e+00 angle pdb=" C3 BMA G 3 " pdb=" C2 BMA G 3 " pdb=" O2 BMA G 3 " ideal model delta sigma weight residual 112.95 106.71 6.24 3.00e+00 1.11e-01 4.33e+00 angle pdb=" CA TYR E 299 " pdb=" CB TYR E 299 " pdb=" CG TYR E 299 " ideal model delta sigma weight residual 113.90 110.22 3.68 1.80e+00 3.09e-01 4.17e+00 ... (remaining 20657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.76: 8891 21.76 - 43.52: 205 43.52 - 65.28: 28 65.28 - 87.04: 22 87.04 - 108.80: 14 Dihedral angle restraints: 9160 sinusoidal: 3922 harmonic: 5238 Sorted by residual: dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.91 108.80 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.93 108.78 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.52 107.23 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 9157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2049 0.056 - 0.113: 315 0.113 - 0.169: 18 0.169 - 0.225: 5 0.225 - 0.282: 4 Chirality restraints: 2391 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.00e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.25e+01 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.19e+01 ... (remaining 2388 not shown) Planarity restraints: 2528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 65 " -0.006 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" C GLN D 65 " 0.019 2.00e-02 2.50e+03 pdb=" O GLN D 65 " -0.007 2.00e-02 2.50e+03 pdb=" N BTYR D 66 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR D 143 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.13e+00 pdb=" N PRO D 144 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 144 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 144 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 143 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO E 144 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO E 144 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 144 " -0.014 5.00e-02 4.00e+02 ... (remaining 2525 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2577 2.77 - 3.30: 14080 3.30 - 3.84: 25289 3.84 - 4.37: 30824 4.37 - 4.90: 52272 Nonbonded interactions: 125042 Sorted by model distance: nonbonded pdb=" O VAL A 248 " pdb=" OG SER A 251 " model vdw 2.241 2.440 nonbonded pdb=" O VAL C 248 " pdb=" OG SER C 251 " model vdw 2.242 2.440 nonbonded pdb=" O ALA D 252 " pdb=" OG1 THR D 256 " model vdw 2.270 2.440 nonbonded pdb=" O ALA B 252 " pdb=" OG1 THR B 256 " model vdw 2.270 2.440 nonbonded pdb=" O ALA E 252 " pdb=" OG1 THR E 256 " model vdw 2.271 2.440 ... (remaining 125037 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' and (resid 7 through 43 or resid 45 through 65 or resid 67 through 44 \ 7)) selection = (chain 'D' and (resid 7 through 43 or resid 45 through 65 or resid 67 through 44 \ 7)) selection = (chain 'E' and (resid 7 through 43 or resid 45 through 65 or resid 67 through 44 \ 7)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 6.400 Check model and map are aligned: 0.440 Set scattering table: 0.000 Process input model: 47.170 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 0.040 15183 Z= 0.166 Angle : 0.457 7.284 20662 Z= 0.213 Chirality : 0.042 0.282 2391 Planarity : 0.003 0.027 2520 Dihedral : 11.197 108.803 5782 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.56 % Allowed : 3.32 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.21), residues: 1748 helix: 2.34 (0.22), residues: 559 sheet: 1.18 (0.25), residues: 468 loop : 0.51 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 241 HIS 0.002 0.000 HIS A 122 PHE 0.006 0.001 PHE E 293 TYR 0.015 0.001 TYR B 299 ARG 0.002 0.000 ARG D 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 356 time to evaluate : 1.549 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 71 GLU