Starting phenix.real_space_refine on Sun Jun 15 02:58:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ql6_14065/06_2025/7ql6_14065.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql6_14065/06_2025/7ql6_14065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ql6_14065/06_2025/7ql6_14065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql6_14065/06_2025/7ql6_14065.map" model { file = "/net/cci-nas-00/data/ceres_data/7ql6_14065/06_2025/7ql6_14065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql6_14065/06_2025/7ql6_14065.cif" } resolution = 3.23 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= 0.002 sd= 0.043 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 10837 2.51 5 N 2603 2.21 5 O 3094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16617 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3125 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 365} Chain breaks: 1 Chain: "B" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3292 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "C" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3466 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 399} Chain breaks: 1 Chain: "D" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2993 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 348} Chain breaks: 1 Chain: "E" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3280 Classifications: {'peptide': 404} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 382} Chain breaks: 1 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'CCE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'CCE': 1} Classifications: {'undetermined': 1} 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: 9.32, per 1000 atoms: 0.56 Number of scatterers: 16617 At special positions: 0 Unit cell: (100.76, 104.195, 179.765, 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 3094 8.00 N 2603 7.00 C 10837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.05 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 6 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 6 " " BMA L 3 " - " MAN L 6 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 5 " " BMA L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG E 501 " - " ASN E 68 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 141 " " NAG H 1 " - " ASN C 143 " " NAG I 1 " - " ASN C 70 " " NAG J 1 " - " ASN C 208 " " NAG K 1 " - " ASN D 141 " " NAG L 1 " - " ASN E 141 " Time building additional restraints: 4.61 Conformation dependent library (CDL) restraints added in 1.9 seconds 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 20 sheets defined 41.3% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.699A pdb=" N VAL A 85 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 232 removed outlier: 4.568A pdb=" N ILE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 262 Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 320 through 323 Processing helix chain 'A' and resid 380 through 431 removed outlier: 4.283A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 68 through 73 removed outlier: 4.246A pdb=" N GLU B 73 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.652A pdb=" N VAL B 85 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 241 removed outlier: 4.522A pdb=" N ILE B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Proline residue: B 227 - end of helix removed outlier: 4.391A pdb=" N PHE B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 267 removed outlier: 3.929A pdb=" N SER B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 306 Processing helix chain 'B' and resid 315 through 324 removed outlier: 3.992A pdb=" N GLU B 324 " --> pdb=" O GLN B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 removed outlier: 4.220A pdb=" N PHE B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 460 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.869A pdb=" N SER C 75 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 245 removed outlier: 4.556A pdb=" N THR C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.667A pdb=" N LEU C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 249 Processing helix chain 'C' and resid 255 through 277 removed outlier: 3.722A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 315 removed outlier: 3.526A pdb=" N ARG C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 416 through 478 Proline residue: C 463 - end of helix Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 218 through 230 removed outlier: 4.178A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 235 removed outlier: 4.343A pdb=" N TYR D 234 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 264 Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 319 removed outlier: 4.080A pdb=" N ILE D 317 " --> pdb=" O ARG D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 421 removed outlier: 4.496A pdb=" N GLU D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N HIS D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.254A pdb=" N GLU E 73 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 219 through 226 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 243 removed outlier: 3.619A pdb=" N VAL E 240 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE E 242 " --> pdb=" O LEU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 271 Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 318 through 327 Processing helix chain 'E' and resid 328 through 334 Processing helix chain 'E' and resid 420 through 470 removed outlier: 3.561A pdb=" N SER E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 118 Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118 removed outlier: 6.404A pdb=" N ILE A 49 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 43 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU