Starting phenix.real_space_refine on Thu Jul 31 16:13:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l31_23148/07_2025/7l31_23148.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l31_23148/07_2025/7l31_23148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l31_23148/07_2025/7l31_23148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l31_23148/07_2025/7l31_23148.map" model { file = "/net/cci-nas-00/data/ceres_data/7l31_23148/07_2025/7l31_23148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l31_23148/07_2025/7l31_23148.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 83 5.16 5 C 8883 2.51 5 N 2170 2.21 5 O 2460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13596 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2698 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2697 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2674 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2663 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "E" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2613 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 17, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 78 Unusual residues: {'NAG': 2, 'SY9': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.83, per 1000 atoms: 0.65 Number of scatterers: 13596 At special positions: 0 Unit cell: (91.3, 90.47, 128.65, 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 83 16.00 O 2460 8.00 N 2170 7.00 C 8883 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 216 " distance=2.04 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS D 205 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 45 " " NAG A 502 " - " ASN A 76 " " NAG B 501 " - " ASN B 45 " " NAG B 502 " - " ASN B 76 " " NAG C 501 " - " ASN C 45 " " NAG C 502 " - " ASN C 76 " " NAG D 501 " - " ASN D 45 " " NAG D 502 " - " ASN D 76 " " NAG E 501 " - " ASN E 220 " Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.9 seconds 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 23 sheets defined 36.0% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.811A pdb=" N ASP A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 81 Processing helix chain 'A' and resid 96 through 100 removed outlier: 4.039A pdb=" N SER A 99 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 100 " --> pdb=" O LEU A 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 100' Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 235 through 250 removed outlier: 3.705A pdb=" N PHE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 281 Processing helix chain 'A' and resid 290 through 315 Processing helix chain 'A' and resid 384 through 416 Proline residue: A 400 - end of helix removed outlier: 3.599A pdb=" N ILE A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 235 through 251 removed outlier: 3.828A pdb=" N PHE B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 277 Processing helix chain 'B' and resid 288 through 315 removed outlier: 4.032A pdb=" N VAL B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 416 removed outlier: 3.585A pdb=" N ALA B 388 " --> pdb=" O PHE B 384 " (cutoff:3.500A) Proline residue: B 400 - end of helix removed outlier: 3.609A pdb=" N PHE B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 26 Processing helix chain 'C' and resid 151 through 154 removed outlier: 3.649A pdb=" N MET C 154 " --> pdb=" O ASN C 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 234 through 251 removed outlier: 3.798A pdb=" N SER C 238 " --> pdb=" O MET C 234 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE C 251 " --> pdb=" O VAL C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 258 Processing helix chain 'C' and resid 259 through 276 Processing helix chain 'C' and resid 288 through 316 removed outlier: 3.633A pdb=" N ARG C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 412 Proline residue: C 400 - end of helix Processing helix chain 'D' and resid 16 through 25 Processing helix chain 'D' and resid 78 through 81 removed outlier: 3.832A pdb=" N ALA D 81 " --> pdb=" O SER D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 81' Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.842A pdb=" N LEU D 97 " --> pdb=" O PRO D 94 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP D 98 " --> pdb=" O SER D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 94 through 98' Processing helix chain 'D' and resid 151 through 154 removed outlier: 3.624A pdb=" N MET D 154 " --> pdb=" O ASN D 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 151 through 154' Processing helix chain 'D' and resid 228 through 234 Processing helix chain 'D' and resid 234 through 251 removed outlier: 3.874A pdb=" N PHE D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE D 251 " --> pdb=" O VAL D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 279 removed outlier: 4.283A pdb=" N ALA D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 315 removed outlier: 3.849A pdb=" N TRP D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU D 298 " --> pdb=" O MET D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 415 Proline residue: D 400 - end of helix removed outlier: 4.163A pdb=" N THR D 413 " --> pdb=" O PHE D 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 92 through 95 removed outlier: 4.126A pdb=" N LYS E 95 " --> pdb=" O PRO E 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 110 through 116 removed outlier: 3.525A pdb=" N TYR E 113 " --> pdb=" O PRO E 110 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS E 114 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU E 116 " --> pdb=" O TYR E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 170 Processing helix chain 'E' and resid 244 through 249 Processing helix chain 'E' and resid 252 through 265 Processing