Starting phenix.real_space_refine on Tue Aug 26 05:54:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9awj_43925/08_2025/9awj_43925_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9awj_43925/08_2025/9awj_43925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9awj_43925/08_2025/9awj_43925_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9awj_43925/08_2025/9awj_43925_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9awj_43925/08_2025/9awj_43925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9awj_43925/08_2025/9awj_43925.map" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 80 5.16 5 C 11055 2.51 5 N 2656 2.21 5 O 3210 1.98 5 H 16488 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33491 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6468 Classifications: {'peptide': 399} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 378} Chain breaks: 1 Chain: "E" Number of atoms: 6627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 6627 Classifications: {'peptide': 408} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 381} Chain breaks: 2 Chain: "C" Number of atoms: 6466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6466 Classifications: {'peptide': 399} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 378} Chain breaks: 1 Chain: "D" Number of atoms: 6922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 6922 Classifications: {'peptide': 427} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 396} Chain breaks: 1 Chain: "B" Number of atoms: 6440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 6440 Classifications: {'peptide': 408} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 384} Chain breaks: 1 Chain: "H" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "K" 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: "F" 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: "L" 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: "G" 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: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {'ACH': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Chain: "A" 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} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N POV A 502 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV A 502 " occ=0.75 residue: pdb=" N POV E 601 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV E 601 " occ=0.75 Time building chain proxies: 4.63, per 1000 atoms: 0.14 Number of scatterers: 33491 At special positions: 0 Unit cell: (102.85, 109.395, 172.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 2 15.00 O 3210 8.00 N 2656 7.00 C 11055 6.00 H 16488 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 152 " - pdb=" SG CYS E 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 490 " 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 ALPHA1-2 " MAN H 5 " - " MAN H 6 " " MAN H 7 " - " MAN H 8 " " MAN H 9 " - " MAN H 10 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN K 4 " - " MAN K 5 " ALPHA1-3 " BMA H 3 " - " MAN H 9 " " MAN H 4 " - " MAN H 5 " " BMA J 3 " - " MAN J 8 " " MAN J 4 " - " MAN J 7 " " BMA K 3 " - " MAN K 4 " " MAN K 6 " - " MAN K 7 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA H 3 " - " MAN H 4 " " MAN H 4 " - " MAN H 7 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA K 3 " - " MAN K 6 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " 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 J 2 " - " BMA J 3 " " 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 F 1 " - " ASN D 96 " " NAG G 1 " - " ASN B 86 " " NAG H 1 " - " ASN A 161 " " NAG I 1 " - " ASN E 165 " " NAG J 1 " - " ASN C 161 " " NAG K 1 " - " ASN D 163 " " NAG L 1 " - " ASN B 161 " Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 912.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3912 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 19 sheets defined 44.9% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 removed outlier: 3.521A pdb=" N PHE A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.904A pdb=" N GLY A 93 " --> pdb=" O ASP A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 238 through 251 removed outlier: 3.644A pdb=" N THR A 249 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.524A pdb=" N SER A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 283 Processing helix chain 'A' and resid 292 through 320 Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 389 through 456 removed outlier: 3.594A pdb=" N ALA A 432 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLY A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 87 through 90 removed outlier: 3.785A pdb=" N SER E 90 " --> pdb=" O TYR E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 90' Processing helix chain 'E' and resid 92 through 97 removed outlier: 4.071A pdb=" N GLU E 97 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 109 No H-bonds generated for 'chain 'E' and resid 107 through 109' Processing helix chain 'E' and resid 246 through 253 Processing helix chain 'E' and resid 253 through 267 Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 271 through 275 removed outlier: 3.501A pdb=" N GLY E 275 " --> pdb=" O PRO E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 296 Processing helix chain 'E' and resid 307 through 335 Processing helix chain 'E' and resid 344 through 353 Processing helix chain 'E' and resid 354 through 360 removed outlier: 3.792A pdb=" N TYR E 358 " --> pdb=" O LYS E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 496 Processing helix chain 'C' and resid 22 through 32 Processing helix chain 'C' and resid 88 through 93 removed outlier: 