Starting phenix.real_space_refine on Tue Apr 9 19:46:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/04_2024/8hsj_34999_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/04_2024/8hsj_34999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/04_2024/8hsj_34999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/04_2024/8hsj_34999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/04_2024/8hsj_34999_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/04_2024/8hsj_34999_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 8 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 42 5.16 5 Be 6 3.05 5 C 10800 2.51 5 N 3132 2.21 5 O 3228 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17244 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "D" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "E" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "F" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.96, per 1000 atoms: 0.52 Number of scatterers: 17244 At special positions: 0 Unit cell: (136.74, 130.38, 90.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 42 16.00 P 12 15.00 Mg 6 11.99 F 18 9.00 O 3228 8.00 N 3132 7.00 C 10800 6.00 Be 6 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.45 Conformation dependent library (CDL) restraints added in 3.0 seconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4032 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 26 sheets defined 40.0% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 92 through 98 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.565A pdb=" N LYS A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 243 through 263 removed outlier: 3.775A pdb=" N GLU A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 300 through 309 removed outlier: 4.019A pdb=" N PHE A 303 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 375 through 378 No H-bonds generated for 'chain 'A' and resid 375 through 378' Processing helix chain 'A' and resid 381 through 394 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.872A pdb=" N ARG A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'B' and resid 92 through 98 Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.677A pdb=" N LYS B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 133 through 137' Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 191 through 204 removed outlier: 3.512A pdb=" N LYS B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 228 Processing helix chain 'B' and resid 243 through 263 removed outlier: 3.944A pdb=" N GLU B 263 " --> pdb=" O ARG B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 375 through 378 No H-bonds generated for 'chain 'B' and resid 375 through 378' Processing helix chain 'B' and resid 381 through 394 Processing helix chain 'B' and resid 399 through 412 removed outlier: 4.303A pdb=" N ARG B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.518A pdb=" N LYS C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 133 through 137' Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 191 through 204 removed outlier: 3.579A pdb=" N LYS C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 228 Processing helix chain 'C' and resid 243 through 263 removed outlier: 4.865A pdb=" N GLU C 263 " --> pdb=" O ARG C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 299 through 309 removed outlier: 4.134A pdb=" N PHE C 303 " --> pdb=" O ALA C 300 " (cutoff:3.500A) Proline residue: C 304 - end of helix Processing helix chain 'C' and resid 333 through 343 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 375 through 378 No H-bonds generated for 'chain 'C' and resid 375 through 378' Processing helix chain 'C' and resid 381 through 394 Processing helix chain 'C' and resid 399 through 412 removed outlier: 3.696A pdb=" N ALA C 411 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'D' and resid 92 through 98 Processing helix chain 'D' and resid 133 through 137 removed outlier: 3.543A pdb=" N LYS D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 133 through 137' Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'D' and resid 191 through 204 removed outlier: 3.529A pdb=" N LYS D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 228 Processing helix chain 'D' and resid 243 through 263 removed outlier: 3.718A pdb=" N GLU D 263 " --> pdb=" O ARG D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 299 through 309 removed outlier: 3.528A pdb=" N PHE D 303 " --> pdb=" O ALA D 300 " (cutoff:3.500A) Proline residue: D 304 - end of helix Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 375 through 378 No