cc_start: 0.8401 (pt0) cc_final: 0.7747 (pt0) REVERT: A 105 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8565 (mmmm) REVERT: A 197 ARG cc_start: 0.8040 (ttp-110) cc_final: 0.7730 (mpt-90) REVERT: B 9 MET cc_start: 0.8364 (mtp) cc_final: 0.7483 (pmm) REVERT: B 115 MET cc_start: 0.7671 (ttp) cc_final: 0.7123 (ttp) REVERT: B 215 LYS cc_start: 0.8773 (tttt) cc_final: 0.8476 (tppt) REVERT: B 306 PHE cc_start: 0.7000 (t80) cc_final: 0.6685 (t80) REVERT: C 42 LEU cc_start: 0.9037 (mt) cc_final: 0.8744 (mt) REVERT: C 177 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8532 (mp0) REVERT: C 223 MET cc_start: 0.7852 (mmm) cc_final: 0.7425 (mmm) REVERT: D 55 MET cc_start: 0.8908 (mtt) cc_final: 0.8602 (mmm) REVERT: D 153 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8626 (mm-30) REVERT: D 190 GLU cc_start: 0.7689 (tt0) cc_final: 0.7393 (tt0) REVERT: D 215 LYS cc_start: 0.8855 (tttt) cc_final: 0.8613 (tmmt) REVERT: D 224 GLN cc_start: 0.8172 (tp40) cc_final: 0.7678 (tp40) REVERT: D 268 LEU cc_start: 0.7808 (mp) cc_final: 0.7504 (mp) REVERT: D 306 PHE cc_start: 0.7852 (t80) cc_final: 0.7607 (t80) REVERT: E 306 PHE cc_start: 0.7877 (t80) cc_final: 0.7664 (t80) REVERT: E 426 TRP cc_start: 0.7966 (t60) cc_final: 0.7720 (t60) REVERT: N 426 GLN cc_start: 0.7868 (tt0) cc_final: 0.7565 (tp-100) REVERT: N 432 ARG cc_start: 0.8024 (ttm170) cc_final: 0.7185 (ttm110) REVERT: N 472 ASN cc_start: 0.7958 (t0) cc_final: 0.7722 (t0) outliers start: 9 outliers final: 4 residues processed: 360 average time/residue: 0.3262 time to fit residues: 161.1716 Evaluate side-chains 211 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 207 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 255 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 73 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS B 267 HIS C 152 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15183 Z= 0.287 Angle : 0.626 9.289 20662 Z= 0.326 Chirality : 0.044 0.211 2391 Planarity : 0.004 0.037 2520 Dihedral : 8.065 78.442 2462 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.44 % Allowed : 8.83 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.21), residues: 1748 helix: 2.25 (0.21), residues: 563 sheet: 0.83 (0.24), residues: 491 loop : 0.43 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 123 HIS 0.004 0.001 HIS B 267 PHE 0.013 0.002 PHE B 11 TYR 0.027 0.002 TYR D 299 ARG 0.013 0.001 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 214 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8530 (mmtp) REVERT: A 130 MET cc_start: 0.7403 (ttm) cc_final: 0.7103 (ttm) REVERT: A 197 ARG cc_start: 0.8040 (ttp-110) cc_final: 0.7738 (mpt-90) REVERT: A 285 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8521 (mmmm) REVERT: B 9 MET cc_start: 0.8488 (mtp) cc_final: 0.8235 (pmm) REVERT: B 115 MET cc_start: 0.7556 (ttp) cc_final: 0.7228 (ttp) REVERT: C 71 GLU cc_start: 0.7949 (pm20) cc_final: 0.7577 (pm20) REVERT: C 102 MET cc_start: 0.6581 (mmp) cc_final: 0.5460 (mmm) REVERT: C 123 TRP cc_start: 0.7196 (m100) cc_final: 0.6853 (m100) REVERT: C 150 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7903 (tm-30) REVERT: C 152 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7715 (mm110) REVERT: C 177 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8572 (mp0) REVERT: C 223 MET cc_start: 0.8158 (mmm) cc_final: 0.7563 (mmm) REVERT: C 239 GLN cc_start: 0.8040 (mm110) cc_final: 0.7803 (mm-40) REVERT: D 9 MET cc_start: 0.8394 (mpp) cc_final: 0.8175 (mpp) REVERT: D 18 LYS cc_start: 0.9175 (pttp) cc_final: 0.8399 (pptt) REVERT: D 55 MET cc_start: 0.8920 (mtt) cc_final: 0.8615 (mtp) REVERT: D 215 LYS cc_start: 0.8943 (tttt) cc_final: 0.8696 (tptp) REVERT: D 224 GLN cc_start: 0.8009 (tp40) cc_final: 0.7392 (tp40) REVERT: D 235 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9219 (mp) REVERT: D 274 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7845 (mmtm) REVERT: D 306 PHE cc_start: 0.7923 (t80) cc_final: 0.7633 (t80) REVERT: E 55 MET cc_start: 0.8573 (mtp) cc_final: 0.8325 (mmm) REVERT: E 227 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8424 (mmt) REVERT: N 1 GLN cc_start: 0.8703 (pm20) cc_final: 0.8490 (pm20) REVERT: N 421 MET cc_start: 0.7523 (mmm) cc_final: 0.7164 (mmm) REVERT: N 426 GLN cc_start: 0.8230 (tt0) cc_final: 0.7756 (tp-100) REVERT: N 432 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7676 (ttm110) REVERT: N 460 ASP cc_start: 0.5904 (OUTLIER) cc_final: 0.5617 (p0) REVERT: N 472 ASN cc_start: 0.8095 (t0) cc_final: 0.7880 (t0) outliers start: 39 outliers final: 22 residues processed: 242 average time/residue: 0.2954 time to fit residues: 101.9547 Evaluate side-chains 219 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 426 TRP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain N residue 460 ASP Chi-restraints excluded: chain N residue 477 ASP Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 141 optimal weight: 0.3980 chunk 157 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS C 156 HIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15183 Z= 0.172 Angle : 0.551 8.987 20662 Z= 0.284 Chirality : 0.043 0.206 2391 Planarity : 0.003 0.042 2520 Dihedral : 7.343 72.775 2458 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.44 % Allowed : 10.08 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.21), residues: 1748 helix: 2.29 (0.21), residues: 561 sheet: 0.95 (0.24), residues: 473 loop : 0.33 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 67 HIS 0.003 0.001 HIS D 267 PHE 0.019 0.001 PHE E 306 TYR 0.025 0.001 TYR D 299 ARG 0.004 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 196 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8457 (mmtp) REVERT: A 130 MET cc_start: 0.7413 (ttm) cc_final: 0.6811 (tpp) REVERT: A 150 GLU cc_start: 0.8290 (tm-30) cc_final: 0.8077 (tm-30) REVERT: B 9 MET cc_start: 0.8573 (mtp) cc_final: 0.8281 (pmm) REVERT: B 115 MET cc_start: 0.7496 (ttp) cc_final: 0.7249 (ttp) REVERT: C 71 GLU cc_start: 0.7916 (pm20) cc_final: 0.7487 (pm20) REVERT: C 123 TRP cc_start: 0.7146 (m100) cc_final: 0.6916 (m100) REVERT: C 150 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7907 (tm-30) REVERT: C 152 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7997 (mm110) REVERT: C 177 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8511 (mp0) REVERT: C 189 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7850 (tm-30) REVERT: C 223 MET cc_start: 0.8066 (mmm) cc_final: 0.7373 (mtp) REVERT: D 9 MET cc_start: 0.8417 (mpp) cc_final: 0.8203 (mpp) REVERT: D 55 MET cc_start: 0.8889 (mtt) cc_final: 0.8631 (mtp) REVERT: D 215 LYS cc_start: 0.9002 (tttt) cc_final: 0.8747 (tptp) REVERT: D 274 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7719 (mmtm) REVERT: E 17 ASP cc_start: 0.8887 (t0) cc_final: 0.8229 (t0) REVERT: E 227 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8418 (mmt) REVERT: N 426 GLN cc_start: 0.8223 (tt0) cc_final: 0.7660 (tp-100) REVERT: N 432 ARG cc_start: 0.8093 (ttm170) cc_final: 0.7704 (ttm110) REVERT: N 472 ASN cc_start: 0.8325 (t0) cc_final: 0.8041 (t0) outliers start: 39 outliers final: 18 residues processed: 223 average time/residue: 0.2763 time to fit residues: 89.7313 Evaluate side-chains 199 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 180 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS E 267 HIS N 414 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15183 Z= 0.228 Angle : 0.575 9.330 20662 Z= 0.292 Chirality : 0.044 0.246 2391 Planarity : 