Starting phenix.real_space_refine on Sun Jun 15 15:41:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ql5_14064/06_2025/7ql5_14064.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql5_14064/06_2025/7ql5_14064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ql5_14064/06_2025/7ql5_14064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql5_14064/06_2025/7ql5_14064.map" model { file = "/net/cci-nas-00/data/ceres_data/7ql5_14064/06_2025/7ql5_14064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql5_14064/06_2025/7ql5_14064.cif" } resolution = 2.5 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= 0.004 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 84 5.16 5 C 11139 2.51 5 N 2614 2.21 5 O 3180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 17028 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3173 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 390, 3165 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 370} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 390, 3165 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 370} Chain breaks: 1 bond proxies already assigned to first conformer: 3240 Chain: "B" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3239 Classifications: {'peptide': 399} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Chain: "C" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3430 Classifications: {'peptide': 423} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 395} Chain breaks: 1 Chain: "D" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3010 Classifications: {'peptide': 371} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 351} Chain breaks: 1 Chain: "E" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3297 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 384} Chain breaks: 1 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 135 Unusual residues: {'NCT': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'NCT': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {'NAG': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 11.40, per 1000 atoms: 0.67 Number of scatterers: 17028 At special positions: 0 Unit cell: (101.721, 103.375, 176.151, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 P 11 15.00 O 3180 8.00 N 2614 7.00 C 11139 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=2.08 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=2.02 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 7 " " MAN F 4 " - " MAN F 5 " " 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 6 " " 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: 4.80 Conformation dependent library (CDL) restraints added in 2.2 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: 49 helices and 19 sheets defined 42.9% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.964A pdb=" N ARG A 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.138A pdb=" N GLY A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.744A pdb=" N SER A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 232 removed outlier: 4.546A 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 324 removed outlier: 5.675A pdb=" N ILE A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Proline residue: A 321 - end of helix removed outlier: 3.701A pdb=" N MET A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 432 removed outlier: 3.624A pdb=" N TRP A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 removed outlier: 3.682A pdb=" N THR B 6 " --> pdb=" O VAL B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.535A pdb=" N VAL B 85 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 180 removed outlier: 3.979A pdb=" N PHE B 180 " --> pdb=" O LYS B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 180' Processing helix chain 'B' and resid 224 through 238 Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 247 through 267 Processing helix chain 'B' and resid 278 through 306 Processing helix chain 'B' and resid 315 through 331 Proline residue: B 327 - end of helix Processing helix chain 'B' and resid 406 through 459 removed outlier: 3.546A pdb=" N ASP B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 removed outlier: 4.034A pdb=" N ARG C 6 " --> pdb=" O ASN C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.912A pdb=" N SER C 75 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 246 removed outlier: 4.487A pdb=" N THR C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.687A pdb=" N LEU C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 255 through 277 removed outlier: 3.924A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 314 Processing helix chain 'C' and resid 323 through 339 removed outlier: 5.510A pdb=" N LEU C 334 " --> pdb=" O PHE C 330 " (cutoff:3.500A) Proline residue: C 335 - end of helix Processing helix chain 'C' and resid 420 through 478 removed outlier: 4.267A pdb=" N ASP C 424 " --> pdb=" O LYS C 420 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 430 " --> pdb=" O THR C 426 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 431 " --> pdb=" O ASN C 427 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C 462 " --> pdb=" O MET C 458 " (cutoff:3.500A) Proline residue: C 463 - end of helix Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 68 through 73 removed outlier: 3.946A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.569A pdb=" N VAL D 85 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 235 removed outlier: 4.634A pdb=" N ILE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 3.637A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR D 234 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 240 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 Processing helix chain 'D' and resid 379 through 425 Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 68 through 73 removed outlier: 3.939A 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 174 through 178 removed outlier: 4.171A pdb=" N PHE E 178 " --> pdb=" O PRO E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 226 Processing helix chain 'E' and resid 226 through 237 Processing helix chain 'E' and resid 238 through 243 removed outlier: 3.563A pdb=" N TYR E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 273 Processing helix chain 'E' and resid 281 through 310 removed outlier: 3.574A pdb=" N ARG E 310 " --> pdb=" O ASN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 333 Proline residue: E 330 - end of helix Processing helix chain 'E' and resid 420 through 472 removed outlier: 3.682A pdb=" N GLN E 430 " --> pdb=" O SER E 426 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN E 431 " --> pdb=" O THR E 427 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU E 436 " --> pdb=" O ASP E 432 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP E 453 " --> pdb=" O LYS E 449 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE E 454 " --> pdb=" O ALA E 450 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.105A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.105A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 49 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL A 43 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU A 51 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG A 55 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU A 37 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG A 57 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU A 35 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLN A 59 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL A 33 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ILE A 61 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE A 31 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 6.077A pdb=" N TYR A 198 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TRP A 187 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP A 200 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR A 202 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY A 183 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS A 204 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR A 181 " --> pdb=" O HIS A 204 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 206 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.987A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU B 49 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU B 43 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR B 51 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE B 55 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU B 37 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN B 57 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU B 35 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA B 59 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL B 33 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N THR B 61 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL B 31 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 121 through 127 removed outlier: 6.254A pdb=" N GLU B 49 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU B 43 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR B 51 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE B 55 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU B 37 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN B 57 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU B 35 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA B 59 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL B 33 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N THR B 61 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL B 31 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N VAL B 174 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 35 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.469A pdb=" N SER B 148 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLU B 205 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN B 214 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE B 188 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.469A pdb=" N SER B 148 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLU B 205 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 82 removed outlier: 4.712A pdb=" N GLY C 116 " --> pdb=" O ASP C 64 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 82 removed outlier: 4.712A pdb=" N GLY C 116 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR C 51 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU C 45 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR C 53 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP C 57 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU C 39 " --> pdb=" O TRP C 57 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP C 59 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LEU C 37 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA C 61 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU C 35 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N TYR C 63 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ILE C 33 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 