H-bonds generated for 'chain 'D' and resid 375 through 378' Processing helix chain 'D' and resid 381 through 394 Processing helix chain 'D' and resid 399 through 410 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'E' and resid 92 through 98 Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 162 through 171 Processing helix chain 'E' and resid 191 through 204 removed outlier: 3.554A pdb=" N LYS E 203 " --> pdb=" O ASN E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 228 Processing helix chain 'E' and resid 243 through 263 removed outlier: 5.450A pdb=" N GLU E 263 " --> pdb=" O ARG E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 300 through 309 Proline residue: E 304 - end of helix Processing helix chain 'E' and resid 333 through 343 Processing helix chain 'E' and resid 354 through 358 Processing helix chain 'E' and resid 375 through 378 No H-bonds generated for 'chain 'E' and resid 375 through 378' Processing helix chain 'E' and resid 381 through 394 Processing helix chain 'E' and resid 399 through 412 removed outlier: 4.516A pdb=" N ARG E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 419 Processing helix chain 'F' and resid 92 through 98 Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 142 through 144 No H-bonds generated for 'chain 'F' and resid 142 through 144' Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'F' and resid 191 through 204 removed outlier: 3.573A pdb=" N LYS F 203 " --> pdb=" O ASN F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 228 Processing helix chain 'F' and resid 243 through 263 removed outlier: 3.571A pdb=" N GLU F 263 " --> pdb=" O ARG F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 284 Processing helix chain 'F' and resid 299 through 309 removed outlier: 4.047A pdb=" N PHE F 303 " --> pdb=" O ALA F 300 " (cutoff:3.500A) Proline residue: F 304 - end of helix Processing helix chain 'F' and resid 333 through 343 Processing helix chain 'F' and resid 354 through 358 Processing helix chain 'F' and resid 375 through 378 No H-bonds generated for 'chain 'F' and resid 375 through 378' Processing helix chain 'F' and resid 381 through 396 removed outlier: 4.144A pdb=" N ALA F 395 " --> pdb=" O ARG F 391 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASP F 396 " --> pdb=" O LYS F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 412 removed outlier: 3.658A pdb=" N ALA F 411 " --> pdb=" O LEU F 407 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 419 Processing sheet with id= A, first strand: chain 'A' and resid 62 through 65 Processing sheet with id= B, first strand: chain 'A' and resid 74 through 76 Processing sheet with id= C, first strand: chain 'A' and resid 348 through 351 Processing sheet with id= D, first strand: chain 'A' and resid 319 through 324 removed outlier: 6.828A pdb=" N LYS A 209 " --> pdb=" O MET A 268 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LEU A 270 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE A 211 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASP A 272 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU A 213 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU A 233 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU A 214 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE A 235 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP A 216 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N SER A 237 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 109 through 111 removed outlier: 5.479A pdb=" N ARG A 111 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU A 122 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 62 through 64 Processing sheet with id= G, first strand: chain 'B' and resid 74 through 76 Processing sheet with id= H, first strand: chain 'B' and resid 180 through 183 removed outlier: 6.207A pdb=" N MET B 348 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL B 183 " --> pdb=" O MET B 348 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU B 350 " --> pdb=" O VAL B 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 319 through 324 removed outlier: 6.802A pdb=" N LYS B 209 " --> pdb=" O MET B 268 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU B 270 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 211 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASP B 272 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 213 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU B 233 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU B 214 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B 235 