0.004 0.088 2520 Dihedral : 6.650 66.707 2458 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.44 % Allowed : 10.33 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.21), residues: 1748 helix: 2.30 (0.21), residues: 565 sheet: 0.89 (0.24), residues: 467 loop : 0.24 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 67 HIS 0.002 0.001 HIS C 122 PHE 0.021 0.001 PHE B 306 TYR 0.029 0.002 TYR D 299 ARG 0.009 0.001 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 185 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7383 (ttm) cc_final: 0.6733 (tpp) REVERT: A 150 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7906 (tm-30) REVERT: C 58 TYR cc_start: 0.8127 (t80) cc_final: 0.7565 (t80) REVERT: C 70 MET cc_start: 0.9032 (mtp) cc_final: 0.8467 (mmm) REVERT: C 71 GLU cc_start: 0.7939 (pm20) cc_final: 0.7388 (pm20) REVERT: C 150 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7957 (tm-30) REVERT: C 152 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8071 (mm110) REVERT: C 177 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8571 (mp0) REVERT: C 223 MET cc_start: 0.8166 (mmm) cc_final: 0.7419 (mtp) REVERT: D 9 MET cc_start: 0.8483 (mpp) cc_final: 0.8282 (mpp) REVERT: D 55 MET cc_start: 0.8905 (mtt) cc_final: 0.8570 (mtp) REVERT: D 79 LEU cc_start: 0.8862 (mt) cc_final: 0.8587 (mp) REVERT: D 215 LYS cc_start: 0.9032 (tttt) cc_final: 0.8769 (tptp) REVERT: E 227 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8405 (mmt) REVERT: N 425 ARG cc_start: 0.8371 (ptt180) cc_final: 0.7895 (ptt180) REVERT: N 426 GLN cc_start: 0.8280 (tt0) cc_final: 0.7683 (tp-100) REVERT: N 432 ARG cc_start: 0.8191 (ttm170) cc_final: 0.7797 (ttm110) REVERT: N 449 ASP cc_start: 0.8655 (m-30) cc_final: 0.8333 (p0) REVERT: N 472 ASN cc_start: 0.8492 (t0) cc_final: 0.8291 (t0) REVERT: N 474 LYS cc_start: 0.8399 (mmmm) cc_final: 0.7990 (ttpp) outliers start: 39 outliers final: 25 residues processed: 214 average time/residue: 0.2646 time to fit residues: 82.5110 Evaluate side-chains 200 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain N residue 409 CYS Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS D 265 ASN E 267 HIS N 507 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15183 Z= 0.304 Angle : 0.585 10.439 20662 Z= 0.302 Chirality : 0.044 0.257 2391 Planarity : 0.004 0.060 2520 Dihedral : 6.399 62.176 2458 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.38 % Allowed : 10.96 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.21), residues: 1748 helix: 2.17 (0.21), residues: 568 sheet: 0.63 (0.24), residues: 492 loop : 0.21 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP E 241 HIS 0.003 0.001 HIS C 122 PHE 0.023 0.002 PHE D 306 TYR 0.028 0.002 TYR D 299 ARG 0.010 0.001 ARG E 428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 173 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.9100 (mmtt) cc_final: 0.8727 (mmtp) REVERT: A 130 MET cc_start: 0.7411 (ttm) cc_final: 0.6657 (tpp) REVERT: A 150 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8032 (tm-30) REVERT: C 58 TYR cc_start: 0.8014 (t80) cc_final: 0.7113 (t80) REVERT: C 70 MET cc_start: 0.9110 (mtp) cc_final: 0.8180 (mmm) REVERT: C 71 GLU cc_start: 0.8075 (pm20) cc_final: 0.7603 (pm20) REVERT: C 130 MET cc_start: 0.6928 (ttp) cc_final: 0.6630 (tmm) REVERT: C 150 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8034 (tm-30) REVERT: C 152 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8026 (mm110) REVERT: C 177 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8538 (mp0) REVERT: C 223 MET cc_start: 0.8185 (mmm) cc_final: 0.7488 (mtt) REVERT: C 239 GLN cc_start: 0.8014 (tp-100) cc_final: 0.7794 (mm-40) REVERT: D 55 MET cc_start: 0.9015 (mtt) cc_final: 0.8711 (mtp) REVERT: D 79 LEU cc_start: 0.8875 (mt) cc_final: 0.8610 (mp) REVERT: D 165 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7081 (pp20) REVERT: D 215 LYS cc_start: 0.9065 (tttt) cc_final: 0.8767 (tptp) REVERT: D 224 GLN cc_start: 0.8068 (tp40) cc_final: 0.7804 (tp40) REVERT: E 155 GLU cc_start: 0.8068 (tt0) cc_final: 0.7811 (tt0) REVERT: E 274 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7865 (mmtm) REVERT: N 425 ARG cc_start: 0.8457 (ptt180) cc_final: 0.7939 (ptt180) REVERT: N 426 GLN cc_start: 0.8302 (tt0) cc_final: 0.7640 (tp-100) REVERT: N 432 ARG cc_start: 0.8333 (ttm170) cc_final: 0.7657 (ttm110) REVERT: N 449 ASP cc_start: 0.8747 (m-30) cc_final: 0.8441 (p0) REVERT: N 465 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8316 (p) REVERT: N 472 ASN cc_start: 0.8728 (t0) cc_final: 0.8506 (t0) REVERT: N 482 TYR cc_start: 0.8416 (m-10) cc_final: 0.7763 (m-10) outliers start: 38 outliers final: 25 residues processed: 201 average time/residue: 0.2874 time to fit residues: 86.7835 Evaluate side-chains 194 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain N residue 465 THR Chi-restraints excluded: chain N residue 477 ASP Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 99 optimal weight: 0.2980 chunk 41 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 163 optimal weight: 10.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS D 217 ASN E 267 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15183 Z= 0.211 Angle : 0.542 10.933 20662 Z= 0.275 Chirality : 0.043 0.253 2391 Planarity : 0.003 0.030 2520 Dihedral : 6.010 56.904 2458 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.88 % Allowed : 11.77 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1748 helix: 2.26 (0.22), residues: 565 sheet: 0.69 (0.24), residues: 487 loop : 0.17 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 241 HIS 0.003 0.001 HIS A 122 PHE 0.016 0.001 PHE B 306 TYR 0.026 0.001 TYR D 299 ARG 0.004 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8891 (mmtp) REVERT: A 130 MET cc_start: 0.7338 (ttm) cc_final: 0.6670 (tpp) REVERT: A 150 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8023 (tm-30) REVERT: B 26 ARG cc_start: 0.8480 (mtm180) cc_final: 0.8184 (mtm-85) REVERT: C 70 MET cc_start: 0.9102 (mtp) cc_final: 0.8355 (mmm) REVERT: C 71 GLU cc_start: 0.8138 (pm20) cc_final: 0.7660 (pm20) REVERT: C 130 MET cc_start: 0.6874 (ttp) cc_final: 0.6527 (tmm) REVERT: C 150 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8040 (tm-30) REVERT: C 152 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8031 (mm110) REVERT: C 177 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8536 (mp0) REVERT: C 223 MET cc_start: 0.8189 (mmm) cc_final: 0.7461 (mtt) REVERT: D 55 MET cc_start: 0.8996 (mtt) cc_final: 0.8726 (mtp) REVERT: D 215 LYS cc_start: 0.9057 (tttt) cc_final: 0.8781 (tptp) REVERT: D 224 GLN cc_start: 0.8089 (tp40) cc_final: 0.7793 (tp40) REVERT: E 182 GLU cc_start: 0.7175 (mp0) cc_final: 0.6973 (mp0) REVERT: E 274 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7847 (mmtm) REVERT: N 425 ARG cc_start: 0.8465 (ptt180) cc_final: 0.8091 (ptt180) REVERT: N 426 GLN cc_start: 0.8337 (tt0) cc_final: 0.7603 (tp-100) REVERT: N 432 ARG cc_start: 0.8357 (ttm170) cc_final: 0.7756 (ttm110) REVERT: N 449 ASP cc_start: 0.8733 (m-30) cc_final: 0.8377 (p0) REVERT: N 470 MET cc_start: 0.7444 (mmm) cc_final: 0.7199 (mmm) REVERT: N 474 LYS cc_start: 0.8494 (mmmm) cc_final: 0.8108 (tmtt) outliers start: 30 outliers final: 24 residues processed: 194 average time/residue: 0.2603 time to fit residues: 74.8554 Evaluate side-chains 193 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS E 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15183 Z= 0.374 Angle : 0.615 11.041 20662 