11.654A pdb=" N HIS C 65 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 13.919A pdb=" N VAL C 31 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.969A pdb=" N ALA C 150 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN C 213 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 220 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.969A pdb=" N ALA C 150 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN C 213 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 164 through 167 Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.207A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.207A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE D 49 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL D 43 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU D 51 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG D 55 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU D 37 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG D 57 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU D 35 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLN D 59 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL D 33 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ILE D 61 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE D 31 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 91 through 92 removed outlier: 6.143A pdb=" N TYR D 198 " --> pdb=" O TRP D 187 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP D 187 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP D 200 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS D 185 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR D 202 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY D 183 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N HIS D 204 " --> pdb=" O TYR D 181 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR D 181 " --> pdb=" O HIS D 204 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE D 206 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.907A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.907A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA E 49 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU E 43 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR E 51 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TRP E 55 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU E 37 " --> pdb=" O TRP E 55 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU E 57 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU E 35 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLN E 59 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU E 33 " --> pdb=" O GLN E 59 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ASN E 61 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL E 31 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 11.509A pdb=" N TYR E 63 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 13.726A pdb=" N ILE E 29 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.237A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN E 216 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE E 186 " --> pdb=" O GLN E 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.237A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) 877 hydrogen bonds defined for protein. 2543 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: 5.23 Time building geometry restraints manager: 5.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2615 1.32 - 1.45: 4883 1.45 - 1.58: 9793 1.58 - 1.71: 26 1.71 - 1.84: 137 Bond restraints: 17454 Sorted by residual: bond pdb=" C9 NCT A 601 " pdb=" N2 NCT A 601 " ideal model delta sigma weight residual 1.452 1.651 -0.199 2.00e-02 2.50e+03 9.86e+01 bond pdb=" C9 NCT D 601 " pdb=" N2 NCT D 601 " ideal model delta sigma weight residual 1.452 1.647 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" C8 NCT A 601 " pdb=" C9 NCT A 601 " ideal model delta sigma weight residual 1.532 1.352 0.180 2.00e-02 2.50e+03 8.08e+01 bond pdb=" C8 NCT D 601 " pdb=" C9 NCT D 601 " ideal model delta sigma weight residual 1.532 1.353 0.179 2.00e-02 2.50e+03 8.02e+01 bond pdb=" C6 NCT D 601 " pdb=" N2 NCT D 601 " ideal model delta sigma weight residual 1.452 1.331 0.121 2.00e-02 2.50e+03 3.66e+01 ... (remaining 17449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 23247 2.78 - 5.57: 386 5.57 - 8.35: 86 8.35 - 11.13: 29 11.13 - 13.91: 19 Bond angle restraints: 23767 Sorted by residual: angle pdb=" O VAL D 405 " pdb=" C VAL D 405 " pdb=" N ILE D 406 " ideal model delta sigma weight residual 121.87 113.22 8.65 9.70e-01 1.06e+00 7.96e+01 angle pdb=" CA VAL D 405 " pdb=" C VAL D 405 " pdb=" N ILE D 406 " ideal model delta sigma weight residual 117.15 125.84 -8.69 1.14e+00 7.69e-01 5.81e+01 angle pdb=" C TYR B 134 " pdb=" CA TYR B 134 " pdb=" CB TYR B 134 " ideal model delta sigma weight residual 109.83 116.04 -6.21 9.90e-01 1.02e+00 3.94e+01 angle pdb=" O SER E 294 " pdb=" C SER E 294 " pdb=" N MET E 295 " ideal model delta sigma weight residual 122.12 127.48 -5.36 1.06e+00 8.90e-01 2.55e+01 angle pdb=" C CYS A 142 " pdb=" CA CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sigma weight residual 109.48 117.96 -8.48 1.68e+00 3.54e-01 2.55e+01 ... (remaining 23762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 10475 35.22 - 70.43: 307 70.43 - 105.65: 93 105.65 - 140.86: 22 140.86 - 176.08: 2 Dihedral angle restraints: 10899 sinusoidal: 4996 harmonic: 5903 Sorted by residual: dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual -86.00 -44.76 -41.24 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" C27 POV C 602 " pdb=" C28 POV C 602 " pdb=" C29 POV C 602 " pdb="C210 POV C 602 " ideal model delta sinusoidal sigma weight residual 127.48 -56.44 -176.08 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C CYS A 142 " pdb=" N CYS A 142 " pdb=" CA CYS A 142 " pdb=" CB CYS A 142 " ideal model delta harmonic sigma weight residual -122.60 -133.82 11.22 0 2.50e+00 1.60e-01 2.02e+01 ... (remaining 10896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2497 0.075 - 0.151: 298 0.151 - 0.226: 19 0.226 - 0.302: 7 0.302 - 0.377: 3 Chirality restraints: 2824 Sorted by residual: chirality pdb=" CA CYS A 142 " pdb=" N CYS A 142 " pdb=" C CYS A 142 " pdb=" CB CYS A 142 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA PHE D 233 " pdb=" N PHE D 233 " pdb=" C PHE D 233 " pdb=" CB PHE D 233 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+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 -2.59 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 2821 not shown) Planarity restraints: 2862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 137 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" C PHE A 137 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE A 137 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 138 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 417 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C ILE D 417 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE D 417 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS D 418 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 228 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C LEU D 228 " 0.034 2.00e-02 2.50e+03 pdb=" O LEU D 228 " -0.013 2.00e-02 2.50e+03 pdb=" N THR D 229 " -0.012 2.00e-02 2.50e+03 ... (remaining 2859 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1198 2.74 - 3.28: 16851 3.28 - 3.82: 29137 3.82 - 4.36: 35783 4.36 - 4.90: 60378 Nonbonded interactions: 143347 Sorted by model distance: nonbonded pdb=" OG SER D 302 " pdb=" OG1 THR D 305 " model vdw 2.199 3.040 nonbonded pdb=" OD2 ASP A 89 " pdb=" OG1 THR A 150 " model vdw 2.199 3.040 nonbonded pdb=" OD2 ASP A 152 " pdb=" OG1 THR A 154 " model vdw 2.201 3.040 nonbonded pdb=" O ILE A 420 " pdb=" OG SER A 424 " model vdw 2.210 3.040 nonbonded pdb=" O LEU B 92 " pdb=" ND2 ASN B 95 " model vdw 2.210 3.120 ... (remaining 143342 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 226 or resid 228 through 323 or resid 378 throug \ h 425 or (resid 603 through 604 and (name N or name C1 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or nam \ e C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or \ name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 \ or name O32 or name P )))) selection = (chain 'D' and (resid 1 through 226 or resid 228 through 425 or resid 602 throug \ h 603)) } ncs_group { reference = (chain 'F' and (resid 2 or resid 5 through 7)) selection = (chain 'K' and (resid 1 or resid 4 through 6)) selection = (chain 'L' and (resid 1 or resid 4 through 6)) } 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=0.45 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: 2.430 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: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 40.010 Find NCS groups from input model: 0.620 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:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.008 0.199 17498 Z= 0.395 Angle : 0.960 13.913 23892 Z= 0.435 Chirality : 0.050 0.377 2824 Planarity : 0.004 0.040 2854 Dihedral : 18.219 176.076 7038 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.03 % Allowed : 5.66 % Favored : 93.30 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.63 % 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: 0.95 (0.19), residues: 1970 helix: 1.97 (0.19), residues: 732 sheet: 0.32 (0.25), residues: 407 loop : -0.38 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 453 HIS 0.004 0.001 HIS A 104 PHE 0.013 0.001 PHE B 137 TYR 0.015 0.001 TYR D 234 ARG 0.003 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.01229 ( 8) link_NAG-ASN : angle 2.15231 ( 24) link_ALPHA1-6 : bond 0.00505 ( 9) link_ALPHA1-6 : angle 1.65160 ( 27) link_BETA1-4 : bond 0.00885 ( 13) link_BETA1-4 : angle 2.58644 ( 39) link_ALPHA1-3 : bond 0.00455 ( 7) link_ALPHA1-3 : angle 1.74124 ( 21) hydrogen bonds : bond 0.15391 ( 799) hydrogen bonds : angle 5.78584 ( 2543) SS BOND : bond 0.01915 ( 7) SS BOND : angle 3.78267 ( 14) covalent geometry : bond 0.00771 (17454) covalent geometry : angle 0.94696 (23767) *********************** 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 193 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8826 (mmt) cc_final: 0.8608 (tpp) REVERT: A 262 GLU cc_start: 0.7211 (tt0) cc_final: 0.6916 (tp30) REVERT: A 306 HIS cc_start: 0.7498 (m90) cc_final: 0.7226 (m-70) REVERT: B 310 ASN cc_start: 0.7947 (t0) cc_final: 0.7623 (t0) REVERT: D 397 GLU cc_start: 0.5954 (tp30) cc_final: 0.5546 (tm-30) REVERT: E 472 PHE cc_start: 0.7923 (m-80) cc_final: 0.7633 (m-10) outliers start: 19 outliers final: 6 residues processed: 189 average time/residue: 0.9645 time to fit residues: 210.1992 Evaluate side-chains 146 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 154 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 ASN C 98 ASN C 103 HIS D 297 ASN D 306 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.117923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.089159 restraints weight = 28150.174| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.06 