3.982A pdb=" N GLY C 93 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 231 through 238 Processing helix chain 'C' and resid 238 through 251 removed outlier: 4.046A pdb=" N GLY C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 260 removed outlier: 3.598A pdb=" N SER C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C 260 " --> pdb=" O THR C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 260' Processing helix chain 'C' and resid 261 through 281 Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 292 through 320 removed outlier: 3.657A pdb=" N HIS C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'C' and resid 339 through 343 Processing helix chain 'C' and resid 389 through 456 removed outlier: 3.639A pdb=" N PHE C 446 " --> pdb=" O THR C 442 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 34 Processing helix chain 'D' and resid 85 through 88 removed outlier: 3.695A pdb=" N GLN D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 88' Processing helix chain 'D' and resid 90 through 95 removed outlier: 4.071A pdb=" N GLY D 95 " --> pdb=" O GLU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 107 No H-bonds generated for 'chain 'D' and resid 105 through 107' Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 through 231' Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 252 through 262 Processing helix chain 'D' and resid 263 through 269 removed outlier: 3.589A pdb=" N PHE D 267 " --> pdb=" O ASN D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 296 removed outlier: 3.894A pdb=" N LYS D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 334 Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 352 through 359 removed outlier: 3.714A pdb=" N GLU D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 494 Proline residue: D 436 - end of helix Proline residue: D 478 - end of helix removed outlier: 3.585A pdb=" N ASN D 494 " --> pdb=" O GLN D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 513 Processing helix chain 'B' and resid 22 through 33 Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.608A pdb=" N GLY B 93 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.695A pdb=" N TYR B 199 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 247 Processing helix chain 'B' and resid 247 through 257 Processing helix chain 'B' and resid 258 through 264 Processing helix chain 'B' and resid 271 through 294 removed outlier: 3.553A pdb=" N VAL B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 330 Processing helix chain 'B' and resid 339 through 350 Processing helix chain 'B' and resid 418 through 480 removed outlier: 3.572A pdb=" N TRP B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B 477 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.070A pdb=" N HIS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.070A pdb=" N HIS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN A 73 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU A 60 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ARG A 75 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE A 58 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS A 77 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLN A 56 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLN A 79 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLY A 54 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N VAL A 81 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N THR A 52 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL A 49 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASN A 179 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 51 " --> pdb=" O ASN A 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 112 removed outlier: 4.230A pdb=" N THR A 168 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU A 219 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR A 218 " --> pdb=" O TRP A 207 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TRP A 207 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASP A 220 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS A 205 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR A 222 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY A 203 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS A 224 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER A 201 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 226 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 101 through 105 removed outlier: 4.036A pdb=" N SER E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 101 through 105 removed outlier: 4.036A pdb=" N SER E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU E 73 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU E 67 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER E 75 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR E 79 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU E 61 " --> pdb=" O TYR E 79 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP E 81 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LEU E 59 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLU E 83 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE E 57 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR E 85 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL E 55 " --> pdb=" O THR E 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 114 through 116 removed outlier: 6.865A pdb=" N ILE E 241 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 101 removed outlier: 4.284A pdb=" N HIS C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 101 removed outlier: 4.284A pdb=" N HIS C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE C 69 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL C 63 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR C 71 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG C 75 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU C 57 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS C 77 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU C 55 " --> pdb=" O LYS C 77 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLN C 79 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL C 53 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N VAL C 81 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL C 51 " --> pdb=" O VAL C 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 112 removed outlier: 4.219A pdb=" N THR C 168 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU C 219 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR C 218 " --> pdb=" O TRP C 207 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TRP C 207 " --> pdb=" O TYR C 218 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP C 220 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS C 205 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR C 222 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY C 203 " --> pdb=" O THR C 222 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N HIS C 224 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER C 201 " --> pdb=" O HIS C 224 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL C 226 " --> pdb=" O LYS C 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 100 through 103 Processing sheet with id=AB3, first strand: chain 'D' and resid 100 through 103 removed outlier: 6.268A pdb=" N THR D 71 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU D 65 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR D 73 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP D 77 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU D 59 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU D 79 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU D 57 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLY D 81 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU D 55 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N THR D 83 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE D 53 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 112 through 114 removed outlier: 5.252A pdb=" N SER D 170 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLN D 233 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE D 240 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 112 through 114 removed outlier: 5.252A pdb=" N SER D 170 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLN D 233 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 184 through 187 Processing sheet with id=AB7, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.108A pdb=" N TYR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.108A pdb=" N TYR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N THR B 69 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU B 63 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR B 71 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TRP B 75 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU B 57 " --> pdb=" O TRP B 75 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY B 77 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL B 55 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASP B 79 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU B 53 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N GLN B 81 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE B 51 " --> pdb=" O GLN B 81 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 110 through 112 removed outlier: 4.978A pdb=" N SER B 168 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N THR B 228 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 235 " --> pdb=" O ASP B 208 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 110 through 112 removed outlier: 4.978A pdb=" N SER B 168 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N THR B 228 " --> pdb=" O SER B 168 " (cutoff:3.500A) 941 hydrogen bonds defined for protein. 2718 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: 6.14 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 16465 1.04 - 1.23: 374 1.23 - 1.43: 6878 1.43 - 1.63: 10068 1.63 - 1.82: 127 Bond restraints: 33912 Sorted by residual: bond pdb=" ND2 ASN B 86 " pdb="HD22 ASN B 86 " ideal model delta sigma weight residual 0.860 1.020 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" ND2 ASN D 96 " pdb="HD22 ASN D 96 " ideal model delta sigma weight residual 0.860 1.018 -0.158 2.00e-02 2.50e+03 6.27e+01 bond pdb=" NZ LYS A 124 " pdb=" HZ1 LYS A 124 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS B 54 " pdb=" HZ3 LYS B 54 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS E 214 " pdb=" HZ2 LYS E 214 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 33907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.81: 61244 11.81 - 23.61: 5 23.61 - 35.42: 0 35.42 - 47.23: 2 47.23 - 59.03: 1 Bond angle restraints: 61252 Sorted by residual: angle pdb=" CA ALA B 417 " pdb=" N ALA B 417 " pdb=" H ALA B 417 " ideal model delta sigma weight residual 114.00 173.03 -59.03 3.00e+00 1.11e-01 3.87e+02 angle pdb=" CA ILE A 387 " pdb=" N ILE A 387 " pdb=" H ILE A 387 " ideal model delta sigma weight residual 114.00 156.51 -42.51 3.00e+00 1.11e-01 2.01e+02 angle pdb=" CA GLY E 231 " pdb=" N GLY E 231 " pdb=" H GLY E 231 " ideal model delta sigma weight residual 114.00 153.04 -39.04 3.00e+00 1.11e-01 1.69e+02 angle pdb="HD21 ASN B 86 " pdb=" ND2 ASN