Z= 0.315 Chirality : 0.045 0.260 2391 Planarity : 0.004 0.031 2520 Dihedral : 6.048 54.520 2458 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.32 % Allowed : 11.33 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.21), residues: 1748 helix: 2.03 (0.22), residues: 564 sheet: 0.50 (0.24), residues: 493 loop : -0.02 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 241 HIS 0.008 0.001 HIS D 191 PHE 0.021 0.002 PHE D 307 TYR 0.030 0.002 TYR D 299 ARG 0.005 0.001 ARG E 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8760 (mtt) cc_final: 0.8454 (mtt) REVERT: A 105 LYS cc_start: 0.9219 (mmtt) cc_final: 0.8891 (mmtp) REVERT: A 150 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 199 TYR cc_start: 0.7702 (p90) cc_final: 0.7341 (p90) REVERT: B 26 ARG cc_start: 0.8683 (mtm180) cc_final: 0.8342 (mtm-85) REVERT: C 70 MET cc_start: 0.9174 (mtp) cc_final: 0.8228 (mmm) REVERT: C 71 GLU cc_start: 0.8160 (pm20) cc_final: 0.7665 (pm20) REVERT: C 130 MET cc_start: 0.6946 (ttp) cc_final: 0.6599 (tmm) REVERT: C 150 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8098 (tm-30) REVERT: C 152 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7993 (mm110) REVERT: C 177 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8601 (mp0) REVERT: C 223 MET cc_start: 0.8301 (mmm) cc_final: 0.7388 (mmm) REVERT: D 18 LYS cc_start: 0.8943 (pptt) cc_final: 0.8561 (pptt) REVERT: D 55 MET cc_start: 0.8988 (mtt) cc_final: 0.8751 (mtp) REVERT: D 165 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7140 (pp20) REVERT: D 215 LYS cc_start: 0.9080 (tttt) cc_final: 0.8739 (tttm) REVERT: D 224 GLN cc_start: 0.8028 (tp40) cc_final: 0.7678 (tp40) REVERT: D 274 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8326 (mmtt) REVERT: N 426 GLN cc_start: 0.8378 (tt0) cc_final: 0.7627 (tp-100) REVERT: N 432 ARG cc_start: 0.8473 (ttm170) cc_final: 0.7770 (ttm110) REVERT: N 449 ASP cc_start: 0.8811 (m-30) cc_final: 0.8489 (p0) REVERT: N 455 PHE cc_start: 0.8028 (m-10) cc_final: 0.7764 (m-10) REVERT: N 465 THR cc_start: 0.8549 (m) cc_final: 0.8273 (p) REVERT: N 470 MET cc_start: 0.7398 (mmm) cc_final: 0.7195 (mmm) outliers start: 37 outliers final: 30 residues processed: 199 average time/residue: 0.2785 time to fit residues: 80.3901 Evaluate side-chains 200 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 169 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain N residue 463 LYS Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 132 optimal weight: 0.4980 chunk 153 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS E 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15183 Z= 0.156 Angle : 0.548 11.377 20662 Z= 0.275 Chirality : 0.042 0.251 2391 Planarity : 0.003 0.031 2520 Dihedral : 5.585 49.181 2458 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.69 % Allowed : 12.59 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.21), residues: 1748 helix: 2.18 (0.22), residues: 565 sheet: 0.73 (0.24), residues: 477 loop : 0.09 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 241 HIS 0.009 0.001 HIS D 191 PHE 0.013 0.001 PHE A 308 TYR 0.026 0.001 TYR B 299 ARG 0.007 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8189 (pt0) cc_final: 0.7845 (pt0) REVERT: A 150 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7987 (tm-30) REVERT: A 199 TYR cc_start: 0.7624 (p90) cc_final: 0.7248 (p90) REVERT: B 26 ARG cc_start: 0.8574 (mtm180) cc_final: 0.8318 (mtm-85) REVERT: C 58 TYR cc_start: 0.8019 (t80) cc_final: 0.7621 (t80) REVERT: C 70 MET cc_start: 0.9130 (mtp) cc_final: 0.8377 (mmm) REVERT: C 71 GLU cc_start: 0.8308 (pm20) cc_final: 0.7740 (pm20) REVERT: C 130 MET cc_start: 0.6951 (ttp) cc_final: 0.6625 (tmm) REVERT: C 150 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8188 (tm-30) REVERT: C 152 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8012 (mm110) REVERT: C 177 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8560 (mp0) REVERT: C 223 MET cc_start: 0.8196 (mmm) cc_final: 0.7452 (mtt) REVERT: D 18 LYS cc_start: 0.8953 (pptt) cc_final: 0.8553 (pptt) REVERT: D 55 MET cc_start: 0.8952 (mtt) cc_final: 0.8736 (mtp) REVERT: D 215 LYS cc_start: 0.9075 (tttt) cc_final: 0.8759 (tttm) REVERT: D 224 GLN cc_start: 0.8121 (tp40) cc_final: 0.7748 (tp40) REVERT: D 274 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8207 (mmtt) REVERT: N 426 GLN cc_start: 0.8379 (tt0) cc_final: 0.7648 (tp-100) REVERT: N 432 ARG cc_start: 0.8360 (ttm170) cc_final: 0.7600 (ttm110) REVERT: N 449 ASP cc_start: 0.8797 (m-30) cc_final: 0.8430 (p0) REVERT: N 455 PHE cc_start: 0.7767 (m-10) cc_final: 0.7376 (m-10) REVERT: N 465 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8145 (p) REVERT: N 470 MET cc_start: 0.7641 (mmm) cc_final: 0.7290 (mmm) REVERT: N 474 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8077 (ttpp) REVERT: N 482 TYR cc_start: 0.8332 (m-10) cc_final: 0.7796 (m-10) outliers start: 27 outliers final: 21 residues processed: 195 average time/residue: 0.2703 time to fit residues: 78.0595 Evaluate side-chains 192 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain N residue 465 THR Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 5.9990 chunk 147 optimal weight: 0.0030 chunk 157 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15183 Z= 0.299 Angle : 0.592 11.825 20662 Z= 0.296 Chirality : 0.044 0.257 2391 Planarity : 0.003 0.029 2520 Dihedral : 5.568 48.361 2458 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.69 % Allowed : 12.90 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.21), residues: 1748 helix: 2.06 (0.22), residues: 566 sheet: 0.54 (0.24), residues: 492 loop : 0.05 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 241 HIS 0.009 0.001 HIS D 191 PHE 0.019 0.001 PHE D 307 TYR 0.035 0.002 TYR B 299 ARG 0.006 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.9242 (mmtt) cc_final: 0.8918 (mmtp) REVERT: A 150 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8003 (tm-30) REVERT: A 199 TYR cc_start: 0.7711 (p90) cc_final: 0.7305 (p90) REVERT: B 26 ARG cc_start: 0.8667 (mtm180) cc_final: 0.8361 (mtm-85) REVERT: C 70 MET cc_start: 0.9166 (mtp) cc_final: 0.8237 (mmm) REVERT: C 71 GLU cc_start: 0.8257 (pm20) cc_final: 0.7721 (pm20) REVERT: C 130 MET cc_start: 0.7006 (ttp) cc_final: 0.6632 (tmm) REVERT: C 150 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8146 (tm-30) REVERT: C 152 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8003 (mm110) REVERT: C 177 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8601 (mp0) REVERT: C 223 MET cc_start: 0.8270 (mmm) cc_final: 0.7503 (mtt) REVERT: D 18 LYS cc_start: 0.8942 (pptt) cc_final: 0.8559 (pptt) REVERT: D 215 LYS cc_start: 0.9093 (tttt) cc_final: 0.8748 (tttm) REVERT: D 274 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8237 (mmtt) REVERT: E 141 ARG cc_start: 0.8502 (mpt-90) cc_final: 0.8268 (mmt90) REVERT: N 426 GLN cc_start: 0.8419 (tt0) cc_final: 0.7649 (tp-100) REVERT: N 432 ARG cc_start: 0.8445 (ttm170) cc_final: 0.7739 (ttm110) REVERT: N 449 ASP cc_start: 0.8851 (m-30) cc_final: 0.8484 (p0) REVERT: N 455 PHE cc_start: 0.7956 (m-10) cc_final: 0.7457 (m-10) REVERT: N 465 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8116 (p) REVERT: N 470 MET cc_start: 0.7456 (mmm) cc_final: 0.7080 (mmm) REVERT: N 474 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8015 (ttpp) outliers start: 27 outliers final: 24 residues processed: 187 average time/residue: 0.2789 time to fit residues: 76.9253 Evaluate side-chains 193 