r_work: 0.3054 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17498 Z= 0.165 Angle : 0.616 9.617 23892 Z= 0.305 Chirality : 0.046 0.241 2824 Planarity : 0.004 0.044 2854 Dihedral : 18.211 174.671 3201 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.63 % Allowed : 8.66 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.19), residues: 1970 helix: 2.19 (0.19), residues: 753 sheet: 0.16 (0.24), residues: 421 loop : -0.39 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 453 HIS 0.006 0.001 HIS A 104 PHE 0.018 0.001 PHE C 294 TYR 0.016 0.001 TYR D 151 ARG 0.003 0.000 ARG E 485 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 8) link_NAG-ASN : angle 1.98625 ( 24) link_ALPHA1-6 : bond 0.00654 ( 9) link_ALPHA1-6 : angle 1.89144 ( 27) link_BETA1-4 : bond 0.00743 ( 13) link_BETA1-4 : angle 2.68068 ( 39) link_ALPHA1-3 : bond 0.01028 ( 7) link_ALPHA1-3 : angle 2.39974 ( 21) hydrogen bonds : bond 0.05198 ( 799) hydrogen bonds : angle 4.72807 ( 2543) SS BOND : bond 0.00831 ( 7) SS BOND : angle 2.73549 ( 14) covalent geometry : bond 0.00370 (17454) covalent geometry : angle 0.59382 (23767) *********************** 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 178 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8932 (mtp) REVERT: A 262 GLU cc_start: 0.7870 (tt0) cc_final: 0.7445 (tp30) REVERT: A 273 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7476 (mp) REVERT: A 306 HIS cc_start: 0.7549 (m90) cc_final: 0.7304 (m-70) REVERT: C 454 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6747 (m-30) REVERT: D 397 GLU cc_start: 0.6134 (tp30) cc_final: 0.5705 (tm-30) REVERT: E 299 MET cc_start: 0.8324 (ttt) cc_final: 0.7790 (ttp) outliers start: 30 outliers final: 11 residues processed: 164 average time/residue: 1.3337 time to fit residues: 249.8656 Evaluate side-chains 154 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 333 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 20 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 GLN C 267 GLN D 297 ASN D 306 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.117024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088258 restraints weight = 31066.593| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.15 r_work: 0.3038 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17498 Z= 0.161 Angle : 0.585 7.974 23892 Z= 0.291 Chirality : 0.045 0.238 2824 Planarity : 0.004 0.045 2854 Dihedral : 16.442 150.364 3197 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.18 % Allowed : 9.97 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 1970 helix: 2.33 (0.19), residues: 749 sheet: 0.17 (0.24), residues: 423 loop : -0.41 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 453 HIS 0.005 0.001 HIS A 104 PHE 0.018 0.001 PHE C 294 TYR 0.014 0.001 TYR D 151 ARG 0.002 0.000 ARG A 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 8) link_NAG-ASN : angle 1.82155 ( 24) link_ALPHA1-6 : bond 0.00727 ( 9) link_ALPHA1-6 : angle 1.94167 ( 27) link_BETA1-4 : bond 0.00750 ( 13) link_BETA1-4 : angle 2.59564 ( 39) link_ALPHA1-3 : bond 0.01089 ( 7) link_ALPHA1-3 : angle 2.06402 ( 21) hydrogen bonds : bond 0.04905 ( 799) hydrogen bonds : angle 4.56236 ( 2543) SS BOND : bond 0.00815 ( 7) SS BOND : angle 2.41948 ( 14) covalent geometry : bond 0.00365 (17454) covalent geometry : angle 0.56408 (23767) *********************** 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 179 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.9023 (mtp) REVERT: A 262 GLU cc_start: 0.7871 (tt0) cc_final: 0.7436 (tp30) REVERT: A 273 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7396 (mp) REVERT: A 306 HIS cc_start: 0.7544 (m90) cc_final: 0.7312 (m-70) REVERT: D 245 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7690 (pt) REVERT: D 397 GLU cc_start: 0.6141 (tp30) cc_final: 0.5716 (tm-30) REVERT: E 299 MET cc_start: 0.8400 (ttt) cc_final: 0.7883 (ttp) REVERT: E 335 MET cc_start: 0.5183 (mmp) cc_final: 0.4520 (mmp) outliers start: 40 outliers final: 17 residues processed: 163 average time/residue: 0.9989 time to fit residues: 187.7473 Evaluate side-chains 150 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 333 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 54 optimal weight: 2.9990 chunk 159 optimal weight: 0.2980 chunk 127 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 165 optimal weight: 0.3980 chunk 184 optimal weight: 0.0170 chunk 20 optimal weight: 8.9990 chunk 182 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN B 159 GLN D 306 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.120460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.092252 restraints weight = 30681.805| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.14 r_work: 0.3106 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17498 Z= 0.107 Angle : 0.527 7.745 23892 Z= 0.258 Chirality : 0.044 0.234 2824 Planarity : 0.004 0.046 2854 Dihedral : 14.686 119.906 3197 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.23 % Allowed : 10.89 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.19), residues: 1970 helix: 2.47 (0.19), residues: 761 sheet: 0.26 (0.24), residues: 423 loop : -0.39 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 60 HIS 0.003 0.001 HIS B 306 PHE 0.012 0.001 PHE C 294 TYR 0.014 0.001 TYR D 151 ARG 0.001 0.000 ARG C 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 8) link_NAG-ASN : angle 1.56177 ( 24) link_ALPHA1-6 : bond 0.00846 ( 9) link_ALPHA1-6 : angle 1.92669 ( 27) link_BETA1-4 : bond 0.00744 ( 13) link_BETA1-4 : angle 