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ASP B 216 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N SER B 237 " --> pdb=" O ASP B 216 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 62 through 64 Processing sheet with id= K, first strand: chain 'C' and resid 74 through 76 Processing sheet with id= L, first strand: chain 'C' and resid 348 through 351 Processing sheet with id= M, first strand: chain 'C' and resid 319 through 324 removed outlier: 6.748A pdb=" N LYS C 209 " --> pdb=" O MET C 268 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU C 270 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE C 211 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASP C 272 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 213 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU C 233 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU C 214 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE C 235 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ASP C 216 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N SER C 237 " --> pdb=" O ASP C 216 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 109 through 111 removed outlier: 3.580A pdb=" N LYS C 124 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ARG C 111 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LEU C 122 " --> pdb=" O ARG C 111 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 62 through 65 Processing sheet with id= P, first strand: chain 'D' and resid 66 through 68 Processing sheet with id= Q, first strand: chain 'D' and resid 348 through 351 Processing sheet with id= R, first strand: chain 'D' and resid 319 through 324 removed outlier: 6.811A pdb=" N LYS D 209 " --> pdb=" O MET D 268 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU D 270 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE D 211 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ASP D 272 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU D 213 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU D 233 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU D 214 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE D 235 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ASP D 216 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N SER D 237 " --> pdb=" O ASP D 216 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 62 through 64 Processing sheet with id= T, first strand: chain 'E' and resid 74 through 76 removed outlier: 3.526A pdb=" N ALA E 88 " --> pdb=" O LEU E 76 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 180 through 183 removed outlier: 6.230A pdb=" N MET E 348 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL E 183 " --> pdb=" O MET E 348 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU E 350 " --> pdb=" O VAL E 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 319 through 324 removed outlier: 6.662A pdb=" N LYS E 209 " --> pdb=" O MET E 268 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LEU E 270 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE E 211 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ASP E 272 " --> pdb=" O ILE E 211 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU E 213 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU E 233 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU E 214 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE E 235 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP E 216 " --> pdb=" O ILE E 235 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N SER E 237 " --> pdb=" O ASP E 216 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 63 through 65 Processing sheet with id= X, first strand: chain 'F' and resid 66 through 68 Processing sheet with id= Y, first strand: chain 'F' and resid 348 through 352 Processing sheet with id= Z, first strand: chain 'F' and resid 319 through 324 removed outlier: 6.767A pdb=" N LYS F 209 " --> pdb=" O MET F 268 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU F 270 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE F 211 " --> pdb=" O LEU F 270 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASP F 272 " --> pdb=" O ILE F 211 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU F 213 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU F 233 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU F 214 " --> pdb=" O GLU F 233 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE F 235 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N ASP F 216 " --> pdb=" O ILE F 235 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N SER F 237 " --> pdb=" O ASP F 216 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.17 Time building geometry restraints manager: 7.