helix chain 'E' and resid 266 through 268 No H-bonds generated for 'chain 'E' and resid 266 through 268' Processing helix chain 'E' and resid 275 through 294 removed outlier: 4.518A pdb=" N SER E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 331 removed outlier: 3.815A pdb=" N VAL E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 474 removed outlier: 3.952A pdb=" N TYR E 454 " --> pdb=" O ARG E 450 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA E 457 " --> pdb=" O LEU E 453 " (cutoff:3.500A) Proline residue: E 460 - end of helix removed outlier: 3.907A pdb=" N PHE E 465 " --> pdb=" O PHE E 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.985A pdb=" N LEU A 125 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP A 64 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER A 57 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ARG A 66 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE A 55 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN A 68 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASN A 76 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASN A 45 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL A 44 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLU A 176 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL A 46 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115 removed outlier: 6.100A pdb=" N GLU A 110 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER A 144 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY A 112 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP A 64 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER A 57 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ARG A 66 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE A 55 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN A 68 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASN A 76 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASN A 45 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN A 184 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107 removed outlier: 5.999A pdb=" N THR A 215 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS A 216 " --> pdb=" O CYS A 205 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 196 removed outlier: 3.613A pdb=" N GLU A 224 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 91 removed outlier: 5.661A pdb=" N ASP B 64 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER B 57 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG B 66 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 55 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN B 68 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN B 76 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASN B 45 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL B 44 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N GLU B 176 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL B 46 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 91 removed outlier: 5.661A pdb=" N ASP B 64 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER B 57 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG B 66 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 55 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN B 68 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN B 76 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASN B 45 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N GLN B 184 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE B 50 " --> pdb=" O GLN B 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 105 through 107 Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 107 Processing sheet with id=AA9, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.552A pdb=" N LEU C 92 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU C 125 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR C 140 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA C 113 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR C 142 " --> pdb=" O LYS C 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.552A pdb=" N LEU C 92 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU C 125 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ASP C 64 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER C 57 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG C 66 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE C 55 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN C 68 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN C 76 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASN C 45 " --> pdb=" O ASN C 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 105 through 107 Processing sheet with id=AB3, first strand: chain 'C' and resid 105 through 107 Processing sheet with id=AB4, first strand: chain 'C' and resid 207 through 208 Processing sheet with id=AB5, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.184A pdb=" N LEU D 125 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG D 66 " --> pdb=" O PHE D 55 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE D 55 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN D 68 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ASN D 76 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN D 45 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 110 through 114 removed outlier: 6.332A pdb=" N GLU D 110 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N SER D 144 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY D 112 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG D 66 " --> pdb=" O PHE D 55 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE D 55 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN D 68 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ASN