B 86 " pdb="HD22 ASN B 86 " ideal model delta sigma weight residual 120.00 141.69 -21.69 3.00e+00 1.11e-01 5.23e+01 angle pdb=" N PHE A 345 " pdb=" CA PHE A 345 " pdb=" C PHE A 345 " ideal model delta sigma weight residual 113.01 104.43 8.58 1.20e+00 6.94e-01 5.11e+01 ... (remaining 61247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.78: 15676 25.78 - 51.57: 693 51.57 - 77.35: 157 77.35 - 103.14: 49 103.14 - 128.92: 8 Dihedral angle restraints: 16583 sinusoidal: 9311 harmonic: 7272 Sorted by residual: dihedral pdb=" CB CYS A 148 " pdb=" SG CYS A 148 " pdb=" SG CYS A 162 " pdb=" CB CYS A 162 " ideal model delta sinusoidal sigma weight residual 93.00 -177.94 -89.06 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" CA CYS C 162 " pdb=" C CYS C 162 " pdb=" N SER C 163 " pdb=" CA SER C 163 " ideal model delta harmonic sigma weight residual -180.00 -146.72 -33.28 0 5.00e+00 4.00e-02 4.43e+01 dihedral pdb=" C3 POV E 601 " pdb=" C31 POV E 601 " pdb=" O31 POV E 601 " pdb=" C32 POV E 601 " ideal model delta sinusoidal sigma weight residual 172.61 43.69 128.92 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 16580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.192: 2850 0.192 - 0.384: 12 0.384 - 0.576: 0 0.576 - 0.768: 1 0.768 - 0.960: 3 Chirality restraints: 2866 Sorted by residual: chirality pdb=" C1 MAN H 4 " pdb=" O6 BMA H 3 " pdb=" C2 MAN H 4 " pdb=" O5 MAN H 4 " both_signs ideal model delta sigma weight residual False 2.40 2.18 0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.13e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 2.99e+01 ... (remaining 2863 not shown) Planarity restraints: 4818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.333 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG G 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.159 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.507 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " 0.316 2.00e-02 2.50e+03 2.68e-01 9.00e+02 pdb=" C7 NAG G 2 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " -0.468 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.303 2.00e-02 2.50e+03 2.59e-01 8.36e+02 pdb=" C7 NAG F 1 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.170 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.454 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.052 2.00e-02 2.50e+03 ... (remaining 4815 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.87: 69 1.87 - 2.55: 28976 2.55 - 3.24: 103588 3.24 - 3.92: 135017 3.92 - 4.60: 211882 Nonbonded interactions: 479532 Sorted by model distance: nonbonded pdb="HD21 ASN C 161 " pdb=" O5 NAG J 1 " model vdw 1.189 1.960 nonbonded pdb="HD21 ASN A 161 " pdb=" O5 NAG H 1 " model vdw 1.446 1.960 nonbonded pdb=" HH TYR B 35 " pdb=" H TRP B 106 " model vdw 1.523 2.100 nonbonded pdb=" HG CYS D 256 " pdb="HD21 LEU D 312 " model vdw 1.598 2.440 nonbonded pdb=" HE1 PHE D 261 " pdb=" HG1 THR D 484 " model vdw 1.603 2.100 ... (remaining 479527 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 21 through 147 or (resid 148 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 149 through 161 or (resid 162 and (name N or name CA or name C or na \ me O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or res \ id 163 through 501)) selection = chain 'C' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = (chain 'H' and (resid 2 or resid 5 through 10)) selection = (chain 'J' and (resid 1 or resid 4 through 9)) } 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=0.75 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: 9.960 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: 0.200 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.580 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.006 0.233 17469 Z= 0.304 Angle : 0.904 21.904 23895 Z= 0.436 Chirality : 0.059 0.960 2866 Planarity : 0.012 0.286 2899 Dihedral : 16.942 128.923 6931 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.43 % Allowed : 13.02 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.18), residues: 2019 helix: 1.85 (0.18), residues: 788 sheet: -0.56 (0.23), residues: 412 loop : -0.26 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 463 TYR 0.015 0.001 TYR A 401 PHE 0.032 0.002 PHE C 304 TRP 0.018 0.001 TRP B 159 HIS 0.025 0.002 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00529 (17424) covalent geometry : angle 0.81876 (23766) SS BOND : bond 0.00290 ( 6) SS BOND : angle 1.69596 ( 12) hydrogen bonds : bond 0.10863 ( 857) hydrogen bonds : angle 5.23445 ( 2718) link_ALPHA1-2 : bond 0.00367 ( 6) link_ALPHA1-2 : angle 1.38742 ( 18) link_ALPHA1-3 : bond 0.00368 ( 7) link_ALPHA1-3 : angle 1.68928 ( 21) link_ALPHA1-6 : bond 0.00388 ( 7) link_ALPHA1-6 : angle 1.25848 ( 21) link_BETA1-4 : bond 0.02083 ( 12) link_BETA1-4 : angle 2.24870 ( 36) link_NAG-ASN : bond 0.16454 ( 7) link_NAG-ASN : angle 12.46877 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 222 time to evaluate : 0.745 Fit side-chains REVERT: E 354 LYS cc_start: 0.8363 (mmtt) cc_final: 0.7798 (ttpt) REVERT: C 258 ASP cc_start: 0.8245 (m-30) cc_final: 0.8027 (m-30) REVERT: D 480 MET cc_start: 0.8560 (ttm) cc_final: 0.8355 (ttm) REVERT: D 490 GLN cc_start: 0.8248 (mm-40) cc_final: 0.8048 (mp10) REVERT: B 321 ASN cc_start: 0.8645 (t0) cc_final: 0.8442 (t160) outliers start: 8 outliers final: 6 residues processed: 229 average time/residue: 1.0974 time to fit residues: 283.9397 Evaluate side-chains 203 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 197 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 336 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 278 ASN B 