A 51 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG A 55 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU A 37 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG A 57 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU A 35 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN A 59 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL A 33 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ILE A 61 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ILE A 31 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 80 Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.848A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP A 180 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 80 removed outlier: 4.180A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 80 removed outlier: 4.180A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLU B 49 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU B 43 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR B 51 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE B 55 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU B 37 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASN B 57 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU B 35 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA B 59 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL B 33 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N THR B 61 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL B 31 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.777A pdb=" N GLN B 214 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE B 188 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 82 Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 82 removed outlier: 6.239A pdb=" N THR C 51 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU C 45 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR C 53 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TRP C 57 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LEU C 39 " --> pdb=" O TRP C 57 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP C 59 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU C 37 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA C 61 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU C 35 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N TYR C 63 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE C 33 " --> pdb=" O TYR C 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.015A pdb=" N ALA C 150 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLN C 213 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG C 222 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE C 192 " --> pdb=" O ARG C 222 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.015A pdb=" N ALA C 150 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLN C 213 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 164 through 167 Processing sheet with id=AB5, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AB6, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.295A pdb=" N ILE D 49 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL D 43 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU D 51 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ARG D 55 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU D 37 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG D 57 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU D 35 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLN D 59 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL D 33 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ILE D 61 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE D 31 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 91 through 92 removed outlier: 3.785A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE D 205 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR D 198 " --> pdb=" O TRP D 187 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP D 187 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP D 200 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS D 185 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR D 202 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY D 183 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS D 204 " --> pdb=" O TYR D 181 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR D 181 " --> pdb=" O HIS D 204 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE D 206 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.243A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.243A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA E 49 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU E 43 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR E 51 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP E 55 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LEU E 37 " --> pdb=" O TRP E 55 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU E 57 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU E 35 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLN E 59 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU E 33 " --> pdb=" O GLN E 59 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N ASN E 61 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL E 31 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.096A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.096A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) 867 hydrogen bonds defined for protein. 2517 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: 5.19 Time building geometry restraints manager: 5.