D 76 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN D 45 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN D 184 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 105 through 107 Processing sheet with id=AB8, first strand: chain 'D' and resid 156 through 157 Processing sheet with id=AB9, first strand: chain 'D' and resid 207 through 209 removed outlier: 3.841A pdb=" N GLY D 212 " --> pdb=" O TYR D 209 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 105 through 108 removed outlier: 4.515A pdb=" N LEU E 141 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP E 148 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR E 79 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE E 65 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL E 58 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE E 192 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 105 through 108 removed outlier: 4.515A pdb=" N LEU E 141 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP E 148 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR E 79 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE E 65 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN E 200 " --> pdb=" O ILE E 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 121 through 123 removed outlier: 3.572A pdb=" N ARG E 241 " --> pdb=" O ASP E 210 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 121 through 123 Processing sheet with id=AC5, first strand: chain 'E' and resid 223 through 224 752 hydrogen bonds defined for protein. 2193 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: 4.56 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3463 1.33 - 1.46: 3094 1.46 - 1.58: 7274 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 13966 Sorted by residual: bond pdb=" N VAL D 58 " pdb=" CA VAL D 58 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 9.86e+00 bond pdb=" N GLY B 203 " pdb=" CA GLY B 203 " ideal model delta sigma weight residual 1.443 1.480 -0.037 1.17e-02 7.31e+03 9.85e+00 bond pdb=" C ALA A 256 " pdb=" N PRO A 257 " ideal model delta sigma weight residual 1.337 1.368 -0.032 1.06e-02 8.90e+03 8.88e+00 bond pdb=" N LYS B 207 " pdb=" CA LYS B 207 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.25e-02 6.40e+03 8.78e+00 bond pdb=" N ILE D 264 " pdb=" CA ILE D 264 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.34e+00 ... (remaining 13961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 18451 2.22 - 4.45: 476 4.45 - 6.67: 86 6.67 - 8.89: 29 8.89 - 11.12: 7 Bond angle restraints: 19049 Sorted by residual: angle pdb=" C TYR C 235 " pdb=" N ILE C 236 " pdb=" CA ILE C 236 " ideal model delta sigma weight residual 120.24 123.39 -3.15 6.30e-01 2.52e+00 2.50e+01 angle pdb=" C TYR B 235 " pdb=" N ILE B 236 " pdb=" CA ILE B 236 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.15e+01 angle pdb=" N THR E 166 " pdb=" CA THR E 166 " pdb=" C THR E 166 " ideal model delta sigma weight residual 113.30 107.27 6.03 1.34e+00 5.57e-01 2.03e+01 angle pdb=" C VAL C 118 " pdb=" N THR C 119 " pdb=" CA THR C 119 " ideal model delta sigma weight residual 121.54 129.82 -8.28 1.91e+00 2.74e-01 1.88e+01 angle pdb=" N ALA A 256 " pdb=" CA ALA A 256 " pdb=" C ALA A 256 " ideal model delta sigma weight residual 109.81 118.92 -9.11 2.21e+00 2.05e-01 1.70e+01 ... (remaining 19044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.66: 7892 20.66 - 41.32: 605 41.32 - 61.98: 92 61.98 - 82.64: 17 82.64 - 103.30: 7 Dihedral angle restraints: 8613 sinusoidal: 3628 harmonic: 4985 Sorted by residual: dihedral pdb=" CA CYS E 175 " pdb=" C CYS E 175 " pdb=" N LYS E 176 " pdb=" CA LYS E 176 " ideal model delta harmonic sigma weight residual -180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CB CYS E 161 " pdb=" SG CYS E 161 " pdb=" SG CYS E 175 " pdb=" CB CYS E 175 " ideal model delta sinusoidal sigma weight residual -86.00 -39.07 -46.93 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CA ILE A 69 " pdb=" C ILE A 69 " pdb=" N PHE A 70 " pdb=" CA PHE A 70 " ideal model delta harmonic sigma weight residual 180.00 152.45 27.55 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 8610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1973 0.086 - 0.172: 198 0.172 - 0.259: 16 0.259 - 0.345: 13 0.345 - 0.431: 7 Chirality restraints: 2207 Sorted by residual: chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 76 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" NAY SY9 A 503 " pdb=" CAS SY9 A 503 " pdb=" CAV SY9 A 503 " pdb=" CAX SY9 A 503 " both_signs ideal model delta sigma weight residual False -2.12 -2.54 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" NAY SY9 D 504 " pdb=" CAS SY9 D 504 " pdb=" CAV SY9 D 504 " pdb=" CAX SY9 D 504 " both_signs ideal model delta sigma weight residual False -2.12 -2.53 0.40 2.00e-01 2.50e+01 4.07e+00 ... (remaining 2204 not shown) Planarity restraints: 2354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 45 " -0.006 2.00e-02 2.50e+03 2.50e-02 7.81e+00 pdb=" CG ASN C 45 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN C 45 " -0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN C 45 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG C 501 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 193 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C GLN D 193 " 0.045 2.00e-02 2.50e+03 pdb=" O GLN D 193 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE D 194 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 134 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C VAL E 134 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL E 134 " 0.017 2.00e-02 2.50e+03 pdb=" N THR E 135 " 0.015 2.00e-02 2.50e+03 ... (remaining 2351 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2374 