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.125885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.089396 restraints weight = 64089.111| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.22 r_work: 0.3057 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17469 Z= 0.133 Angle : 0.884 40.262 23895 Z= 0.361 Chirality : 0.047 0.648 2866 Planarity : 0.005 0.075 2899 Dihedral : 11.648 126.614 3026 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.07 % Allowed : 12.80 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.18), residues: 2019 helix: 2.28 (0.18), residues: 792 sheet: -0.26 (0.24), residues: 399 loop : -0.18 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 463 TYR 0.009 0.001 TYR B 344 PHE 0.029 0.001 PHE A 345 TRP 0.008 0.001 TRP B 80 HIS 0.006 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00295 (17424) covalent geometry : angle 0.56554 (23766) SS BOND : bond 0.00568 ( 6) SS BOND : angle 3.49104 ( 12) hydrogen bonds : bond 0.04620 ( 857) hydrogen bonds : angle 4.32571 ( 2718) link_ALPHA1-2 : bond 0.00342 ( 6) link_ALPHA1-2 : angle 1.58948 ( 18) link_ALPHA1-3 : bond 0.00624 ( 7) link_ALPHA1-3 : angle 1.97494 ( 21) link_ALPHA1-6 : bond 0.00589 ( 7) link_ALPHA1-6 : angle 1.80010 ( 21) link_BETA1-4 : bond 0.00403 ( 12) link_BETA1-4 : angle 2.09547 ( 36) link_NAG-ASN : bond 0.00386 ( 7) link_NAG-ASN : angle 22.45084 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 MET cc_start: 0.8886 (tpp) cc_final: 0.8648 (tpp) REVERT: C 258 ASP cc_start: 0.8349 (m-30) cc_final: 0.8051 (m-30) REVERT: D 303 MET cc_start: 0.8720 (mmt) cc_final: 0.8499 (mpt) REVERT: D 480 MET cc_start: 0.8396 (ttm) cc_final: 0.8196 (ttm) REVERT: D 490 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8019 (mp10) REVERT: B 321 ASN cc_start: 0.8678 (t0) cc_final: 0.8472 (t160) outliers start: 20 outliers final: 14 residues processed: 212 average time/residue: 1.0029 time to fit residues: 242.3610 Evaluate side-chains 211 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain E residue 266 PHE Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 491 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 18 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 125 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 349 GLN D 116 ASN B 169 GLN B 278 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.086803 restraints weight = 64276.083| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.22 r_work: 0.3037 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17469 Z= 0.151 Angle : 0.875 41.283 23895 Z= 0.351 Chirality : 0.045 0.401 2866 Planarity : 0.004 0.067 2899 Dihedral : 10.368 120.160 3021 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.61 % Allowed : 11.78 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.19), residues: 2019 helix: 2.55 (0.18), residues: 791 sheet: -0.17 (0.25), residues: 403 loop : -0.09 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 101 TYR 0.008 0.001 TYR D 133 PHE 0.016 0.001 PHE C 304 TRP 0.009 0.001 TRP B 80 HIS 0.006 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00337 (17424) covalent geometry : angle 0.53043 (23766) SS BOND : bond 0.00294 ( 6) SS BOND : angle 1.58236 ( 12) hydrogen bonds : bond 0.04320 ( 857) hydrogen bonds : angle 4.03048 ( 2718) link_ALPHA1-2 : bond 0.00353 ( 6) link_ALPHA1-2 : angle 1.59711 ( 18) link_ALPHA1-3 : bond 0.00883 ( 7) link_ALPHA1-3 : angle 1.83554 ( 21) link_ALPHA1-6 : bond 0.00818 ( 7) link_ALPHA1-6 : angle 1.79344 ( 21) link_BETA1-4 : bond 0.00385 ( 12) link_BETA1-4 : angle 2.15887 ( 36) link_NAG-ASN : bond 0.00507 ( 7) link_NAG-ASN : angle 23.11202 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 460 LEU cc_start: 0.8146 (mt) cc_final: 0.7774 (tp) REVERT: C 258 ASP cc_start: 0.8376 (m-30) cc_final: 0.8062 (m-30) REVERT: B 452 LYS cc_start: 0.6658 (mtpm) cc_final: 0.6210 (mttp) outliers start: 30 outliers final: 14 residues processed: 218 average time/residue: 1.0185 time to fit residues: 253.1618 Evaluate side-chains 209 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 266 PHE Chi-restraints excluded: chain E residue 446 TYR Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 491 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 181 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 ASN B 278 ASN B 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.086093 restraints weight = 64170.666| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.22 r_work: 0.3028 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17469 Z= 0.169 Angle : 0.870 41.632 23895 Z= 0.351 Chirality : 0.046 0.476 2866 Planarity : 0.004 0.063 2899 Dihedral : 9.802 117.337 3017 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.45 % Allowed : 12.10 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.19), residues: 2019 helix: 2.58 (0.18), residues: 792 sheet: -0.15 (0.25), residues: 414 loop : -0.08 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 101 TYR 0.008 0.001 TYR B 344 PHE 0.013 0.001 PHE A 32 TRP 0.009 0.001 TRP B 80 HIS 0.005 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00388 (17424) covalent geometry : angle 0.53211 (23766) SS BOND : bond 0.00314 ( 6) SS BOND : angle 1.92000 ( 12) hydrogen bonds : bond 0.04326 ( 857) hydrogen bonds : angle 3.97298 ( 2718) link_ALPHA1-2 : bond 0.00303 ( 6) link_ALPHA1-2 : angle 1.64290 ( 18) link_ALPHA1-3 : bond 0.00706 ( 7) link_ALPHA1-3 : angle 1.84684 ( 21) link_ALPHA1-6 : bond 0.00831 ( 7) link_ALPHA1-6 : angle 1.86657 ( 21) link_BETA1-4 : bond 0.00353 ( 12) link_BETA1-4 : angle 2.03246 ( 36) link_NAG-ASN : bond 0.00354 ( 7) link_NAG-ASN : angle 22.84204 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 455 