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2598 1.32 - 1.46: 5259 1.46 - 1.59: 9060 1.59 - 1.73: 0 1.73 - 1.86: 135 Bond restraints: 17052 Sorted by residual: bond pdb=" C5 CCE A 601 " pdb=" N6 CCE A 601 " ideal model delta sigma weight residual 1.340 1.453 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C5 CCE D 601 " pdb=" N6 CCE D 601 " ideal model delta sigma weight residual 1.340 1.452 -0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" CA ALA D 96 " pdb=" CB ALA D 96 " ideal model delta sigma weight residual 1.537 1.479 0.058 1.67e-02 3.59e+03 1.21e+01 bond pdb=" C PRO E 479 " pdb=" O PRO E 479 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.30e-02 5.92e+03 1.21e+01 bond pdb=" C3 BMA G 3 " pdb=" O3 BMA G 3 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 1.01e+01 ... (remaining 17047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 22881 2.24 - 4.49: 312 4.49 - 6.73: 73 6.73 - 8.97: 4 8.97 - 11.22: 4 Bond angle restraints: 23274 Sorted by residual: angle pdb=" N PRO E 481 " pdb=" CA PRO E 481 " pdb=" C PRO E 481 " ideal model delta sigma weight residual 113.47 120.62 -7.15 1.43e+00 4.89e-01 2.50e+01 angle pdb=" N PHE B 468 " pdb=" CA PHE B 468 " pdb=" C PHE B 468 " ideal model delta sigma weight residual 113.56 107.05 6.51 1.39e+00 5.18e-01 2.20e+01 angle pdb=" C PRO B 467 " pdb=" CA PRO B 467 " pdb=" CB PRO B 467 " ideal model delta sigma weight residual 111.85 106.17 5.68 1.42e+00 4.96e-01 1.60e+01 angle pdb=" N ALA D 96 " pdb=" CA ALA D 96 " pdb=" C ALA D 96 " ideal model delta sigma weight residual 114.04 109.33 4.71 1.24e+00 6.50e-01 1.44e+01 angle pdb=" N TYR B 134 " pdb=" CA TYR B 134 " pdb=" CB TYR B 134 " ideal model delta sigma weight residual 114.10 110.32 3.78 1.00e+00 1.00e+00 1.43e+01 ... (remaining 23269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.56: 10055 22.56 - 45.12: 355 45.12 - 67.68: 53 67.68 - 90.23: 56 90.23 - 112.79: 39 Dihedral angle restraints: 10558 sinusoidal: 4656 harmonic: 5902 Sorted by residual: dihedral pdb=" CA CYS A 142 " pdb=" C CYS A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA PHE B 137 " pdb=" C PHE B 137 " pdb=" N ASP B 138 " pdb=" CA ASP B 138 " ideal model delta harmonic sigma weight residual -180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA CYS D 192 " pdb=" C CYS D 192 " pdb=" N CYS D 193 " pdb=" CA CYS D 193 " ideal model delta harmonic sigma weight residual -180.00 -159.08 -20.92 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 10555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2417 0.064 - 0.127: 353 0.127 - 0.191: 21 0.191 - 0.255: 6 0.255 - 0.318: 9 Chirality restraints: 2806 Sorted by residual: chirality pdb=" CA VAL C 31 " pdb=" N VAL C 31 " pdb=" C VAL C 31 " pdb=" CB VAL C 31 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2803 not shown) Planarity restraints: 2837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 92 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C LEU D 92 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU D 92 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR D 93 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 121 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO C 122 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 122 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 122 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 215 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C VAL D 215 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL D 215 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL D 216 " 0.010 2.00e-02 2.50e+03 ... (remaining 2834 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3651 2.79 - 3.31: 16118 3.31 - 3.84: 28024 3.84 - 4.37: 33076 4.37 - 4.90: 57144 Nonbonded interactions: 138013 Sorted by model distance: nonbonded pdb=" O SER A 226 " pdb=" OG1 THR A 229 " model vdw 2.258 3.040 nonbonded pdb=" O SER D 226 " pdb=" OG1 THR D 229 " model vdw 2.263 3.040 nonbonded pdb=" O ILE A 315 " pdb=" OG1 THR A 319 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR B 220 " pdb=" OE2 GLU C 280 " model vdw 2.276 3.040 nonbonded pdb=" O GLY E 182 " pdb=" NZ LYS E 218 " model vdw 2.294 3.120 ... (remaining 138008 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 1 through 322 or resid 378 through 421 or resid 601)) selection = (chain 'D' and (resid 1 through 322 or resid 378 through 421 or resid 601)) } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 37.220 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 17095 Z= 0.232 Angle : 0.684 11.218 23396 Z= 0.338 Chirality : 0.048 0.318 2806 Planarity : 0.004 0.043 2829 Dihedral : 15.259 112.793 6697 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.60 % Allowed : 4.41 % Favored : 94.99 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 1970 helix: 2.24 (0.19), residues: 756 sheet: -0.42 (0.26), residues: 383 loop : -0.83 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 139 HIS 0.003 0.001 HIS D 385 PHE 0.015 0.001 PHE A 284 TYR 0.012 0.001 TYR D 93 ARG 0.003 0.000 ARG A 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 8) link_NAG-ASN : angle 1.64672 ( 24) link_ALPHA1-6 : bond 0.00473 ( 9) link_ALPHA1-6 : angle 1.67005 ( 27) link_BETA1-4 : bond 0.00399 ( 13) link_BETA1-4 : angle 1.83869 ( 39) link_ALPHA1-3 : bond 0.00404 ( 6) link_ALPHA1-3 : angle 2.42297 ( 18) hydrogen bonds : bond 0.11351 ( 793) hydrogen bonds : angle 5.32146 ( 2517) SS BOND : bond 0.00867 ( 7) SS BOND : angle 2.79357 ( 14) covalent geometry : bond 0.00450 (17052) covalent geometry : angle 0.67065 (23274) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 360 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8486 (m-40) cc_final: 0.8016 (m110) REVERT: A 238 ASP cc_start: 0.7441 (t0) cc_final: 0.7205 (t0) REVERT: A 252 SER cc_start: 0.9239 (m) cc_final: 0.9016 (p) REVERT: B 250 SER cc_start: 0.8933 (t) cc_final: 0.8694 (m) REVERT: B 442 VAL cc_start: 0.8220 (t) cc_final: 0.7923 (p) REVERT: C 296 MET cc_start: 0.7766 (mtp) cc_final: 0.7482 (mtp) REVERT: C 473 PHE cc_start: 0.7717 (m-10) cc_final: 0.6986 (t80) REVERT: D 144 MET cc_start: 0.6649 (mtt) cc_final: 0.6332 (mtp) REVERT: D 277 TYR cc_start: 0.7499 (m-10) cc_final: 0.6252 (t80) REVERT: D 309 PRO cc_start: 0.8181 (Cg_exo) cc_final: 0.7401 (Cg_endo) REVERT: D 410 LEU cc_start: 0.8580 (mm) cc_final: 0.8258 (mm) REVERT: E 239 LEU cc_start: 0.8737 (tp) cc_final: 0.8484 (tp) REVERT: E 269 ILE cc_start: 0.8887 (mm) cc_final: 0.8683 (mm) REVERT: E 310 ARG cc_start: 0.6103 (mtt180) cc_final: 0.5886 (mtt90) REVERT: E 443 ILE cc_start: 0.7641 (mm) cc_final: 0.7407 (mm) REVERT: E 448 ASP cc_start: 0.7728 (m-30) cc_final: 0.7288 (m-30) REVERT: E 467 PHE cc_start: 0.7418 (m-10) cc_final: 0.6981 (t80) outliers start: 11 outliers final: 3 residues processed: 368 average time/residue: 0.2455 time to fit residues: 140.8935 Evaluate side-chains 200 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 197 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 110 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 59 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 134 HIS ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 GLN B 159 GLN B 310 ASN B 429 GLN C 231 ASN C 267 GLN C 276 GLN C 445 ASN ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.115914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.091202 restraints weight = 32639.838| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.95 r_work: 0.3125 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17095 Z= 0.158 Angle : 0.620 9.566 23396 Z= 0.303 Chirality : 0.045 0.276 2806 Planarity : 0.004 0.044 2829 Dihedral : 13.782 93.506 2852 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.34 % Allowed : 10.13 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 1970 helix: 2.16 (0.19), residues: 749 sheet: -0.64 (0.25), residues: 391 loop : -0.76 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 197 HIS 0.005 0.001 HIS A 408 PHE 0.019 0.001 PHE C 478 TYR 0.012 0.001 TYR E 117 ARG 0.005 0.000 ARG A 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 8) link_NAG-ASN : angle 1.61234 ( 24) link_ALPHA1-6 : bond 0.00651 ( 9) link_ALPHA1-6 : angle 2.27951 ( 27) link_BETA1-4 : bond 0.00426 ( 13) link_BETA1-4 : angle 2.16608 ( 39) link_ALPHA1-3 : bond 0.00835 ( 6) link_ALPHA1-3 : angle 3.56268 ( 18) hydrogen bonds : bond 0.04032 ( 793) hydrogen bonds : angle 4.40170 ( 2517) SS BOND : bond 0.00795 ( 7) SS BOND : angle 2.16940 ( 14) covalent geometry : bond 0.00361 (17052) covalent geometry : angle 0.59763 (23274) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8909 (m-40) cc_final: 0.8551 (m110) REVERT: A 179 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.7964 (mttm) REVERT: A 238 ASP cc_start: 0.8231 (t0) cc_final: 0.7932 (t0) REVERT: A 241 GLU cc_start: 0.7215 (mt-10) cc_final: 0.7008 (mt-10) REVERT: A 252 SER cc_start: 0.9134 (m) cc_final: 0.8860 (p) REVERT: A 308 MET cc_start: 0.8023 (ttp) cc_final: 0.7642 (ttp) REVERT: A 324 MET cc_start: 0.7925 (tmm) cc_final: 0.6482 (pmm) REVERT: B 94 ASN cc_start: 0.8711 (t0) cc_final: 0.7354 (t0) REVERT: B 250 SER cc_start: 0.9183 (t) cc_final: 0.8798 (m) REVERT: C 257 MET cc_start: 0.7721 (mmm) cc_final: 0.7219 (tpp) REVERT: C 445 ASN cc_start: 0.7313 (OUTLIER) cc_final: 0.6826 (t0) REVERT: C 473 PHE cc_start: 0.7734 (m-10) cc_final: 0.6845 (t80) REVERT: D 33 VAL cc_start: 0.8789 (t) cc_final: 0.8442 (p) REVERT: D 144 MET cc_start: 0.7330 (mtt) cc_final: 0.6948 (mmt) REVERT: D 277 TYR cc_start: 0.7761 (m-10) cc_final: 0.6278 (t80) REVERT: D 309 PRO cc_start: 0.7279 (Cg_exo) cc_final: 0.7010 (Cg_endo) REVERT: D 410 LEU cc_start: 0.8486 (mm) cc_final: 0.8174 (mm) REVERT: E 239 LEU cc_start: 0.8676 (tp) cc_final: 0.8393 (tp) outliers start: 43 outliers final: 22 residues processed: 233 average time/residue: 0.2263 time to fit residues: 86.7780 Evaluate side-chains 216 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 296 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 151 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.113929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.089540 restraints weight = 32413.158| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.90 r_work: 0.3097 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17095 Z= 0.145 Angle : 0.579 8.723 23396 Z= 0.281 Chirality : 0.044 0.249 2806 Planarity : 0.004 0.045 2829 Dihedral : 12.001 84.828 2850 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.40 % Allowed : 11.11 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.19), residues: 1970 helix: 2.19 (0.19), residues: 756 sheet: -0.56 (0.25), residues: 399 loop : -0.72 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 311 HIS 0.003 0.001 HIS A 104 PHE 0.019 0.001 PHE C 471 TYR 0.011 0.001 TYR A 277 ARG 0.005 0.000 ARG D 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00120 ( 8) link_NAG-ASN : angle 1.62147 ( 24) link_ALPHA1-6 : bond 0.00838 ( 9) link_ALPHA1-6 : angle 2.09059 ( 27) link_BETA1-4 : bond 0.00513 ( 13) link_BETA1-4 : angle 1.84689 ( 39) link_ALPHA1-3 : bond 0.01108 ( 6) link_ALPHA1-3 : angle 2.72835 ( 18) hydrogen bonds : bond 0.03875 ( 793) hydrogen bonds : angle 4.24668 ( 2517) SS BOND : bond 0.00747 ( 7) SS BOND : angle 1.97372 ( 14) covalent geometry : bond 0.00322 (17052) covalent geometry : angle 0.56191 (23274) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 1.830 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8903 (m-40) cc_final: 0.8558 (m110) REVERT: A 179 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8311 (mtmm) REVERT: A 238 ASP cc_start: 0.8371 (t0) cc_final: 0.8079 (t0) REVERT: A 252 SER cc_start: 0.9156 (m) cc_final: 0.8945 (p) REVERT: A 308 MET cc_start: 0.8119 (ttp) cc_final: 0.7419 (ttp) REVERT: A 324 MET cc_start: 0.7795 (tmm) cc_final: 0.7063 (pmm) REVERT: B 94 ASN cc_start: 0.8725 (t0) cc_final: 0.7432 (t0) REVERT: B 250 SER cc_start: 0.9199 (t) cc_final: 0.8865 (m) REVERT: B 285 MET cc_start: 0.7823 (mmm) cc_final: 0.6595 (tmm) REVERT: C 249 LEU cc_start: 0.7381 (mp) cc_final: 0.7045 (mp) REVERT: C 340 MET cc_start: 0.5610 (OUTLIER) cc_final: 0.5405 (mmt) REVERT: C 445 ASN cc_start: 0.7683 (m-40) cc_final: 0.7364 (t0) REVERT: C 465 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8275 (ptp) REVERT: C 473 PHE cc_start: 0.7750 (m-10) cc_final: 0.6822 (t80) REVERT: C 499 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7205 (mtm180) REVERT: D 33 VAL cc_start: 0.8759 (t) cc_final: 0.8416 (p) REVERT: D 108 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8234 (pp) REVERT: D 144 MET cc_start: 0.7381 (mtt) cc_final: 0.6984 (mmt) REVERT: D 231 LEU cc_start: 0.7762 (mt) cc_final: 0.7400 (mp) REVERT: D 277 TYR cc_start: 0.7738 (m-10) cc_final: 0.6193 (t80) REVERT: D 309 PRO cc_start: 0.7173 (Cg_exo) cc_final: 0.6852 (Cg_endo) REVERT: D 410 LEU cc_start: 0.8546 (mm) cc_final: 0.8249 (mm) REVERT: E 239 LEU cc_start: 0.8607 (tp) cc_final: 0.8344 (tp) REVERT: E 310 ARG cc_start: 0.5613 (mtt90) cc_final: 0.5231 (mtt90) outliers start: 44 outliers final: 24 residues processed: 232 average time/residue: 0.2313 time to fit residues: 86.5149 Evaluate side-chains 214 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 458 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 96 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 118 optimal weight: 0.0050 chunk 78 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.111566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.086725 restraints weight = 32797.545| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.91 r_work: 0.3048 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17095 Z= 0.162 Angle : 0.597 8.628 23396 Z= 0.288 Chirality : 0.045 0.295 2806 Planarity : 0.004 0.102 2829 Dihedral : 10.363 82.160 2849 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.83 % Allowed : 11.70 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 1970 helix: 2.07 (0.19), residues: 762 sheet: -0.58 (0.25), residues: 407 loop : -0.73 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 311 HIS 0.006 0.001 HIS A 186 PHE 0.025 0.001 PHE C 478 TYR 0.013 0.001 TYR A 277 ARG 0.005 0.000 ARG A 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 8) link_NAG-ASN : angle 1.71247 ( 24) link_ALPHA1-6 : bond 0.01039 ( 9) link_ALPHA1-6 : angle 2.00479 ( 27) link_BETA1-4 : bond 0.00465 ( 13) link_BETA1-4 : angle 2.00993 ( 39) link_ALPHA1-3 : bond 0.01569 ( 6) link_ALPHA1-3 : angle 2.20378 ( 18) hydrogen bonds : bond 0.03819 ( 793) hydrogen bonds : angle 4.21462 ( 2517) SS BOND : bond 0.00743 ( 7) SS BOND : angle 2.03880 ( 14) covalent geometry : bond 0.00366 (17052) covalent geometry : angle 0.58136 (23274) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 2.115 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8922 (m-40) cc_final: 0.8535 (m110) REVERT: A 238 ASP cc_start: 0.8450 (t0) cc_final: 0.8124 (t0) REVERT: A 252 SER cc_start: 0.9160 (m) cc_final: 0.8940 (p) REVERT: A 280 PHE cc_start: 0.7713 (t80) cc_final: 0.6654 (m-10) REVERT: B 94 ASN cc_start: 0.8718 (t0) cc_final: 0.7500 (t0) REVERT: B 247 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7836 (mt-10) REVERT: B 285 MET cc_start: 0.7810 (mmm) cc_final: 0.6740 (tmm) REVERT: B 314 MET cc_start: 0.7476 (tpp) cc_final: 0.6319 (tpp) REVERT: B 462 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8968 (m) REVERT: C 249 LEU cc_start: 0.7494 (mp) cc_final: 0.7110 (mp) REVERT: C 255 GLU cc_start: 0.7973 (tp30) cc_final: 0.7282 (tp30) REVERT: C 445 ASN cc_start: 0.7354 (m-40) cc_final: 0.6931 (t0) REVERT: C 465 MET cc_start: 0.8720 (ptp) cc_final: 0.8318 (ptp) REVERT: C 473 PHE cc_start: 0.7821 (m-10) cc_final: 0.6851 (t80) REVERT: C 499 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7179 (mtm180) REVERT: D 108 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8326 (pp) REVERT: D 144 MET cc_start: 0.7526 (mtt) cc_final: 0.7082 (mmt) REVERT: D 277 TYR cc_start: 0.7510 (m-10) cc_final: 0.6010 (t80) REVERT: D 311 TRP cc_start: 0.7558 (p-90) cc_final: 0.7343 (p-90) REVERT: D 410 LEU cc_start: 0.8564 (mm) cc_final: 0.8289 (mm) REVERT: E 239 LEU cc_start: 0.8645 (tp) cc_final: 0.8395 (tp) REVERT: E 310 ARG cc_start: 0.6063 (mtt90) cc_final: 0.5671 (mtt90) outliers start: 52 outliers final: 28 residues processed: 233 average time/residue: 0.2358 time to fit residues: 89.4156 Evaluate side-chains 214 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 296 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 16 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.085053 restraints weight = 33282.789| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.85 r_work: 0.3017 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17095 Z= 0.185 Angle : 0.603 9.001 23396 Z= 0.293 Chirality : 0.045 0.218 2806 Planarity : 0.004 0.046 2829 Dihedral : 9.752 75.989 2849 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.05 % Allowed : 12.36 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 1970 helix: 2.01 (0.19), residues: 766 sheet: -0.67 (0.25), residues: 400 loop : -0.75 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 311 HIS 0.004 0.001 HIS E 172 PHE 0.020 0.001 PHE C 471 TYR 0.012 0.001 TYR E 15 ARG 0.008 0.000 ARG A 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 8) link_NAG-ASN : angle 1.80935 ( 24) link_ALPHA1-6 : bond 0.00797 ( 9) link_ALPHA1-6 : angle 2.04506 ( 27) link_BETA1-4 : bond 0.00544 ( 13) link_BETA1-4 : angle 1.96395 ( 39) link_ALPHA1-3 : bond 0.01080 ( 6) link_ALPHA1-3 : angle 2.20999 ( 18) hydrogen bonds : bond 0.03828 ( 793) hydrogen bonds : angle 4.25312 ( 2517) SS BOND : bond 0.00751 ( 7) SS BOND : angle 2.17329 ( 14) covalent geometry : bond 0.00427 (17052) covalent geometry : angle 0.58636 (23274) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 195 time to evaluate : 1.809 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8925 (m-40) cc_final: 0.8543 (m110) REVERT: A 238 ASP cc_start: 0.8520 (t0) cc_final: 0.8195 (t0) REVERT: A 252 SER cc_start: 0.9165 (m) cc_final: 0.8941 (p) REVERT: A 280 PHE cc_start: 0.7761 (t80) cc_final: 0.6675 (m-10) REVERT: A 324 MET cc_start: 0.7882 (tmm) cc_final: 0.6825 (pmm) REVERT: B 94 ASN cc_start: 0.8735 (t0) cc_final: 0.7506 (t0) REVERT: B 285 MET cc_start: 0.7747 (mmm) cc_final: 0.6760 (tmm) REVERT: C 249 LEU cc_start: 0.7602 (mp) cc_final: 0.7235 (mp) REVERT: C 261 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7632 (mp) REVERT: C 293 MET cc_start: 0.8247 (mmm) cc_final: 0.8004 (mmm) REVERT: C 340 MET cc_start: 0.4695 (mmm) cc_final: 0.4392 (mmm) REVERT: C 445 ASN cc_start: 0.7312 (m-40) cc_final: 0.6885 (t0) REVERT: C 459 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6822 (m-80) REVERT: C 465 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8374 (ptp) REVERT: C 499 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7254 (mtm180) REVERT: D 144 MET cc_start: 0.7582 (mtt) cc_final: 0.7312 (mtp) REVERT: D 410 LEU cc_start: 0.8664 (mm) cc_final: 0.8401 (mm) REVERT: E 239 LEU cc_start: 0.8638 (tp) cc_final: 0.8394 (tp) REVERT: E 310 ARG cc_start: 0.6187 (mtt90) cc_final: 0.5713 (mtt180) outliers start: 56 outliers final: 34 residues processed: 232 average time/residue: 0.2256 time to fit residues: 85.7734 Evaluate side-chains 216 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 44 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 179 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 184 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.087441 restraints weight = 32891.166| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.84 r_work: 0.3062 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17095 Z= 0.117 Angle : 0.558 10.578 23396 Z= 0.268 Chirality : 0.044 0.218 2806 Planarity : 0.004 0.041 2829 Dihedral : 8.771 65.370 2849 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.01 % Allowed : 13.94 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1970 helix: 2.19 (0.19), residues: 756 sheet: -0.76 (0.25), residues: 412 loop : -0.64 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 311 HIS 0.003 0.001 HIS C 60 PHE 0.018 0.001 PHE C 471 TYR 0.012 0.001 TYR E 117 ARG 0.006 0.000 ARG A 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 8) link_NAG-ASN : angle 1.65290 ( 24) link_ALPHA1-6 : bond 0.01155 ( 9) link_ALPHA1-6 : angle 1.80809 ( 27) link_BETA1-4 : bond 0.00500 ( 13) link_BETA1-4 : angle 1.86022 ( 39) link_ALPHA1-3 : bond 0.01256 ( 6) link_ALPHA1-3 : angle 1.97884 ( 18) hydrogen bonds : bond 0.03496 ( 793) hydrogen bonds : angle 4.09231 ( 2517) SS BOND : bond 0.00718 ( 7) SS BOND : angle 1.89400 ( 14) covalent geometry : bond 0.00254 (17052) covalent geometry : angle 0.54301 (23274) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 1.751 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8933 (m-40) cc_final: 0.8547 (m110) REVERT: A 238 ASP cc_start: 0.8489 (t0) cc_final: 0.8196 (t0) REVERT: A 252 SER cc_start: 0.9157 (m) cc_final: 0.8945 (p) REVERT: A 280 PHE cc_start: 0.7709 (t80) cc_final: 0.6617 (m-10) REVERT: A 324 MET cc_start: 0.7733 (tmm) cc_final: 0.6781 (pmm) REVERT: B 94 ASN cc_start: 0.8459 (t0) cc_final: 0.7227 (t0) REVERT: B 285 MET cc_start: 0.7739 (mmm) cc_final: 0.6736 (tmm) REVERT: C 249 LEU cc_start: 0.7735 (mp) cc_final: 0.7200 (mp) REVERT: C 261 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7732 (mp) REVERT: C 340 MET cc_start: 0.5162 (mmm) cc_final: 0.4807 (mmm) REVERT: C 445 ASN cc_start: 0.7224 (m-40) cc_final: 0.6809 (t0) REVERT: C 465 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8392 (ptp) REVERT: C 499 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7167 (mtm180) REVERT: D 144 MET cc_start: 0.7538 (mtt) cc_final: 0.7245 (mtp) REVERT: D 410 LEU cc_start: 0.8707 (mm) cc_final: 0.8429 (mm) REVERT: E 234 SER cc_start: 0.8676 (t) cc_final: 0.8460 (t) REVERT: E 239 LEU cc_start: 0.8601 (tp) cc_final: 0.8367 (tp) REVERT: E 275 GLU cc_start: 0.8258 (mp0) cc_final: 0.7957 (mp0) REVERT: E 310 ARG cc_start: 0.6247 (mtt90) cc_final: 0.5820 (mtt90) outliers start: 37 outliers final: 22 residues processed: 226 average time/residue: 0.2231 time to fit residues: 82.1967 Evaluate side-chains 211 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 84 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.110627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.086325 restraints weight = 32825.542| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.87 r_work: 0.3041 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17095 Z= 0.141 Angle : 0.564 8.495 23396 Z= 0.272 Chirality : 0.044 0.229 2806 Planarity : 0.004 0.037 2829 Dihedral : 8.164 60.139 2849 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.50 % Allowed : 13.88 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1970 helix: 2.16 (0.19), residues: 763 sheet: -0.69 (0.25), residues: 405 loop : -0.68 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 311 HIS 0.003 0.001 HIS C 60 PHE 0.020 0.001 PHE A 284 TYR 0.009 0.001 TYR E 117 ARG 0.004 0.000 ARG A 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 8) link_NAG-ASN : angle 1.66044 ( 24) link_ALPHA1-6 : bond 0.01032 ( 9) link_ALPHA1-6 : angle 1.81870 ( 27) link_BETA1-4 : bond 0.00516 ( 13) link_BETA1-4 : angle 1.92811 ( 39) link_ALPHA1-3 : bond 0.01120 ( 6) link_ALPHA1-3 : angle 2.03448 ( 18) hydrogen bonds : bond 0.03552 ( 793) hydrogen bonds : angle 4.10591 ( 