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5908 1.34 - 1.46: 3223 1.46 - 1.58: 8275 1.58 - 1.69: 18 1.69 - 1.81: 84 Bond restraints: 17508 Sorted by residual: bond pdb=" BE BEF C1002 " pdb=" F2 BEF C1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" BE BEF A1002 " pdb=" F2 BEF A1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" BE BEF B1002 " pdb=" F2 BEF B1002 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" BE BEF D1002 " pdb=" F2 BEF D1002 " ideal model delta sigma weight residual 1.476 1.558 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" BE BEF E1002 " pdb=" F2 BEF E1002 " ideal model delta sigma weight residual 1.476 1.557 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 17503 not shown) Histogram of bond angle deviations from ideal: 98.88 - 106.42: 585 106.42 - 113.96: 10152 113.96 - 121.49: 8723 121.49 - 129.03: 4153 129.03 - 136.57: 75 Bond angle restraints: 23688 Sorted by residual: angle pdb=" C ALA B 136 " pdb=" N LYS B 137 " pdb=" CA LYS B 137 " ideal model delta sigma weight residual 120.28 131.12 -10.84 1.44e+00 4.82e-01 5.66e+01 angle pdb=" OG1 THR A 288 " pdb=" CB THR A 288 " pdb=" CG2 THR A 288 " ideal model delta sigma weight residual 109.30 120.07 -10.77 2.00e+00 2.50e-01 2.90e+01 angle pdb=" CA THR A 288 " pdb=" CB THR A 288 " pdb=" CG2 THR A 288 " ideal model delta sigma weight residual 110.50 119.02 -8.52 1.70e+00 3.46e-01 2.51e+01 angle pdb=" F2 BEF C1002 " pdb=" BE BEF C1002 " pdb=" F3 BEF C1002 " ideal model delta sigma weight residual 119.96 105.35 14.61 3.00e+00 1.11e-01 2.37e+01 angle pdb=" F2 BEF F1002 " pdb=" BE BEF F1002 " pdb=" F3 BEF F1002 " ideal model delta sigma weight residual 119.96 107.18 12.78 3.00e+00 1.11e-01 1.81e+01 ... (remaining 23683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 10598 35.40 - 70.80: 210 70.80 - 106.20: 12 106.20 - 141.60: 6 141.60 - 177.00: 4 Dihedral angle restraints: 10830 sinusoidal: 4602 harmonic: 6228 Sorted by residual: dihedral pdb=" O1B ADP C1000 " pdb=" O3A ADP C1000 " pdb=" PB ADP C1000 " pdb=" PA ADP C1000 " ideal model delta sinusoidal sigma weight residual -60.00 117.00 -177.00 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP D1000 " pdb=" O3A ADP D1000 " pdb=" PB ADP D1000 " pdb=" PA ADP D1000 " ideal model delta sinusoidal sigma weight residual 300.00 130.52 169.48 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O1B ADP E1000 " pdb=" O3A ADP E1000 " pdb=" PB ADP E1000 " pdb=" PA ADP E1000 " ideal model delta sinusoidal sigma weight residual -60.00 85.53 -145.53 1 2.00e+01 2.50e-03 4.38e+01 ... (remaining 10827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 2716 0.270 - 0.539: 1 0.539 - 0.809: 0 0.809 - 1.079: 0 1.079 - 1.348: 1 Chirality restraints: 2718 Sorted by residual: chirality pdb=" CB THR A 288 " pdb=" CA THR A 288 " pdb=" OG1 THR A 288 " pdb=" CG2 THR A 288 " both_signs ideal model delta sigma weight residual False 2.55 1.20 1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" CA SER C 164 " pdb=" N SER C 164 " pdb=" C SER C 164 " pdb=" CB SER C 164 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA VAL E 106 " pdb=" N VAL E 106 " pdb=" C VAL E 106 " pdb=" CB VAL E 106 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 2715 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 286 " -0.089 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO E 287 " 0.235 5.00e-02 4.00e+02 pdb=" CA PRO E 287 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO E 287 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 286 " -0.086 5.00e-02 4.00e+02 1.31e-01 2.75e+01 pdb=" N PRO A 287 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 286 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO B 287 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " -0.063 5.00e-02 4.00e+02 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 224 2.41 - 3.03: 11922 3.03 - 3.66: 26549 3.66 - 4.28: 39964 4.28 - 4.90: 62921 Nonbonded interactions: 141580 Sorted by model distance: nonbonded pdb=" OE1 GLU C 217 " pdb="MG MG C1001 " model vdw 1.788 2.170 nonbonded pdb=" O1A ADP D1000 " pdb="MG MG D1001 " model vdw 1.792 2.170 nonbonded pdb=" O5' ADP C1000 " pdb="MG MG C1001 " model vdw 1.798 2.170 nonbonded pdb=" O5' ADP E1000 " pdb="MG MG E1001 " model vdw 1.820 2.170 nonbonded pdb=" O1A ADP A1000 " pdb="MG MG A1001 " model vdw 1.850 2.170 ... (remaining 141575 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.620 