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6307 (mp0) REVERT: E 460 LEU cc_start: 0.8207 (mt) cc_final: 0.7785 (tp) REVERT: C 258 ASP cc_start: 0.8444 (m-30) cc_final: 0.8091 (m-30) REVERT: C 320 HIS cc_start: 0.6788 (m-70) cc_final: 0.6525 (m170) outliers start: 27 outliers final: 12 residues processed: 214 average time/residue: 0.9948 time to fit residues: 242.4272 Evaluate side-chains 213 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 446 TYR Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 311 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 87 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 0.0060 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 349 GLN D 61 ASN D 116 ASN B 278 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.122982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.085756 restraints weight = 64258.911| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.23 r_work: 0.3020 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17469 Z= 0.169 Angle : 0.872 42.024 23895 Z= 0.350 Chirality : 0.046 0.464 2866 Planarity : 0.004 0.062 2899 Dihedral : 9.418 111.510 3017 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.23 % Allowed : 12.75 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.19), residues: 2019 helix: 2.66 (0.18), residues: 792 sheet: -0.11 (0.25), residues: 414 loop : -0.08 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 101 TYR 0.008 0.001 TYR D 133 PHE 0.013 0.001 PHE C 304 TRP 0.008 0.001 TRP B 80 HIS 0.004 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00390 (17424) covalent geometry : angle 0.53157 (23766) SS BOND : bond 0.00290 ( 6) SS BOND : angle 1.80879 ( 12) hydrogen bonds : bond 0.04295 ( 857) hydrogen bonds : angle 3.92871 ( 2718) link_ALPHA1-2 : bond 0.00299 ( 6) link_ALPHA1-2 : angle 1.63117 ( 18) link_ALPHA1-3 : bond 0.00731 ( 7) link_ALPHA1-3 : angle 1.77235 ( 21) link_ALPHA1-6 : bond 0.00832 ( 7) link_ALPHA1-6 : angle 1.90923 ( 21) link_BETA1-4 : bond 0.00337 ( 12) link_BETA1-4 : angle 2.02781 ( 36) link_NAG-ASN : bond 0.00402 ( 7) link_NAG-ASN : angle 22.95289 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 455 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: E 460 LEU cc_start: 0.8230 (mt) cc_final: 0.7752 (tp) REVERT: C 258 ASP cc_start: 0.8434 (m-30) cc_final: 0.8068 (m-30) REVERT: C 320 HIS cc_start: 0.6914 (m-70) cc_final: 0.6680 (m170) REVERT: D 69 GLU cc_start: 0.8443 (mp0) cc_final: 0.8200 (mp0) REVERT: B 449 ARG cc_start: 0.6907 (mtp85) cc_final: 0.6609 (mtm110) outliers start: 23 outliers final: 16 residues processed: 222 average time/residue: 1.0142 time to fit residues: 257.2492 Evaluate side-chains 221 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 446 TYR Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 491 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 185 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.0170 chunk 118 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 349 GLN E 450 GLN D 116 ASN B 278 ASN B 283 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.122626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.085432 restraints weight = 64149.713| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.25 r_work: 0.3019 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17469 Z= 0.154 Angle : 0.867 42.227 23895 Z= 0.347 Chirality : 0.045 0.453 2866 Planarity : 0.004 0.060 2899 Dihedral : 9.056 105.857 3017 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.55 % Allowed : 12.69 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.19), residues: 2019 helix: 2.74 (0.18), residues: 792 sheet: -0.09 (0.25), residues: 414 loop : -0.06 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 466 TYR 0.008 0.001 TYR B 344 PHE 0.012 0.001 PHE C 304 TRP 0.009 0.001 TRP B 80 HIS 0.004 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00355 (17424) covalent geometry : angle 0.52108 (23766) SS BOND : bond 0.00259 ( 6) SS BOND : angle 1.70170 ( 12) hydrogen bonds : bond 0.04197 ( 857) hydrogen bonds : angle 3.89564 ( 2718) link_ALPHA1-2 : bond 0.00282 ( 6) link_ALPHA1-2 : angle 1.62213 ( 18) link_ALPHA1-3 : bond 0.00718 ( 7) link_ALPHA1-3 : angle 1.77765 ( 21) link_ALPHA1-6 : bond 0.00865 ( 7) link_ALPHA1-6 : angle 1.94395 ( 21) link_BETA1-4 : bond 0.00337 ( 12) link_BETA1-4 : angle 1.95496 ( 36) link_NAG-ASN : bond 0.00419 ( 7) link_NAG-ASN : angle 23.01925 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 155 GLN cc_start: 0.7878 (mt0) cc_final: 0.7575 (mt0) REVERT: E 362 LYS cc_start: 0.8586 (pttm) cc_final: 0.8277 (ptpt) REVERT: E 455 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6425 (mp0) REVERT: C 258 ASP cc_start: 0.8402 (m-30) cc_final: 0.8032 (m-30) REVERT: D 69 GLU cc_start: 0.8529 (mp0) cc_final: 0.8265 (mp0) REVERT: D 313 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8178 (mm) REVERT: B 449 ARG cc_start: 0.6893 (mtp85) cc_final: 0.6583 (mtm110) outliers start: 29 outliers final: 16 residues processed: 227 average time/residue: 1.0101 time to fit residues: 262.5777 Evaluate side-chains 222 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 446 TYR Chi-restraints excluded: chain E residue 450 GLN Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 491 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 166 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 97 optimal weight: 0.0870 chunk 131 optimal weight: 0.0030 chunk 22 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 349 GLN D 116 ASN B 278 ASN B 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.086061 restraints weight = 64082.666| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.22 