2.33798 ( 39) link_ALPHA1-3 : bond 0.01236 ( 7) link_ALPHA1-3 : angle 1.80784 ( 21) hydrogen bonds : bond 0.03940 ( 799) hydrogen bonds : angle 4.19766 ( 2543) SS BOND : bond 0.00734 ( 7) SS BOND : angle 1.59902 ( 14) covalent geometry : bond 0.00224 (17454) covalent geometry : angle 0.50941 (23767) *********************** 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 182 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7815 (tt0) cc_final: 0.7362 (tp30) REVERT: B 332 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7538 (mt) REVERT: D 127 TYR cc_start: 0.8759 (t80) cc_final: 0.8400 (t80) REVERT: D 245 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7713 (pt) REVERT: D 397 GLU cc_start: 0.6045 (tp30) cc_final: 0.5566 (tm-30) REVERT: E 299 MET cc_start: 0.8354 (ttt) cc_final: 0.7856 (ttp) outliers start: 41 outliers final: 14 residues processed: 166 average time/residue: 1.1777 time to fit residues: 224.0212 Evaluate side-chains 146 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 468 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 0.0270 chunk 166 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 ASN D 297 ASN D 306 HIS E 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.091812 restraints weight = 31040.764| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.15 r_work: 0.3096 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17498 Z= 0.114 Angle : 0.531 7.407 23892 Z= 0.260 Chirality : 0.044 0.232 2824 Planarity : 0.004 0.046 2854 Dihedral : 14.101 118.218 3196 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.96 % Allowed : 11.60 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1970 helix: 2.53 (0.19), residues: 762 sheet: 0.30 (0.24), residues: 421 loop : -0.41 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 60 HIS 0.003 0.001 HIS A 104 PHE 0.012 0.001 PHE C 294 TYR 0.012 0.001 TYR D 151 ARG 0.002 0.000 ARG B 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 8) link_NAG-ASN : angle 1.59116 ( 24) link_ALPHA1-6 : bond 0.00881 ( 9) link_ALPHA1-6 : angle 1.90956 ( 27) link_BETA1-4 : bond 0.00737 ( 13) link_BETA1-4 : angle 2.32863 ( 39) link_ALPHA1-3 : bond 0.01170 ( 7) link_ALPHA1-3 : angle 1.92569 ( 21) hydrogen bonds : bond 0.03942 ( 799) hydrogen bonds : angle 4.17606 ( 2543) SS BOND : bond 0.00741 ( 7) SS BOND : angle 1.69967 ( 14) covalent geometry : bond 0.00245 (17454) covalent geometry : angle 0.51254 (23767) *********************** 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 172 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8715 (p0) cc_final: 0.8422 (p0) REVERT: A 262 GLU cc_start: 0.7817 (tt0) cc_final: 0.7346 (tp30) REVERT: D 245 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7684 (pt) REVERT: D 262 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: D 397 GLU cc_start: 0.6094 (tp30) cc_final: 0.5611 (tm-30) REVERT: E 299 MET cc_start: 0.8364 (ttt) cc_final: 0.7863 (ttp) outliers start: 36 outliers final: 17 residues processed: 160 average time/residue: 1.3513 time to fit residues: 245.3287 Evaluate side-chains 156 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 41 optimal weight: 4.9990 chunk 170 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 GLN C 445 ASN D 297 ASN D 306 HIS E 471 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.118248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.090010 restraints weight = 28015.621| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.05 r_work: 0.3072 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17498 Z= 0.136 Angle : 0.556 8.340 23892 Z= 0.273 Chirality : 0.045 0.233 2824 Planarity : 0.004 0.045 2854 Dihedral : 13.620 118.327 3196 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.07 % Allowed : 11.71 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1970 helix: 2.48 (0.19), residues: 763 sheet: 0.27 (0.24), residues: 423 loop : -0.44 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 311 HIS 0.012 0.001 HIS E 471 PHE 0.013 0.001 PHE D 256 TYR 0.013 0.001 TYR A 151 ARG 0.002 0.000 ARG A 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 8) link_NAG-ASN : angle 1.69920 ( 24) link_ALPHA1-6 : bond 0.00926 ( 9) link_ALPHA1-6 : angle 1.88130 ( 27) link_BETA1-4 : bond 0.00732 ( 13) link_BETA1-4 : angle 2.42944 ( 39) link_ALPHA1-3 : bond 0.01120 ( 7) link_ALPHA1-3 : angle 1.89661 ( 21) hydrogen bonds : bond 0.04165 ( 799) hydrogen bonds : angle 4.25985 ( 2543) SS BOND : bond 0.00770 ( 7) SS BOND : angle 1.91224 ( 14) covalent geometry : bond 0.00304 (17454) covalent geometry : angle 0.53777 (23767) *********************** 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 174 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7838 (tt0) cc_final: 0.7382 (tp30) REVERT: B 425 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7116 (mtpt) REVERT: B 456 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8229 (tp) REVERT: D 105 MET cc_start: 0.8716 (mpp) cc_final: 0.8496 (mmt) REVERT: D 245 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7808 (pt) REVERT: D 262 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: D 397 GLU cc_start: 0.6102 (tp30) cc_final: 0.5603 (tm-30) REVERT: D 423 VAL cc_start: 0.5599 (OUTLIER) cc_final: 0.5177 (m) REVERT: E 299 MET cc_start: 0.8354 (ttt) cc_final: 0.7842 (ttp) outliers start: 38 outliers final: 18 residues processed: 160 average time/residue: 1.0836 time to fit residues: 198.0598 Evaluate side-chains 154 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 333 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 185 