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 46.780 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.170 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 17508 Z= 0.299 Angle : 0.801 14.612 23688 Z= 0.428 Chirality : 0.049 1.348 2718 Planarity : 0.007 0.136 3084 Dihedral : 14.726 176.999 6798 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.71 % Favored : 95.96 % Rotamer: Outliers : 4.93 % Allowed : 8.99 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 2154 helix: -0.24 (0.17), residues: 870 sheet: -0.48 (0.29), residues: 342 loop : -0.67 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 388 HIS 0.004 0.001 HIS A 351 PHE 0.010 0.001 PHE F 307 TYR 0.009 0.001 TYR A 105 ARG 0.007 0.000 ARG E 259 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 454 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.8740 (tp) cc_final: 0.8495 (tt) REVERT: A 252 PHE cc_start: 0.8342 (m-10) cc_final: 0.8130 (m-10) REVERT: A 259 ARG cc_start: 0.8781 (tpp-160) cc_final: 0.8504 (mmp80) REVERT: A 397 MET cc_start: 0.7142 (mtt) cc_final: 0.6767 (tpp) REVERT: A 403 MET cc_start: 0.7843 (tmm) cc_final: 0.7401 (mmm) REVERT: B 163 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7017 (pp) REVERT: B 348 MET cc_start: 0.7628 (tmm) cc_final: 0.7273 (ppp) REVERT: B 357 GLU cc_start: 0.5927 (tm-30) cc_final: 0.5245 (mt-10) REVERT: B 374 ARG cc_start: 0.8045 (mmt180) cc_final: 0.7844 (mmp80) REVERT: B 416 ASN cc_start: 0.9505 (t0) cc_final: 0.9293 (t0) REVERT: C 60 ARG cc_start: 0.2302 (OUTLIER) cc_final: 0.1939 (tmm160) REVERT: C 105 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.5443 (p90) REVERT: C 221 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7998 (mt-10) REVERT: C 349 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.5828 (pp20) REVERT: C 351 HIS cc_start: 0.6618 (m-70) cc_final: 0.6110 (t-90) REVERT: C 396 ASP cc_start: 0.7804 (m-30) cc_final: 0.7550 (p0) REVERT: D 194 LEU cc_start: 0.8698 (tp) cc_final: 0.8442 (tt) REVERT: D 221 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8038 (mt-10) REVERT: D 235 ILE cc_start: 0.7698 (mm) cc_final: 0.7252 (tp) REVERT: D 297 ASP cc_start: 0.5083 (OUTLIER) cc_final: 0.4715 (m-30) REVERT: D 349 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.5968 (pp20) REVERT: D 351 HIS cc_start: 0.6355 (m-70) cc_final: 0.6018 (t-90) REVERT: D 403 MET cc_start: 0.7914 (mmm) cc_final: 0.7685 (mtm) REVERT: E 65 TYR cc_start: 0.4501 (OUTLIER) cc_final: 0.3847 (m-80) REVERT: E 349 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.4979 (pp20) REVERT: E 351 HIS cc_start: 0.6532 (m-70) cc_final: 0.5980 (t-90) REVERT: E 410 LEU cc_start: 0.7547 (mt) cc_final: 0.7293 (pp) REVERT: F 125 VAL cc_start: 0.0616 (OUTLIER) cc_final: -0.1453 (t) REVERT: F 221 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8207 (mt-10) REVERT: F 259 ARG cc_start: 0.8660 (tpp-160) cc_final: 0.8359 (mmm-85) REVERT: F 296 LEU cc_start: 0.8440 (mt) cc_final: 0.8221 (mp) REVERT: F 297 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.6658 (m-30) REVERT: F 349 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.4356 (tt0) REVERT: F 351 HIS cc_start: 0.6547 (m-70) cc_final: 0.5964 (t-90) outliers start: 90 outliers final: 16 residues processed: 528 average time/residue: 0.4434 time to fit residues: 311.5297 Evaluate side-chains 267 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 240 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 388 TRP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 349 GLU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 297 ASP Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 396 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 196 optimal weight: 0.8980 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 148 GLN A 246 HIS B 70 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN C 148 GLN C 246 HIS ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN D 148 GLN D 246 HIS ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 ASN E 70 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN E 230 GLN ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 HIS ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 17508 Z= 0.344 Angle : 0.848 10.012 23688 Z= 0.415 Chirality : 0.047 0.196 2718 Planarity : 0.007 0.136 3084 Dihedral : 11.891 169.982 2525 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 25.55 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.06 % Favored : 96.56 % Rotamer: Outliers : 4.50 % Allowed : 16.67 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.18), residues: 2154 helix: -0.18 (0.17), residues: 