2517) SS BOND : bond 0.00729 ( 7) SS BOND : angle 2.01110 ( 14) covalent geometry : bond 0.00320 (17052) covalent geometry : angle 0.54849 (23274) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8950 (m-40) cc_final: 0.8544 (m110) REVERT: A 238 ASP cc_start: 0.8487 (t0) cc_final: 0.8167 (t0) REVERT: A 280 PHE cc_start: 0.7687 (t80) cc_final: 0.6635 (m-10) REVERT: A 281 THR cc_start: 0.8874 (m) cc_final: 0.8647 (t) REVERT: A 324 MET cc_start: 0.7691 (tmm) cc_final: 0.6790 (pmm) REVERT: B 94 ASN cc_start: 0.8503 (t0) cc_final: 0.7302 (t0) REVERT: B 268 ASP cc_start: 0.8933 (t70) cc_final: 0.8627 (t70) REVERT: B 285 MET cc_start: 0.7797 (mmm) cc_final: 0.6791 (tmm) REVERT: C 249 LEU cc_start: 0.7806 (mp) cc_final: 0.7540 (mp) REVERT: C 261 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7682 (mp) REVERT: C 340 MET cc_start: 0.5019 (mmm) cc_final: 0.4660 (mmm) REVERT: C 445 ASN cc_start: 0.7284 (m-40) cc_final: 0.6861 (t0) REVERT: C 465 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8339 (ptp) REVERT: C 499 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7188 (mtm180) REVERT: D 144 MET cc_start: 0.7597 (mtt) cc_final: 0.7309 (mtp) REVERT: D 278 MET cc_start: 0.7787 (ttp) cc_final: 0.7567 (ttp) REVERT: D 410 LEU cc_start: 0.8778 (mm) cc_final: 0.8472 (mm) REVERT: E 239 LEU cc_start: 0.8606 (tp) cc_final: 0.8378 (tp) REVERT: E 275 GLU cc_start: 0.8301 (mp0) cc_final: 0.7998 (mp0) REVERT: E 310 ARG cc_start: 0.6482 (mtt90) cc_final: 0.5993 (mtt180) outliers start: 46 outliers final: 32 residues processed: 221 average time/residue: 0.2470 time to fit residues: 90.1466 Evaluate side-chains 222 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 458 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 135 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 187 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN D 208 GLN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.110667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.086570 restraints weight = 32741.585| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.82 r_work: 0.3045 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17095 Z= 0.134 Angle : 0.558 7.847 23396 Z= 0.270 Chirality : 0.044 0.223 2806 Planarity : 0.004 0.040 2829 Dihedral : 7.591 57.603 2849 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.34 % Allowed : 14.48 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1970 helix: 2.13 (0.19), residues: 769 sheet: -0.77 (0.25), residues: 411 loop : -0.62 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 311 HIS 0.003 0.001 HIS C 60 PHE 0.025 0.001 PHE A 284 TYR 0.010 0.001 TYR E 117 ARG 0.004 0.000 ARG A 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 8) link_NAG-ASN : angle 1.65772 ( 24) link_ALPHA1-6 : bond 0.01044 ( 9) link_ALPHA1-6 : angle 1.69335 ( 27) link_BETA1-4 : bond 0.00543 ( 13) link_BETA1-4 : angle 1.88288 ( 39) link_ALPHA1-3 : bond 0.01031 ( 6) link_ALPHA1-3 : angle 1.90199 ( 18) hydrogen bonds : bond 0.03495 ( 793) hydrogen bonds : angle 4.08919 ( 2517) SS BOND : bond 0.00727 ( 7) SS BOND : angle 1.97140 ( 14) covalent geometry : bond 0.00304 (17052) covalent geometry : angle 0.54354 (23274) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8945 (m-40) cc_final: 0.8536 (m110) REVERT: A 238 ASP cc_start: 0.8330 (t0) cc_final: 0.8048 (t0) REVERT: A 280 PHE cc_start: 0.7601 (t80) cc_final: 0.6545 (m-10) REVERT: A 324 MET cc_start: 0.7574 (tmm) cc_final: 0.6604 (pmm) REVERT: B 94 ASN cc_start: 0.8463 (t0) cc_final: 0.7266 (t0) REVERT: B 268 ASP cc_start: 0.8906 (t70) cc_final: 0.8457 (t0) REVERT: B 285 MET cc_start: 0.7790 (mmm) cc_final: 0.6790 (tmm) REVERT: C 249 LEU cc_start: 0.7776 (mp) cc_final: 0.7537 (mp) REVERT: C 340 MET cc_start: 0.5208 (mmm) cc_final: 0.4867 (mmm) REVERT: C 445 ASN cc_start: 0.7244 (m-40) cc_final: 0.6829 (t0) REVERT: C 465 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8416 (ptp) REVERT: C 473 PHE cc_start: 0.7731 (m-10) cc_final: 0.6763 (t80) REVERT: C 499 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7202 (mtt180) REVERT: D 308 MET cc_start: 0.6771 (tpt) cc_final: 0.6535 (tpt) REVERT: D 410 LEU cc_start: 0.8787 (mm) cc_final: 0.8482 (mm) REVERT: E 239 LEU cc_start: 0.8593 (tp) cc_final: 0.8372 (tp) REVERT: E 246 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7347 (pp30) REVERT: E 275 GLU cc_start: 0.8185 (mp0) cc_final: 0.7906 (mp0) REVERT: E 310 ARG cc_start: 0.6394 (mtt90) cc_final: 0.5905 (mtt180) outliers start: 43 outliers final: 30 residues processed: 223 average time/residue: 0.2305 time to fit residues: 83.9129 Evaluate side-chains 219 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 78 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.110553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.086561 restraints weight = 32911.208| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.82 r_work: 0.3045 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17095 Z= 0.134 Angle : 0.558 8.581 23396 Z= 0.270 Chirality : 0.044 0.234 2806 Planarity : 0.004 0.037 2829 Dihedral : 7.357 58.892 2849 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.34 % Allowed : 14.64 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1970 helix: 2.19 (0.19), residues: 763 sheet: -0.78 (0.25), residues: 411 loop : -0.61 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 311 HIS 0.003 0.001 HIS C 60 PHE 0.016 0.001 PHE A 284 TYR 0.009 0.001 TYR E 117 ARG 0.004 0.000 ARG A 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 8) link_NAG-ASN : angle 1.63899 ( 24) link_ALPHA1-6 : bond 0.01019 ( 9) link_ALPHA1-6 : angle 1.64671 ( 27) link_BETA1-4 : bond 0.00555 ( 13) link_BETA1-4 : angle 1.85497 ( 39) link_ALPHA1-3 : bond 0.00958 ( 6) link_ALPHA1-3 : angle 1.85351 ( 18) hydrogen bonds : bond 0.03476 ( 793) hydrogen