2.77 - 3.30: 12355 3.30 - 3.83: 22064 3.83 - 4.37: 25066 4.37 - 4.90: 45072 Nonbonded interactions: 106931 Sorted by model distance: nonbonded pdb=" OG SER B 285 " pdb=" O GLN C 226 " model vdw 2.232 3.040 nonbonded pdb=" O ALA A 289 " pdb=" OH TYR A 410 " model vdw 2.233 3.040 nonbonded pdb=" O PHE B 409 " pdb=" OG1 THR B 413 " model vdw 2.242 3.040 nonbonded pdb=" O ASP B 121 " pdb=" OD1 ASP B 121 " model vdw 2.245 3.040 nonbonded pdb=" OG1 THR E 185 " pdb=" OD1 ASP E 187 " model vdw 2.252 3.040 ... (remaining 106926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 18 or (resid 19 and (name N or name CA or name \ C or name O or name CB )) or resid 20 through 21 or (resid 22 and (name N or nam \ e CA or name C or name O or name CB )) or resid 23 through 33 or (resid 34 and ( \ name N or name CA or name C or name O or name CB )) or resid 35 through 59 or (r \ esid 60 and (name N or name CA or name C or name O or name CB )) or resid 61 thr \ ough 175 or (resid 176 and (name N or name CA or name C or name O or name CB )) \ or resid 177 through 186 or (resid 187 and (name N or name CA or name C or name \ O or name CB )) or resid 188 through 250 or (resid 251 and (name N or name CA or \ name C or name O or name CB )) or resid 252 through 253 or (resid 254 through 2 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 257 through \ 305 or (resid 306 and (name N or name CA or name C or name O or name CB )) or r \ esid 307 through 315 or (resid 316 through 398 and (name N or name CA or name C \ or name O or name CB )) or resid 399 through 400 or (resid 401 through 402 and ( \ name N or name CA or name C or name O or name CB )) or resid 403 through 408 or \ (resid 409 and (name N or name CA or name C or name O or name CB )) or resid 410 \ through 419 or resid 501 through 503)) selection = (chain 'B' and ((resid 15 and (name N or name CA or name C or name O or name CB \ )) or resid 16 through 18 or (resid 19 and (name N or name CA or name C or name \ O or name CB )) or resid 20 through 21 or (resid 22 and (name N or name CA or na \ me C or name O or name CB )) or resid 23 through 33 or (resid 34 and (name N or \ name CA or name C or name O or name CB )) or resid 35 through 175 or (resid 176 \ and (name N or name CA or name C or name O or name CB )) or resid 177 through 18 \ 6 or (resid 187 and (name N or name CA or name C or name O or name CB )) or resi \ d 188 through 250 or (resid 251 and (name N or name CA or name C or name O or na \ me CB )) or resid 252 through 305 or (resid 306 and (name N or name CA or name C \ or name O or name CB )) or resid 307 through 315 or (resid 316 through 398 and \ (name N or name CA or name C or name O or name CB )) or resid 399 through 400 or \ (resid 401 through 402 and (name N or name CA or name C or name O or name CB )) \ or resid 403 through 404 or (resid 405 and (name N or name CA or name C or name \ O or name CB )) or resid 406 through 408 or (resid 409 and (name N or name CA o \ r name C or name O or name CB )) or resid 410 through 419 or resid 501 through 5 \ 03)) selection = (chain 'C' and ((resid 15 and (name N or name CA or name C or name O or name CB \ )) or resid 16 through 21 or (resid 22 and (name N or name CA or name C or name \ O or name CB )) or resid 23 through 59 or (resid 60 and (name N or name CA or na \ me C or name O or name CB )) or resid 61 through 175 or (resid 176 and (name N o \ r name CA or name C or name O or name CB )) or resid 177 through 186 or (resid 1 \ 87 and (name N or name CA or name C or name O or name CB )) or resid 188 through \ 305 or (resid 306 and (name N or name CA or name C or name O or name CB )) or r \ esid 307 through 386 or (resid 387 through 398 and (name N or name CA or name C \ or name O or name CB )) or resid 399 through 404 or (resid 405 and (name N or na \ me CA or name C or name O or name CB )) or resid 406 through 419 or resid 501 th \ rough 503)) selection = (chain 'D' and ((resid 15 and (name N or name CA or name C or name O or name CB \ )) or resid 16 through 59 or (resid 60 and (name N or name CA or name C or name \ O or name CB )) or resid 61 through 250 or (resid 251 and (name N or name CA or \ name C or name O or name CB )) or resid 252 or (resid 253 through 256 and (name \ N or name CA or name C or name O or name CB )) or resid 257 through 400 or (resi \ d 401 through 402 and (name N or name CA or name C or name O or name CB )) or re \ sid 403 through 404 or (resid 405 and (name N or name CA or name C or name O or \ name CB )) or resid 406 through 408 or (resid 409 and (name N or name CA or name \ C or name O or name CB )) or resid 410 through 419 or resid 501 through 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.750 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.005 0.052 13981 Z= 0.264 Angle : 0.916 11.118 19088 Z= 0.475 Chirality : 0.061 0.431 2207 Planarity : 0.006 0.062 2345 Dihedral : 14.722 103.296 5361 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.28 % Allowed : 10.68 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.17), residues: 1666 helix: -1.41 (0.18), residues: 561 sheet: -3.12 (0.21), residues: 434 loop : -3.41 (0.20), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 293 HIS 0.003 0.001 HIS E 132 PHE 0.025 0.002 PHE B 70 TYR 0.019 0.002 TYR E 303 ARG 0.005 0.000 ARG E 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 9) link_NAG-ASN : angle 3.66758 ( 27) hydrogen bonds : bond 0.10608 ( 628) hydrogen bonds : angle 6.59789 ( 2193) SS BOND : bond 0.00351 ( 6) SS BOND : angle 2.74365 ( 12) covalent geometry : bond 0.00540 (13966) covalent geometry : angle 0.90431 (19049) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 302 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8346 (tpp) cc_final: 0.8025 (mmm) REVERT: B 157 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8587 (mm-40) REVERT: B 227 MET cc_start: 0.7778 (ttp) cc_final: 0.7505 (ttp) REVERT: C 220 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8290 (mttp) REVERT: E 180 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8221 (mt-10) REVERT: E 297 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6515 (mt-10) REVERT: E 319 PHE cc_start: 0.7743 (t80) cc_final: 0.7436 (m-10) outliers start: 4 outliers final: 3 residues processed: 306 average time/residue: 0.2684 time to fit residues: 116.9030 Evaluate side-chains 241 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 165 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 30.0000 chunk 125 optimal weight: 0.4980 chunk 69 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 0.0040 chunk 149 optimal weight: 3.9990 overall best weight: 1.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 252 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN B 74 GLN B 233 GLN B 252 ASN C 68 ASN C 74 GLN C 116 HIS C 222 HIS D 233 GLN D 312 ASN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.133454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.109275 restraints weight = 19371.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.112232 restraints weight = 11863.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.114190 restraints weight = 8567.011| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13981 Z= 0.139 Angle : 0.669 10.332 19088 Z= 0.330 Chirality : 0.045 0.373 2207 Planarity : 0.005 0.052 2345 Dihedral : 7.418 61.592 2329 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.84 % Allowed : 16.99 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.19), residues: 1666 helix: 0.25 (0.21), residues: 562 sheet: -2.63 (0.22), residues: 433 loop : -3.05 (0.21), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 246 HIS 0.004 0.001 HIS B 116 PHE 0.016 0.001 PHE B 70 TYR 0.017 0.002 TYR E 230 ARG 0.008 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 9) link_NAG-ASN : angle 2.94713 ( 27) hydrogen bonds : bond 0.03298 ( 628) hydrogen bonds : angle 5.03213 ( 2193) SS BOND : bond 0.00208 ( 6) SS BOND : angle 2.19905 ( 12) covalent geometry : bond 0.00315 (13966) covalent geometry : angle 0.65816 (19049) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 248 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8252 (t0) cc_final: 0.7925 (t0) REVERT: C 220 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8312 (mttp) REVERT: C 240 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6521 (tt) REVERT: D 197 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8596 (mtmm) REVERT: D 253 MET cc_start: 0.6181 (pmm) cc_final: 0.5747 (pmm) REVERT: E 297 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6619 (mt-10) REVERT: E 319 PHE cc_start: 0.7718 (t80) cc_final: 0.7421 (m-10) outliers start: 41 outliers final: 31 residues processed: 272 average time/residue: 0.2527 time to fit residues: 101.7907 Evaluate side-chains 253 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 262 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 252 ASN A 273 GLN B 53 ASN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN E 67 ASN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.129966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.105512 restraints weight = 19656.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.108375 restraints weight = 12175.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.110265 restraints weight = 8884.305| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13981 Z= 0.244 Angle : 0.717 9.891 19088 Z= 0.354 Chirality : 0.047 0.414 2207 Planarity : 0.005 0.047 2345 Dihedral : 6.650 56.903 2327 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.20 % Allowed : 19.07 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.20), residues: 1666 helix: 0.67 (0.22), residues: 566 sheet: -2.51 (0.22), residues: 429 loop : -2.83 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 246 HIS 0.003 0.001 HIS B 116 PHE 0.031 0.002 PHE D 249 TYR 0.022 0.002 TYR A 85 ARG 0.007 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 9) link_NAG-ASN : angle 3.39794 ( 27) hydrogen bonds : bond 0.03564 ( 628) hydrogen bonds : angle 4.99914 ( 2193) SS BOND : bond 0.00198 ( 6) SS BOND : angle 2.79034 ( 12) covalent geometry : bond 0.00577 (13966) covalent geometry : angle 0.70324 (19049) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 227 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7272 (mt0) REVERT: A 407 ASN cc_start: 0.8281 (t0) cc_final: 0.7944 (t0) REVERT: B 93 ASP cc_start: 0.7345 (t0) cc_final: 0.7045 (m-30) REVERT: B 260 VAL cc_start: 0.7249 (OUTLIER) cc_final: 0.7042 (t) REVERT: C 96 MET cc_start: 0.7849 (ptp) cc_final: 0.7604 (ptp) REVERT: C 220 LYS cc_start: 0.8544 (mtmt) cc_final: 0.8158 (mttp) REVERT: C 233 GLN cc_start: 0.7742 (tt0) cc_final: 0.7524 (tt0) REVERT: D 253 MET cc_start: 0.5884 (pmm) cc_final: 0.5622 (pmm) REVERT: E 319 PHE cc_start: 0.7831 (t80) cc_final: 0.7459 (m-10) outliers start: 75 outliers final: 49 residues processed: 275 average time/residue: 0.2255 time to fit residues: 93.9810 Evaluate side-chains 262 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 211 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 459 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 0.2980 chunk 101 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 252 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN E 208 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106546 restraints weight = 19541.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.109286 restraints weight = 12082.