r_work: 0.3027 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17469 Z= 0.131 Angle : 0.865 42.428 23895 Z= 0.344 Chirality : 0.045 0.441 2866 Planarity : 0.004 0.058 2899 Dihedral : 8.757 102.276 3017 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.29 % Allowed : 13.02 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.19), residues: 2019 helix: 2.78 (0.18), residues: 792 sheet: -0.08 (0.25), residues: 413 loop : -0.03 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 466 TYR 0.008 0.001 TYR B 344 PHE 0.011 0.001 PHE C 276 TRP 0.009 0.001 TRP B 80 HIS 0.003 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00298 (17424) covalent geometry : angle 0.51399 (23766) SS BOND : bond 0.00224 ( 6) SS BOND : angle 1.46979 ( 12) hydrogen bonds : bond 0.04101 ( 857) hydrogen bonds : angle 3.85380 ( 2718) link_ALPHA1-2 : bond 0.00299 ( 6) link_ALPHA1-2 : angle 1.59754 ( 18) link_ALPHA1-3 : bond 0.00741 ( 7) link_ALPHA1-3 : angle 1.75284 ( 21) link_ALPHA1-6 : bond 0.00876 ( 7) link_ALPHA1-6 : angle 1.94897 ( 21) link_BETA1-4 : bond 0.00340 ( 12) link_BETA1-4 : angle 1.86399 ( 36) link_NAG-ASN : bond 0.00460 ( 7) link_NAG-ASN : angle 23.17522 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 155 GLN cc_start: 0.7871 (mt0) cc_final: 0.7564 (mt0) REVERT: E 362 LYS cc_start: 0.8576 (pttm) cc_final: 0.8269 (ptpt) REVERT: E 455 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6543 (mp0) REVERT: C 124 LYS cc_start: 0.7859 (tttt) cc_final: 0.7030 (mtmt) REVERT: C 258 ASP cc_start: 0.8417 (m-30) cc_final: 0.8036 (m-30) REVERT: C 344 MET cc_start: 0.3537 (mmm) cc_final: 0.3261 (mmp) REVERT: D 69 GLU cc_start: 0.8518 (mp0) cc_final: 0.8248 (mp0) REVERT: D 313 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8172 (mm) REVERT: B 449 ARG cc_start: 0.6893 (mtp85) cc_final: 0.6584 (mtm110) outliers start: 24 outliers final: 18 residues processed: 225 average time/residue: 0.9714 time to fit residues: 250.3376 Evaluate side-chains 228 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 349 GLN Chi-restraints excluded: chain E residue 446 TYR Chi-restraints excluded: chain E residue 450 GLN Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 311 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 144 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 GLN D 116 ASN B 278 ASN B 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.085536 restraints weight = 63962.405| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.21 r_work: 0.3018 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17469 Z= 0.179 Angle : 0.873 42.287 23895 Z= 0.351 Chirality : 0.046 0.455 2866 Planarity : 0.004 0.058 2899 Dihedral : 8.665 98.951 3017 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.23 % Allowed : 13.23 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.19), residues: 2019 helix: 2.76 (0.18), residues: 792 sheet: -0.06 (0.25), residues: 414 loop : -0.06 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 463 TYR 0.008 0.001 TYR B 344 PHE 0.013 0.001 PHE C 276 TRP 0.009 0.001 TRP B 80 HIS 0.004 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00417 (17424) covalent geometry : angle 0.53412 (23766) SS BOND : bond 0.00308 ( 6) SS BOND : angle 1.79012 ( 12) hydrogen bonds : bond 0.04245 ( 857) hydrogen bonds : angle 3.89107 ( 2718) link_ALPHA1-2 : bond 0.00273 ( 6) link_ALPHA1-2 : angle 1.64868 ( 18) link_ALPHA1-3 : bond 0.00685 ( 7) link_ALPHA1-3 : angle 1.77818 ( 21) link_ALPHA1-6 : bond 0.00821 ( 7) link_ALPHA1-6 : angle 1.99397 ( 21) link_BETA1-4 : bond 0.00351 ( 12) link_BETA1-4 : angle 2.02732 ( 36) link_NAG-ASN : bond 0.00385 ( 7) link_NAG-ASN : angle 22.94994 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8668 (tt0) REVERT: E 155 GLN cc_start: 0.7870 (mt0) cc_final: 0.7570 (mt0) REVERT: E 362 LYS cc_start: 0.8656 (pttm) cc_final: 0.8342 (ptpt) REVERT: E 455 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6427 (mp0) REVERT: C 258 ASP cc_start: 0.8419 (m-30) cc_final: 0.8032 (m-30) REVERT: C 344 MET cc_start: 0.3582 (mmm) cc_final: 0.3355 (mmp) REVERT: D 69 GLU cc_start: 0.8509 (mp0) cc_final: 0.8231 (mp0) REVERT: D 313 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8169 (mm) REVERT: B 449 ARG cc_start: 0.6874 (mtp85) cc_final: 0.6565 (mtm110) outliers start: 23 outliers final: 16 residues processed: 222 average time/residue: 0.9988 time to fit residues: 253.9634 Evaluate side-chains 223 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 446 TYR Chi-restraints excluded: chain E residue 450 GLN Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain B residue 311 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 101 optimal weight: 1.9990 chunk 125 optimal weight: 0.1980 chunk 149 optimal weight: 0.0020 chunk 114 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 159 optimal weight: 0.0980 chunk 81 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN D 116 ASN B 271 GLN B 278 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.124458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.087555 restraints weight = 63767.066| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.21 r_work: 0.3049 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17469 Z= 0.103 Angle : 0.860 42.787 23895 Z= 0.340 Chirality : 0.044 0.408 2866 Planarity : 0.004 0.057 2899 Dihedral : 7.824 95.285 3017 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.29 % Allowed : 13.44 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.19), residues: 2019 helix: 2.94 (0.18), residues: 791 sheet: -0.08 (0.25), residues: 403 loop : 0.05 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 463 TYR 0.007 0.001 TYR D 139 PHE 0.011 