bonds : angle 4.08322 ( 2517) SS BOND : bond 0.00717 ( 7) SS BOND : angle 1.96527 ( 14) covalent geometry : bond 0.00303 (17052) covalent geometry : angle 0.54445 (23274) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8944 (m-40) cc_final: 0.8533 (m110) REVERT: A 238 ASP cc_start: 0.8276 (t0) cc_final: 0.7968 (t0) REVERT: A 280 PHE cc_start: 0.7655 (t80) cc_final: 0.6635 (m-10) REVERT: B 94 ASN cc_start: 0.8449 (t0) cc_final: 0.7225 (t0) REVERT: B 268 ASP cc_start: 0.8806 (t70) cc_final: 0.8432 (t0) REVERT: B 285 MET cc_start: 0.7802 (mmm) cc_final: 0.6782 (tmm) REVERT: C 340 MET cc_start: 0.5197 (mmm) cc_final: 0.4858 (mmm) REVERT: C 445 ASN cc_start: 0.7252 (m-40) cc_final: 0.6828 (t0) REVERT: C 473 PHE cc_start: 0.7751 (m-10) cc_final: 0.6742 (t80) REVERT: C 499 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7164 (mtt180) REVERT: D 178 MET cc_start: 0.9111 (mmp) cc_final: 0.8489 (mmt) REVERT: D 410 LEU cc_start: 0.8801 (mm) cc_final: 0.8497 (mm) REVERT: E 234 SER cc_start: 0.8810 (t) cc_final: 0.8335 (p) REVERT: E 239 LEU cc_start: 0.8551 (tp) cc_final: 0.8350 (tp) REVERT: E 275 GLU cc_start: 0.8169 (mp0) cc_final: 0.7884 (mp0) REVERT: E 310 ARG cc_start: 0.6373 (mtt90) cc_final: 0.5894 (mtt180) outliers start: 43 outliers final: 38 residues processed: 218 average time/residue: 0.2251 time to fit residues: 80.3544 Evaluate side-chains 224 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 458 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 192 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 HIS ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.110551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.086548 restraints weight = 32982.034| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.82 r_work: 0.3045 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17095 Z= 0.133 Angle : 0.564 10.612 23396 Z= 0.273 Chirality : 0.044 0.246 2806 Planarity : 0.004 0.038 2829 Dihedral : 7.249 59.999 2849 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.40 % Allowed : 14.92 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1970 helix: 2.21 (0.19), residues: 763 sheet: -0.80 (0.25), residues: 405 loop : -0.63 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 311 HIS 0.003 0.001 HIS C 60 PHE 0.025 0.001 PHE C 478 TYR 0.009 0.001 TYR B 124 ARG 0.004 0.000 ARG A 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00174 ( 8) link_NAG-ASN : angle 1.63232 ( 24) link_ALPHA1-6 : bond 0.01012 ( 9) link_ALPHA1-6 : angle 1.61652 ( 27) link_BETA1-4 : bond 0.00559 ( 13) link_BETA1-4 : angle 1.85094 ( 39) link_ALPHA1-3 : bond 0.00927 ( 6) link_ALPHA1-3 : angle 1.83186 ( 18) hydrogen bonds : bond 0.03468 ( 793) hydrogen bonds : angle 4.09300 ( 2517) SS BOND : bond 0.00720 ( 7) SS BOND : angle 1.96370 ( 14) covalent geometry : bond 0.00302 (17052) covalent geometry : angle 0.55064 (23274) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8928 (m-40) cc_final: 0.8531 (m110) REVERT: A 238 ASP cc_start: 0.8287 (t0) cc_final: 0.7981 (t0) REVERT: A 280 PHE cc_start: 0.7677 (t80) cc_final: 0.6663 (m-10) REVERT: A 324 MET cc_start: 0.7821 (tmm) cc_final: 0.6548 (pmm) REVERT: B 94 ASN cc_start: 0.8447 (t0) cc_final: 0.7232 (t0) REVERT: B 268 ASP cc_start: 0.8806 (t70) cc_final: 0.8430 (t0) REVERT: B 285 MET cc_start: 0.7811 (mmm) cc_final: 0.6784 (tmm) REVERT: C 340 MET cc_start: 0.5208 (mmm) cc_final: 0.4869 (mmm) REVERT: C 445 ASN cc_start: 0.7226 (m-40) cc_final: 0.6794 (t0) REVERT: C 473 PHE cc_start: 0.7736 (m-10) cc_final: 0.6735 (t80) REVERT: D 178 MET cc_start: 0.9133 (mmp) cc_final: 0.8459 (mmt) REVERT: D 410 LEU cc_start: 0.8796 (mm) cc_final: 0.8506 (mm) REVERT: E 234 SER cc_start: 0.8867 (t) cc_final: 0.8392 (p) REVERT: E 239 LEU cc_start: 0.8564 (tp) cc_final: 0.8354 (tp) REVERT: E 246 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7402 (pp30) REVERT: E 275 GLU cc_start: 0.8123 (mp0) cc_final: 0.7849 (mp0) REVERT: E 310 ARG cc_start: 0.6362 (mtt90) cc_final: 0.5865 (mtt180) outliers start: 44 outliers final: 41 residues processed: 216 average time/residue: 0.2243 time to fit residues: 79.6435 Evaluate side-chains 225 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 458 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 68 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 139 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 GLN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.111423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.087288 restraints weight = 32969.913| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.86 r_work: 0.3059 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17095 Z= 0.118 Angle : 0.548 9.681 23396 Z= 0.266 Chirality : 0.043 0.262 2806 Planarity : 0.004 0.038 2829 Dihedral : 7.042 59.183 2849 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.12 % Allowed : 15.08 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1970 helix: 2.29 (0.19), residues: 757 sheet: -0.73 (0.25), residues: 408 loop : -0.62 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 311 HIS 0.004 0.001 HIS C 60 PHE 0.023 0.001 PHE C 471 TYR 0.010 0.001 TYR E 117 ARG 0.003 0.000 ARG A 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 8) link_NAG-ASN : angle 1.56566 ( 24) link_ALPHA1-6 : bond 0.01026 ( 9) link_ALPHA1-6 : angle 1.57326 ( 27) link_BETA1-4 : bond 0.00575 ( 13) link_BETA1-4 : angle 1.81102 ( 39) link_ALPHA1-3 : bond 0.00903 ( 6) link_ALPHA1-3 : angle 1.76269 ( 18) hydrogen bonds : bond 0.03384 ( 793) hydrogen bonds : angle 4.03153 ( 2517) SS BOND : bond 0.00710 ( 7) SS BOND : angle 1.88638 ( 14) covalent geometry : bond 0.00263 (17052) covalent geometry : angle 0.53567 (23274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7688.34 seconds wall clock time: 134 minutes 18.66 seconds (8058.66 seconds total)