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain N residue 405 LEU Chi-restraints excluded: chain N residue 465 THR Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 174 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15183 Z= 0.202 Angle : 0.563 12.221 20662 Z= 0.280 Chirality : 0.042 0.249 2391 Planarity : 0.003 0.029 2520 Dihedral : 5.363 45.428 2458 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.50 % Allowed : 12.96 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1748 helix: 2.16 (0.22), residues: 563 sheet: 0.54 (0.24), residues: 492 loop : 0.08 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 241 HIS 0.009 0.001 HIS D 191 PHE 0.013 0.001 PHE D 306 TYR 0.026 0.001 TYR B 299 ARG 0.006 0.000 ARG D 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.9241 (mmtt) cc_final: 0.8916 (mmtp) REVERT: A 150 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7972 (tm-30) REVERT: A 199 TYR cc_start: 0.7691 (p90) cc_final: 0.7286 (p90) REVERT: A 276 MET cc_start: 0.9418 (mmm) cc_final: 0.9205 (tpp) REVERT: B 26 ARG cc_start: 0.8662 (mtm180) cc_final: 0.8437 (mtm-85) REVERT: B 55 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8219 (mtt) REVERT: C 58 TYR cc_start: 0.7966 (t80) cc_final: 0.7551 (t80) REVERT: C 70 MET cc_start: 0.9189 (mtp) cc_final: 0.8363 (mmm) REVERT: C 71 GLU cc_start: 0.8305 (pm20) cc_final: 0.7721 (pm20) REVERT: C 150 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8134 (tm-30) REVERT: C 152 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8002 (mm110) REVERT: C 177 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8560 (mp0) REVERT: C 182 GLN cc_start: 0.8612 (tt0) cc_final: 0.8147 (tt0) REVERT: C 223 MET cc_start: 0.8242 (mmm) cc_final: 0.7486 (mtt) REVERT: D 18 LYS cc_start: 0.8959 (pptt) cc_final: 0.8555 (pptt) REVERT: D 55 MET cc_start: 0.9053 (mtt) cc_final: 0.8681 (mmm) REVERT: D 215 LYS cc_start: 0.9091 (tttt) cc_final: 0.8752 (tttm) REVERT: D 274 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8185 (mmtt) REVERT: E 141 ARG cc_start: 0.8452 (mpt-90) cc_final: 0.8229 (mmt90) REVERT: N 426 GLN cc_start: 0.8430 (tt0) cc_final: 0.7668 (tp-100) REVERT: N 432 ARG cc_start: 0.8423 (ttm170) cc_final: 0.7731 (ttm110) REVERT: N 449 ASP cc_start: 0.8835 (m-30) cc_final: 0.8481 (p0) REVERT: N 465 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8072 (p) REVERT: N 470 MET cc_start: 0.7467 (mmm) cc_final: 0.7043 (mmm) REVERT: N 474 LYS cc_start: 0.8446 (mmmt) cc_final: 0.8059 (ttpp) outliers start: 24 outliers final: 18 residues processed: 188 average time/residue: 0.2734 time to fit residues: 74.8417 Evaluate side-chains 190 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain N residue 465 THR Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 128 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 139 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.085448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.057957 restraints weight = 72632.155| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 4.37 r_work: 0.2692 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15183 Z= 0.155 Angle : 0.551 12.152 20662 Z= 0.273 Chirality : 0.042 0.244 2391 Planarity : 0.003 0.078 2520 Dihedral : 5.095 42.185 2456 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.50 % Allowed : 13.15 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.21), residues: 1748 helix: 2.23 (0.22), residues: 560 sheet: 0.72 (0.24), residues: 474 loop : 0.07 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 241 HIS 0.009 0.001 HIS D 191 PHE 0.012 0.001 PHE C 236 TYR 0.026 0.001 TYR B 299 ARG 0.013 0.000 ARG A 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3252.95 seconds wall clock time: 59 minutes 31.26 seconds (3571.26 seconds total)