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.111301 restraints weight = 8863.434| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13981 Z= 0.183 Angle : 0.674 10.311 19088 Z= 0.332 Chirality : 0.046 0.385 2207 Planarity : 0.004 0.050 2345 Dihedral : 6.319 56.908 2327 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.72 % Allowed : 22.05 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.20), residues: 1666 helix: 0.96 (0.22), residues: 566 sheet: -2.33 (0.23), residues: 429 loop : -2.67 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 246 HIS 0.003 0.001 HIS B 116 PHE 0.029 0.001 PHE D 249 TYR 0.016 0.002 TYR E 303 ARG 0.006 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 9) link_NAG-ASN : angle 3.37381 ( 27) hydrogen bonds : bond 0.03340 ( 628) hydrogen bonds : angle 4.85411 ( 2193) SS BOND : bond 0.00185 ( 6) SS BOND : angle 2.78670 ( 12) covalent geometry : bond 0.00429 (13966) covalent geometry : angle 0.65849 (19049) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 231 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8901 (mmm) cc_final: 0.8569 (mmm) REVERT: A 407 ASN cc_start: 0.8230 (t0) cc_final: 0.7890 (t0) REVERT: B 93 ASP cc_start: 0.7253 (t0) cc_final: 0.6988 (m-30) REVERT: B 260 VAL cc_start: 0.7226 (OUTLIER) cc_final: 0.7004 (t) REVERT: C 96 MET cc_start: 0.7850 (ptp) cc_final: 0.7638 (ptp) REVERT: C 220 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8226 (mttp) REVERT: D 253 MET cc_start: 0.5811 (pmm) cc_final: 0.5610 (pmm) REVERT: E 297 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6954 (mt-10) outliers start: 68 outliers final: 50 residues processed: 273 average time/residue: 0.2217 time to fit residues: 92.3585 Evaluate side-chains 269 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN A 273 GLN D 312 ASN E 208 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.131693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.107334 restraints weight = 19653.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.110249 restraints weight = 12128.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112145 restraints weight = 8822.454| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13981 Z= 0.161 Angle : 0.655 9.788 19088 Z= 0.322 Chirality : 0.046 0.428 2207 Planarity : 0.004 0.047 2345 Dihedral : 6.221 57.846 2327 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.92 % Allowed : 23.30 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.20), residues: 1666 helix: 1.07 (0.22), residues: 566 sheet: -2.09 (0.23), residues: 414 loop : -2.64 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 246 HIS 0.002 0.001 HIS D 222 PHE 0.029 0.002 PHE D 249 TYR 0.022 0.001 TYR A 85 ARG 0.006 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 9) link_NAG-ASN : angle 3.36776 ( 27) hydrogen bonds : bond 0.03257 ( 628) hydrogen bonds : angle 4.73433 ( 2193) SS BOND : bond 0.00183 ( 6) SS BOND : angle 2.51350 ( 12) covalent geometry : bond 0.00378 (13966) covalent geometry : angle 0.64021 (19049) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 232 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: A 270 MET cc_start: 0.8803 (mmm) cc_final: 0.8325 (mmm) REVERT: A 407 ASN cc_start: 0.8205 (t0) cc_final: 0.7859 (t0) REVERT: B 93 ASP cc_start: 0.7218 (t0) cc_final: 0.6949 (m-30) REVERT: B 260 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.7018 (t) REVERT: B 409 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.7158 (t80) REVERT: C 96 MET cc_start: 0.7821 (ptp) cc_final: 0.7606 (ptp) REVERT: C 154 MET cc_start: 0.7693 (mpp) cc_final: 0.7216 (ptp) REVERT: C 220 LYS cc_start: 0.8549 (mtmt) cc_final: 0.8253 (mttp) REVERT: D 253 MET cc_start: 0.5700 (pmm) cc_final: 0.5467 (pmm) REVERT: E 297 GLU cc_start: 0.7258 (mt-10) cc_final: 0.7023 (mt-10) outliers start: 71 outliers final: 54 residues processed: 276 average time/residue: 0.2217 time to fit residues: 94.0700 Evaluate side-chains 275 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 330 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS B 233 GLN C 233 GLN D 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.132735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.108055 restraints weight = 19869.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.111067 restraints weight = 12262.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.113016 restraints weight = 8875.461| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13981 Z= 0.138 Angle : 0.662 13.514 19088 Z= 0.325 Chirality : 0.045 0.386 2207 Planarity : 0.004 0.052 2345 Dihedral : 6.029 59.960 2326 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.99 % Allowed : 23.44 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.21), residues: 1666 helix: 1.19 (0.22), residues: 566 sheet: -1.97 (0.23), residues: 426 loop : -2.51 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 246 HIS 0.002 0.000 HIS D 222 PHE 0.030 0.001 PHE D 249 TYR 0.016 0.001 TYR E 303 ARG 0.007 0.000 ARG B 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 9) link_NAG-ASN : angle 3.20924 ( 27) hydrogen bonds : bond 0.03123 ( 628) hydrogen bonds : angle 4.65684 ( 2193) SS BOND : bond 0.00102 ( 6) SS BOND : angle 3.98964 ( 12) covalent geometry : bond 0.00318 (13966) covalent geometry : angle 0.64358 (19049) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 231 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: A 270 MET cc_start: 0.8766 (mmm) cc_final: 0.8372 (mmm) REVERT: A 407 ASN cc_start: 0.8206 (t0) cc_final: 0.7997 (t0) REVERT: B 93 ASP cc_start: 0.7109 (t0) cc_final: 0.6858 (m-30) REVERT: B 260 VAL cc_start: 0.7254 (OUTLIER) cc_final: 0.7036 (t) REVERT: B 278 ARG cc_start: 0.7220 (mtt90) cc_final: 0.6750 (mtt90) REVERT: B 409 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7216 (t80) REVERT: C 154 MET cc_start: 0.7649 (mpp) cc_final: 0.7157 (ptp) outliers start: 72 outliers final: 55 residues processed: 278 average time/residue: 0.2204 time to fit residues: 93.9703 Evaluate side-chains 284 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 227 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 330 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 104 optimal weight: 2.9990 chunk 106 optimal weight: 0.0770 chunk 64 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 159 optimal weight: 2.9990 chunk 156 optimal weight: 30.0000 chunk 88 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 GLN D 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.133774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.109416 restraints weight = 19645.