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 52 optimal weight: 0.0870 chunk 192 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 GLN C 445 ASN D 217 ASN D 297 ASN D 306 HIS E 198 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.120548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.092633 restraints weight = 27896.397| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.05 r_work: 0.3112 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17498 Z= 0.107 Angle : 0.522 7.071 23892 Z= 0.255 Chirality : 0.043 0.234 2824 Planarity : 0.004 0.045 2854 Dihedral : 12.952 116.852 3196 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.02 % Allowed : 12.04 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 1970 helix: 2.58 (0.19), residues: 762 sheet: 0.30 (0.24), residues: 420 loop : -0.39 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 60 HIS 0.003 0.001 HIS B 306 PHE 0.013 0.001 PHE C 294 TYR 0.013 0.001 TYR D 151 ARG 0.002 0.000 ARG B 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 8) link_NAG-ASN : angle 1.55195 ( 24) link_ALPHA1-6 : bond 0.01006 ( 9) link_ALPHA1-6 : angle 1.77925 ( 27) link_BETA1-4 : bond 0.00784 ( 13) link_BETA1-4 : angle 2.29336 ( 39) link_ALPHA1-3 : bond 0.01064 ( 7) link_ALPHA1-3 : angle 1.82447 ( 21) hydrogen bonds : bond 0.03704 ( 799) hydrogen bonds : angle 4.09011 ( 2543) SS BOND : bond 0.00725 ( 7) SS BOND : angle 1.59587 ( 14) covalent geometry : bond 0.00227 (17454) covalent geometry : angle 0.50527 (23767) *********************** 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 179 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8598 (p0) cc_final: 0.8270 (p0) REVERT: A 262 GLU cc_start: 0.7789 (tt0) cc_final: 0.7334 (tp30) REVERT: D 105 MET cc_start: 0.8683 (mpp) cc_final: 0.8469 (mmt) REVERT: D 245 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7714 (pt) REVERT: D 262 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: D 397 GLU cc_start: 0.5982 (tp30) cc_final: 0.5479 (tm-30) REVERT: D 423 VAL cc_start: 0.5588 (OUTLIER) cc_final: 0.5171 (m) REVERT: E 299 MET cc_start: 0.8317 (ttt) cc_final: 0.7802 (ttp) REVERT: E 457 LEU cc_start: 0.8954 (tp) cc_final: 0.8748 (tp) outliers start: 37 outliers final: 17 residues processed: 166 average time/residue: 1.0484 time to fit residues: 199.1738 Evaluate side-chains 155 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 237 VAL 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 333 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 125 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 GLN C 445 ASN D 297 ASN D 306 HIS E 196 ASN E 198 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.116830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.088391 restraints weight = 27957.170| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.05 r_work: 0.3038 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17498 Z= 0.194 Angle : 0.609 7.728 23892 Z= 0.302 Chirality : 0.047 0.230 2824 Planarity : 0.004 0.043 2854 Dihedral : 13.148 119.327 3196 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.85 % Allowed : 12.80 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.19), residues: 1970 helix: 2.44 (0.19), residues: 757 sheet: 0.18 (0.24), residues: 418 loop : -0.42 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 149 HIS 0.005 0.001 HIS A 104 PHE 0.015 0.002 PHE D 256 TYR 0.015 0.002 TYR C 202 ARG 0.003 0.001 ARG B 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 8) link_NAG-ASN : angle 1.86906 ( 24) link_ALPHA1-6 : bond 0.00952 ( 9) link_ALPHA1-6 : angle 1.85829 ( 27) link_BETA1-4 : bond 0.00733 ( 13) link_BETA1-4 : angle 2.59498 ( 39) link_ALPHA1-3 : bond 0.00958 ( 7) link_ALPHA1-3 : angle 1.83714 ( 21) hydrogen bonds : bond 0.04590 ( 799) hydrogen bonds : angle 4.40553 ( 2543) SS BOND : bond 0.00813 ( 7) SS BOND : angle 2.27181 ( 14) covalent geometry : bond 0.00456 (17454) covalent geometry : angle 0.59051 (23767) *********************** 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 161 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7861 (tt0) cc_final: 0.7401 (tp30) REVERT: B 318 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8019 (tt) REVERT: B 425 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7078 (mtpt) REVERT: D 142 CYS cc_start: 0.6617 (OUTLIER) cc_final: 0.6139 (m) REVERT: D 245 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7898 (pt) REVERT: D 397 GLU cc_start: 0.6103 (tp30) cc_final: 0.5587 (tm-30) REVERT: D 423 VAL cc_start: 0.5597 (OUTLIER) cc_final: 0.5180 (m) REVERT: E 299 MET cc_start: 0.8349 (ttt) cc_final: 0.7872 (ttp) outliers start: 34 outliers final: 19 residues processed: 149 average time/residue: 1.0941 time to fit residues: 186.2983 Evaluate side-chains 150 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 237 VAL 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 333 LEU Chi-restraints excluded: chain E residue 468 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 48 optimal weight: 0.0470 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 ASN D 306 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.084537 restraints weight = 35137.182| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.44 r_work: 0.2960 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17498 Z= 0.191 Angle : 0.616 8.158 23892 Z= 0.305 Chirality : 0.047 0.233 2824 Planarity : 0.004 0.044 2854 Dihedral : 13.119 121.014 3196 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.91 % Allowed : 12.80 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 1970 helix: 