0.001 PHE C 304 TRP 0.009 0.001 TRP C 80 HIS 0.005 0.001 HIS C 428 Details of bonding type rmsd covalent geometry : bond 0.00224 (17424) covalent geometry : angle 0.49602 (23766) SS BOND : bond 0.00157 ( 6) SS BOND : angle 1.13975 ( 12) hydrogen bonds : bond 0.03910 ( 857) hydrogen bonds : angle 3.78370 ( 2718) link_ALPHA1-2 : bond 0.00357 ( 6) link_ALPHA1-2 : angle 1.55907 ( 18) link_ALPHA1-3 : bond 0.00760 ( 7) link_ALPHA1-3 : angle 1.63462 ( 21) link_ALPHA1-6 : bond 0.00846 ( 7) link_ALPHA1-6 : angle 1.90578 ( 21) link_BETA1-4 : bond 0.00403 ( 12) link_BETA1-4 : angle 1.73785 ( 36) link_NAG-ASN : bond 0.00564 ( 7) link_NAG-ASN : angle 23.40620 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 362 LYS cc_start: 0.8554 (pttm) cc_final: 0.8250 (ptpt) REVERT: E 455 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: C 124 LYS cc_start: 0.7823 (tttt) cc_final: 0.6995 (mtmt) REVERT: C 258 ASP cc_start: 0.8424 (m-30) cc_final: 0.8039 (m-30) REVERT: C 344 MET cc_start: 0.3613 (mmm) cc_final: 0.3340 (mmp) REVERT: C 421 TYR cc_start: 0.7677 (t80) cc_final: 0.7375 (t80) REVERT: D 69 GLU cc_start: 0.8487 (mp0) cc_final: 0.8156 (mp0) REVERT: D 313 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8149 (mm) outliers start: 24 outliers final: 15 residues processed: 227 average time/residue: 0.9746 time to fit residues: 254.0366 Evaluate side-chains 229 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 446 TYR Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain B residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 106 optimal weight: 0.6980 chunk 135 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN D 452 ASN B 278 ASN B 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.086348 restraints weight = 64374.192| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.21 r_work: 0.3026 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17469 Z= 0.149 Angle : 0.867 42.454 23895 Z= 0.346 Chirality : 0.045 0.445 2866 Planarity : 0.004 0.057 2899 Dihedral : 7.849 93.111 3017 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.96 % Allowed : 14.03 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.19), residues: 2019 helix: 2.92 (0.18), residues: 791 sheet: -0.04 (0.25), residues: 414 loop : 0.04 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 463 TYR 0.007 0.001 TYR B 344 PHE 0.012 0.001 PHE C 276 TRP 0.009 0.001 TRP B 80 HIS 0.004 0.001 HIS C 428 Details of bonding type rmsd covalent geometry : bond 0.00348 (17424) covalent geometry : angle 0.51638 (23766) SS BOND : bond 0.00267 ( 6) SS BOND : angle 1.53681 ( 12) hydrogen bonds : bond 0.04033 ( 857) hydrogen bonds : angle 3.82624 ( 2718) link_ALPHA1-2 : bond 0.00269 ( 6) link_ALPHA1-2 : angle 1.62150 ( 18) link_ALPHA1-3 : bond 0.00700 ( 7) link_ALPHA1-3 : angle 1.65660 ( 21) link_ALPHA1-6 : bond 0.00714 ( 7) link_ALPHA1-6 : angle 1.87247 ( 21) link_BETA1-4 : bond 0.00323 ( 12) link_BETA1-4 : angle 1.91026 ( 36) link_NAG-ASN : bond 0.00425 ( 7) link_NAG-ASN : angle 23.16496 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 155 GLN cc_start: 0.7881 (mt0) cc_final: 0.7581 (mt0) REVERT: E 362 LYS cc_start: 0.8569 (pttm) cc_final: 0.8264 (ptpt) REVERT: E 455 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: C 258 ASP cc_start: 0.8441 (m-30) cc_final: 0.8055 (m-30) REVERT: C 421 TYR cc_start: 0.7680 (t80) cc_final: 0.7370 (t80) REVERT: D 69 GLU cc_start: 0.8520 (mp0) cc_final: 0.8245 (mp0) REVERT: D 313 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8166 (mm) REVERT: B 292 GLN cc_start: 0.8162 (tp40) cc_final: 0.7871 (tt0) outliers start: 18 outliers final: 14 residues processed: 222 average time/residue: 0.9666 time to fit residues: 246.1696 Evaluate side-chains 225 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 446 TYR Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain B residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 112 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 98 optimal weight: 0.0470 chunk 181 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 180 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN D 452 ASN B 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.122958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.085840 restraints weight = 64060.089| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.24 r_work: 0.3031 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17469 Z= 0.146 Angle : 0.865 42.417 23895 Z= 0.346 Chirality : 0.045 0.447 2866 Planarity : 0.004 0.056 2899 Dihedral : 7.781 92.041 3017 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.91 % Allowed : 14.30 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.19), residues: 2019 helix: 2.93 (0.18), residues: 791 sheet: -0.04 (0.25), residues: 414 loop : 0.04 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 463 TYR 0.007 0.001 TYR B 344 PHE 0.012 0.001 PHE C 276 TRP 0.009 0.001 TRP B 80 HIS 0.005 0.001 HIS C 428 Details of bonding type rmsd covalent geometry : bond 0.00336 (17424) covalent geometry : angle 0.51478 (23766) SS BOND : bond 0.00252 ( 6) SS BOND : angle 1.54544 ( 12) hydrogen bonds : bond 0.04064 ( 857) hydrogen bonds : angle 3.83644 ( 2718) link_ALPHA1-2 : bond 0.00282 ( 6) link_ALPHA1-2 : angle 1.62410 ( 18) link_ALPHA1-3 : bond 0.00639 ( 7) link_ALPHA1-3 : angle 1.59595 ( 21) link_ALPHA1-6 : bond 0.00657 ( 7) link_ALPHA1-6 : angle 1.86399 ( 21) link_BETA1-4 : bond 0.00329 ( 12) link_BETA1-4 : angle 1.93748 ( 36) link_NAG-ASN : bond 0.00423 ( 7) link_NAG-ASN : angle 23.11758 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10912.60 seconds wall clock time: 184 minutes 49.79 seconds (11089.79 seconds total)