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.112356 restraints weight = 12092.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.114324 restraints weight = 8734.353| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13981 Z= 0.121 Angle : 0.644 9.981 19088 Z= 0.316 Chirality : 0.044 0.375 2207 Planarity : 0.004 0.046 2345 Dihedral : 5.959 58.953 2326 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.51 % Allowed : 23.79 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.21), residues: 1666 helix: 1.35 (0.22), residues: 562 sheet: -1.83 (0.24), residues: 426 loop : -2.47 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 246 HIS 0.003 0.000 HIS D 208 PHE 0.030 0.001 PHE D 249 TYR 0.025 0.001 TYR D 209 ARG 0.006 0.000 ARG B 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 9) link_NAG-ASN : angle 3.39623 ( 27) hydrogen bonds : bond 0.02967 ( 628) hydrogen bonds : angle 4.53838 ( 2193) SS BOND : bond 0.00202 ( 6) SS BOND : angle 3.37244 ( 12) covalent geometry : bond 0.00277 (13966) covalent geometry : angle 0.62618 (19049) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 233 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8723 (mmm) cc_final: 0.8352 (mmm) REVERT: A 407 ASN cc_start: 0.8157 (t0) cc_final: 0.7934 (t0) REVERT: B 93 ASP cc_start: 0.7078 (t0) cc_final: 0.6819 (m-30) REVERT: B 260 VAL cc_start: 0.7232 (OUTLIER) cc_final: 0.7013 (t) REVERT: B 291 ASP cc_start: 0.8057 (m-30) cc_final: 0.7832 (m-30) REVERT: B 409 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.7069 (t80) REVERT: C 233 GLN cc_start: 0.7810 (tt0) cc_final: 0.7471 (tt0) REVERT: D 207 LYS cc_start: 0.8090 (mttt) cc_final: 0.7837 (tttt) REVERT: E 180 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8131 (mt-10) outliers start: 65 outliers final: 55 residues processed: 275 average time/residue: 0.2236 time to fit residues: 94.0500 Evaluate side-chains 280 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 223 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 330 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 94 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 15 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 13 optimal weight: 0.0040 chunk 64 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 GLN D 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.133208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.108898 restraints weight = 19651.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111903 restraints weight = 11999.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.113907 restraints weight = 8614.966| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13981 Z= 0.124 Angle : 0.653 9.997 19088 Z= 0.317 Chirality : 0.045 0.368 2207 Planarity : 0.004 0.046 2345 Dihedral : 5.918 57.934 2326 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.99 % Allowed : 23.93 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.21), residues: 1666 helix: 1.45 (0.22), residues: 562 sheet: -1.69 (0.24), residues: 426 loop : -2.42 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 246 HIS 0.003 0.000 HIS D 222 PHE 0.029 0.001 PHE D 249 TYR 0.017 0.001 TYR E 303 ARG 0.006 0.000 ARG B 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 9) link_NAG-ASN : angle 3.71955 ( 27) hydrogen bonds : bond 0.02919 ( 628) hydrogen bonds : angle 4.47324 ( 2193) SS BOND : bond 0.00148 ( 6) SS BOND : angle 2.78740 ( 12) covalent geometry : bond 0.00285 (13966) covalent geometry : angle 0.63451 (19049) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 236 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8303 (mmp) cc_final: 0.7958 (mmm) REVERT: A 407 ASN cc_start: 0.8120 (t0) cc_final: 0.7865 (t0) REVERT: B 93 ASP cc_start: 0.7001 (t0) cc_final: 0.6741 (m-30) REVERT: B 260 VAL cc_start: 0.7267 (OUTLIER) cc_final: 0.7044 (t) REVERT: B 291 ASP cc_start: 0.8064 (m-30) cc_final: 0.7835 (m-30) REVERT: B 409 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.7069 (t80) REVERT: C 220 LYS cc_start: 0.8537 (mtmt) cc_final: 0.8183 (mttp) REVERT: C 233 GLN cc_start: 0.7737 (tt0) cc_final: 0.7299 (tt0) REVERT: D 207 LYS cc_start: 0.8017 (mttt) cc_final: 0.7774 (tttt) REVERT: D 218 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7920 (pm20) outliers start: 72 outliers final: 57 residues processed: 284 average time/residue: 0.2233 time to fit residues: 96.5965 Evaluate side-chains 282 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 330 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 141 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 1 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 112 optimal weight: 0.2980 chunk 159 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.133641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.109302 restraints weight = 19451.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.112313 restraints weight = 11869.