2.37 (0.19), residues: 757 sheet: 0.14 (0.24), residues: 418 loop : -0.50 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 311 HIS 0.006 0.001 HIS A 104 PHE 0.015 0.002 PHE E 467 TYR 0.015 0.002 TYR C 202 ARG 0.003 0.001 ARG E 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 8) link_NAG-ASN : angle 1.93597 ( 24) link_ALPHA1-6 : bond 0.00913 ( 9) link_ALPHA1-6 : angle 1.79315 ( 27) link_BETA1-4 : bond 0.00760 ( 13) link_BETA1-4 : angle 2.63376 ( 39) link_ALPHA1-3 : bond 0.00896 ( 7) link_ALPHA1-3 : angle 1.74858 ( 21) hydrogen bonds : bond 0.04664 ( 799) hydrogen bonds : angle 4.46559 ( 2543) SS BOND : bond 0.00828 ( 7) SS BOND : angle 2.28685 ( 14) covalent geometry : bond 0.00447 (17454) covalent geometry : angle 0.59717 (23767) *********************** 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 162 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7862 (tt0) cc_final: 0.7377 (tp30) REVERT: A 273 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7353 (mp) REVERT: B 318 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7950 (tt) REVERT: B 425 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7046 (mtpt) REVERT: B 456 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8195 (tp) REVERT: D 142 CYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6398 (m) REVERT: D 245 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7836 (pt) REVERT: D 397 GLU cc_start: 0.6048 (tp30) cc_final: 0.5549 (tm-30) REVERT: D 423 VAL cc_start: 0.5662 (OUTLIER) cc_final: 0.5243 (m) REVERT: E 299 MET cc_start: 0.8370 (ttt) cc_final: 0.7859 (ttp) outliers start: 35 outliers final: 21 residues processed: 153 average time/residue: 1.0931 time to fit residues: 191.7206 Evaluate side-chains 154 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 237 VAL 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 333 LEU Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 142 optimal weight: 0.0010 chunk 126 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 ASN D 297 ASN D 306 HIS E 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.092120 restraints weight = 28479.863| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.06 r_work: 0.3099 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17498 Z= 0.112 Angle : 0.539 8.158 23892 Z= 0.264 Chirality : 0.044 0.237 2824 Planarity : 0.004 0.046 2854 Dihedral : 12.439 118.471 3196 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.42 % Allowed : 13.40 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1970 helix: 2.52 (0.19), residues: 762 sheet: 0.24 (0.24), residues: 419 loop : -0.40 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 311 HIS 0.003 0.001 HIS A 104 PHE 0.014 0.001 PHE C 294 TYR 0.015 0.001 TYR D 151 ARG 0.002 0.000 ARG B 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 8) link_NAG-ASN : angle 1.58425 ( 24) link_ALPHA1-6 : bond 0.01015 ( 9) link_ALPHA1-6 : angle 1.66909 ( 27) link_BETA1-4 : bond 0.00820 ( 13) link_BETA1-4 : angle 2.32037 ( 39) link_ALPHA1-3 : bond 0.00982 ( 7) link_ALPHA1-3 : angle 1.73800 ( 21) hydrogen bonds : bond 0.03793 ( 799) hydrogen bonds : angle 4.15744 ( 2543) SS BOND : bond 0.00753 ( 7) SS BOND : angle 1.63440 ( 14) covalent geometry : bond 0.00242 (17454) covalent geometry : angle 0.52283 (23767) ********************** 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 162 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8668 (p0) cc_final: 0.8370 (p0) REVERT: A 262 GLU cc_start: 0.7771 (tt0) cc_final: 0.7317 (tp30) REVERT: B 318 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7997 (tt) REVERT: D 142 CYS cc_start: 0.6097 (OUTLIER) cc_final: 0.5686 (m) REVERT: E 299 MET cc_start: 0.8330 (ttt) cc_final: 0.7816 (ttp) outliers start: 26 outliers final: 16 residues processed: 155 average time/residue: 1.0608 time to fit residues: 188.4236 Evaluate side-chains 150 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 237 VAL 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 333 LEU Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 147 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 ASN D 297 ASN D 306 HIS E 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.118380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.090112 restraints weight = 27817.838| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.05 r_work: 0.3068 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17498 Z= 0.145 Angle : 0.578 10.436 23892 Z= 0.283 Chirality : 0.045 0.229 2824 Planarity : 0.004 0.044 2854 Dihedral : 12.410 119.238 3195 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.58 % Allowed : 13.45 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1970 helix: 2.44 (0.19), residues: 763 sheet: 0.22 (0.24), residues: 422 loop : -0.42 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 311 HIS 0.004 0.001 HIS A 104 PHE 0.012 0.001 PHE C 294 TYR 0.012 0.001 TYR D 151 ARG 0.003 0.000 ARG A 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 8) link_NAG-ASN : angle 1.74259 ( 24) link_ALPHA1-6 : bond 0.01005 ( 9) link_ALPHA1-6 : angle 1.69034 ( 27) link_BETA1-4 : bond 0.00756 ( 13) link_BETA1-4 : angle 2.40851 ( 39) link_ALPHA1-3 : bond 0.00928 ( 7) link_ALPHA1-3 : angle 1.75069 ( 21) hydrogen bonds : bond 0.04141 ( 799) hydrogen bonds : angle 4.26500 ( 2543) SS BOND : bond 0.00781 ( 7) SS BOND : angle 1.93368 ( 14) covalent geometry : bond 0.00330 (17454) covalent geometry : angle 0.56128 (23767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16871.68 seconds wall clock time: 298 minutes 36.06 seconds (17916.06 seconds total)