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.114183 restraints weight = 8547.599| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13981 Z= 0.127 Angle : 0.665 13.823 19088 Z= 0.320 Chirality : 0.046 0.568 2207 Planarity : 0.004 0.065 2345 Dihedral : 5.930 57.434 2326 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.58 % Allowed : 24.83 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.21), residues: 1666 helix: 1.56 (0.22), residues: 562 sheet: -1.56 (0.25), residues: 410 loop : -2.42 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 246 HIS 0.003 0.000 HIS D 222 PHE 0.030 0.001 PHE D 249 TYR 0.017 0.001 TYR E 303 ARG 0.006 0.000 ARG B 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 9) link_NAG-ASN : angle 4.30363 ( 27) hydrogen bonds : bond 0.02900 ( 628) hydrogen bonds : angle 4.43787 ( 2193) SS BOND : bond 0.00145 ( 6) SS BOND : angle 2.64398 ( 12) covalent geometry : bond 0.00293 (13966) covalent geometry : angle 0.64197 (19049) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 239 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8379 (mmp) cc_final: 0.8032 (mmm) REVERT: A 407 ASN cc_start: 0.8106 (t0) cc_final: 0.7866 (t0) REVERT: B 93 ASP cc_start: 0.6972 (t0) cc_final: 0.6708 (m-30) REVERT: B 227 MET cc_start: 0.7810 (ttm) cc_final: 0.7599 (ttp) REVERT: B 233 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8389 (tm-30) REVERT: B 260 VAL cc_start: 0.7203 (OUTLIER) cc_final: 0.6985 (t) REVERT: B 278 ARG cc_start: 0.7358 (mpp80) cc_final: 0.7082 (mpp-170) REVERT: B 291 ASP cc_start: 0.8035 (m-30) cc_final: 0.7827 (m-30) REVERT: B 409 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.7058 (t80) REVERT: C 96 MET cc_start: 0.7821 (ptp) cc_final: 0.7523 (ptp) REVERT: C 220 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8188 (mttp) REVERT: D 240 LEU cc_start: 0.8048 (tp) cc_final: 0.7777 (tp) outliers start: 66 outliers final: 60 residues processed: 282 average time/residue: 0.2186 time to fit residues: 93.7442 Evaluate side-chains 290 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 228 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 41 optimal weight: 0.2980 chunk 10 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.134649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.109983 restraints weight = 19505.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.113155 restraints weight = 11543.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115277 restraints weight = 8162.765| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13981 Z= 0.115 Angle : 0.674 10.831 19088 Z= 0.324 Chirality : 0.045 0.556 2207 Planarity : 0.004 0.055 2345 Dihedral : 5.864 57.231 2326 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.16 % Allowed : 25.38 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.21), residues: 1666 helix: 1.62 (0.23), residues: 562 sheet: -1.40 (0.25), residues: 410 loop : -2.37 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 246 HIS 0.003 0.000 HIS D 222 PHE 0.030 0.001 PHE D 249 TYR 0.017 0.001 TYR E 303 ARG 0.006 0.000 ARG D 259 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 9) link_NAG-ASN : angle 3.90929 ( 27) hydrogen bonds : bond 0.02834 ( 628) hydrogen bonds : angle 4.36217 ( 2193) SS BOND : bond 0.00173 ( 6) SS BOND : angle 2.82482 ( 12) covalent geometry : bond 0.00262 (13966) covalent geometry : angle 0.65428 (19049) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 239 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7950 (ptp90) cc_final: 0.7679 (ptp90) REVERT: A 63 MET cc_start: 0.8352 (mmp) cc_final: 0.8085 (mmm) REVERT: A 156 VAL cc_start: 0.9109 (m) cc_final: 0.8879 (p) REVERT: A 407 ASN cc_start: 0.8022 (t0) cc_final: 0.7785 (t0) REVERT: B 93 ASP cc_start: 0.6847 (t0) cc_final: 0.6227 (m-30) REVERT: B 260 VAL cc_start: 0.7493 (OUTLIER) cc_final: 0.7260 (t) REVERT: B 291 ASP cc_start: 0.7976 (m-30) cc_final: 0.7575 (m-30) REVERT: B 409 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.7138 (t80) REVERT: C 220 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8224 (mttp) REVERT: C 234 MET cc_start: 0.8800 (mtm) cc_final: 0.8522 (mtm) REVERT: C 285 SER cc_start: 0.8055 (p) cc_final: 0.7679 (t) outliers start: 60 outliers final: 54 residues processed: 277 average time/residue: 0.2282 time to fit residues: 95.0031 Evaluate side-chains 284 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 228 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 110 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 chunk 79 optimal weight: 0.0470 chunk 144 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 136 optimal weight: 0.0770 overall best weight: 2.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.108722 restraints weight = 19676.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111745 restraints weight = 11951.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.113722 restraints weight = 8588.571| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13981 Z= 0.155 Angle : 0.687 10.051 19088 Z= 0.333 Chirality : 0.046 0.490 2207 Planarity : 0.004 0.045 2345 Dihedral : 5.908 57.363 2326 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.02 % Allowed : 25.73 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1666 helix: 1.57 (0.22), residues: 562 sheet: -1.40 (0.25), residues: 410 loop : -2.34 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 246 HIS 0.003 0.001 HIS D 222 PHE 0.030 0.002 PHE D 249 TYR 0.017 0.002 TYR E 303 ARG 0.011 0.000 ARG B 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 9) link_NAG-ASN : angle 3.72713 ( 27) hydrogen bonds : bond 0.02994 ( 628) hydrogen bonds : angle 4.45142 ( 2193) SS BOND : bond 0.00199 ( 6) SS BOND : angle 2.96699 ( 12) covalent geometry : bond 0.00363 (13966) covalent geometry : angle 0.66933 (19049) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4112.56 seconds wall clock time: 72 minutes 29.49 seconds (4349.49 seconds total)