828 sheet: 0.18 (0.30), residues: 324 loop : -0.42 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 388 HIS 0.010 0.002 HIS D 385 PHE 0.021 0.002 PHE B 307 TYR 0.025 0.002 TYR C 98 ARG 0.011 0.001 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 241 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 ARG cc_start: 0.8808 (tpp-160) cc_final: 0.8582 (tpp80) REVERT: A 290 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7439 (mtt180) REVERT: A 357 GLU cc_start: 0.5780 (tm-30) cc_final: 0.5135 (mm-30) REVERT: A 397 MET cc_start: 0.7976 (mtt) cc_final: 0.7065 (tpp) REVERT: A 405 MET cc_start: 0.5873 (ttp) cc_final: 0.5459 (tmm) REVERT: B 163 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7003 (pp) REVERT: B 225 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.9082 (m-80) REVERT: B 374 ARG cc_start: 0.8093 (mmt180) cc_final: 0.7802 (mmp80) REVERT: C 105 TYR cc_start: 0.5917 (OUTLIER) cc_final: 0.5019 (p90) REVERT: C 221 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7970 (mt-10) REVERT: C 348 MET cc_start: 0.8023 (ppp) cc_final: 0.7304 (ppp) REVERT: C 349 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6006 (pp20) REVERT: C 351 HIS cc_start: 0.6758 (m-70) cc_final: 0.6117 (t-90) REVERT: C 355 ARG cc_start: 0.5598 (ptt180) cc_final: 0.5327 (ptm160) REVERT: D 221 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8161 (mt-10) REVERT: D 235 ILE cc_start: 0.8015 (mm) cc_final: 0.7359 (tp) REVERT: D 342 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7499 (m-10) REVERT: D 348 MET cc_start: 0.7933 (ptm) cc_final: 0.7541 (ptm) REVERT: D 349 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7007 (pp20) REVERT: E 349 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.5322 (pp20) REVERT: E 351 HIS cc_start: 0.6768 (m-70) cc_final: 0.5945 (t-90) REVERT: E 403 MET cc_start: 0.8266 (tmm) cc_final: 0.7932 (ppp) REVERT: E 410 LEU cc_start: 0.7633 (mt) cc_final: 0.7392 (pp) REVERT: F 221 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8149 (mt-10) REVERT: F 351 HIS cc_start: 0.6547 (m-70) cc_final: 0.5828 (t-90) REVERT: F 359 ARG cc_start: 0.8577 (mtp85) cc_final: 0.8287 (mtp-110) REVERT: F 403 MET cc_start: 0.8561 (ptt) cc_final: 0.8208 (ptp) outliers start: 82 outliers final: 47 residues processed: 307 average time/residue: 0.3925 time to fit residues: 167.3801 Evaluate side-chains 244 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 189 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 349 GLU Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 385 HIS Chi-restraints excluded: chain F residue 396 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 ASN ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 17508 Z= 0.301 Angle : 0.783 8.939 23688 Z= 0.383 Chirality : 0.045 0.230 2718 Planarity : 0.007 0.130 3084 Dihedral : 11.039 156.530 2496 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 27.82 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.20 % Favored : 96.43 % Rotamer: Outliers : 5.92 % Allowed : 17.49 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2154 helix: -0.18 (0.17), residues: 834 sheet: 0.13 (0.32), residues: 294 loop : -0.48 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 388 HIS 0.008 0.002 HIS D 385 PHE 0.014 0.002 PHE B 307 TYR 0.025 0.002 TYR F 98 ARG 0.014 0.001 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 197 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ARG cc_start: 0.8456 (ttt180) cc_final: 0.8052 (ttt180) REVERT: A 397 MET cc_start: 0.8019 (mtt) cc_final: 0.7300 (tpp) REVERT: A 405 MET cc_start: 0.5918 (ttp) cc_final: 0.5538 (tmm) REVERT: B 225 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.9039 (m-80) REVERT: B 374 ARG cc_start: 0.8027 (mmt180) cc_final: 0.7736 (mmp80) REVERT: C 105 TYR cc_start: 0.5889 (OUTLIER) cc_final: 0.4977 (p90) REVERT: C 221 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7996 (mt-10) REVERT: C 351 HIS cc_start: 0.6637 (m-70) cc_final: 0.5942 (t-90) REVERT: C 355 ARG cc_start: 0.5729 (ptt180) cc_final: 0.5418 (ptm160) REVERT: D 221 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8176 (mt-10) REVERT: D 235 ILE cc_start: 0.7921 (mm) cc_final: 0.7232 (tp) REVERT: D 348 MET cc_start: 0.7982 (ptm) cc_final: 0.7504 (ptm) REVERT: E 349 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.5369 (pp20) REVERT: E 351 HIS cc_start: 0.6787 (m-70) cc_final: 0.5945 (t-90) REVERT: E 359 ARG cc_start: 0.8677 (mtp85) cc_final: 0.8472 (mtp180) REVERT: E 403 MET cc_start: 0.8229 (tmm) cc_final: 0.7962 (ppp) REVERT: E 410 LEU cc_start: 0.7823 (mt) cc_final: 0.7545 (pp) REVERT: F 221 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8177 (mt-10) REVERT: F 305 LYS cc_start: 0.9470 (mttm) cc_final: 0.9136 (mptt) REVERT: F 351 HIS cc_start: 0.6661 (m-70) cc_final: 0.5654 (t70) REVERT: F 405 MET cc_start: 0.6381 (ptm) cc_final: 0.5538 (ppp) outliers start: 108 outliers final: 66 residues processed: 283 average time/residue: 0.3677 time to fit residues: 147.0476 Evaluate side-chains 248 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 179 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 349 GLU Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 385 HIS Chi-restraints excluded: chain F residue 396 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 197 optimal weight: 0.0670 chunk 208 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 186 optimal weight: 30.0000 chunk 56 optimal weight: 0.9980 overall best weight: 2.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 17508 Z= 0.273 Angle : 0.750 8.743 23688 Z= 0.365 Chirality : 0.044 0.176 2718 Planarity : 0.007 0.125 3084 Dihedral : 10.477 149.665 2486 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.34 % Favored : 96.29 % Rotamer: Outliers : 6.03 % Allowed : 17.76 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2154 helix: -0.10 (0.17), residues: 828 sheet: -0.03 (0.31), residues: 294 loop : -0.39 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 388 HIS 0.008 0.002 HIS D 246 PHE 0.014 0.002 PHE B 307 TYR 0.021 0.002 TYR A 98 ARG 0.009 0.001 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 185 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.9503 (mtpt) cc_final: 0.9224 (ptpp) REVERT: A 359 ARG cc_start: 0.8589 (ttt180) cc_final: 0.8290 (ttt180) REVERT: A 397 MET cc_start: 0.7899 (mtt) cc_final: 0.7334 (tpp) REVERT: A 405 MET cc_start: 0.5978 (ttp) cc_final: 0.5592 (tmm) REVERT: B 225 PHE cc_start: 0.9321 (OUTLIER) cc_final: 0.9035 (m-80) REVERT: B 359 ARG cc_start: 0.8436 (ttm170) cc_final: 0.7639 (ttp80) REVERT: C 105 TYR cc_start: 0.6212 (OUTLIER) cc_final: 0.5275 (p90) REVERT: C 221 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7982 (mt-10) REVERT: C 335 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.5576 (p0) REVERT: C 351 HIS cc_start: 0.6584 (m-70) cc_final: 0.5902 (t-90) REVERT: C 355 ARG cc_start: 0.5605 (ptt180) cc_final: 0.5149 (ptm160) REVERT: D 221 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8090 (mt-10) REVERT: D 305 LYS cc_start: 0.9502 (mtpt) cc_final: 0.9225 (ptpp) REVERT: D 348 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7579 (ptm) REVERT: D 405 MET cc_start: 0.5941 (ttp) cc_final: 0.5674 (tmm) REVERT: E 122 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7175 (mt) REVERT: F 221 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8226 (mt-10) REVERT: F 348 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7393 (ptm) REVERT: F 351 HIS cc_start: 0.6662 (m-70) cc_final: 0.5875 (t70) REVERT: F 359 ARG cc_start: 0.8576 (mtp-110) cc_final: 0.8252 (mtm180) REVERT: F 405 MET cc_start: 0.6501 (ptm) cc_final: 0.5427 (ppp) outliers start: 110 outliers final: 69 residues processed: 274 average time/residue: 0.3573 time to fit residues: 139.9815 Evaluate side-chains 232 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 157 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 391 ARG Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 385 HIS Chi-restraints excluded: chain F residue 396 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.1980 chunk 118 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17508 Z= 0.202 Angle : 0.704 8.020 23688 Z= 0.342 Chirality : 0.044 0.170 2718 Planarity : 0.006 0.121 3084 Dihedral : 9.823 141.748 2478 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.20 % Favored : 96.43 % Rotamer: Outliers : 4.66 % Allowed : 20.45 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2154 helix: 0.04 (0.17), residues: 840 sheet: 0.15 (0.31), residues: 306 loop : -0.31 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 388 HIS 0.004 0.001 HIS D 81 PHE 0.014 0.001 PHE D 252 TYR 0.023 0.002 TYR C 98 ARG 0.007 0.000 ARG F 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 190 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.9506 (mtpt) cc_final: 0.9211 (ptpp) REVERT: A 359 ARG cc_start: 0.8535 (ttt180) cc_final: 0.8326 (ttt180) REVERT: A 397 MET cc_start: 0.7897 (mtt) cc_final: 0.7405 (tpp) REVERT: A 405 MET cc_start: 0.5879 (ttp) cc_final: 0.5475 (tmm) REVERT: B 221 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7759 (pt0) REVERT: B 222 VAL cc_start: 0.8688 (t) cc_final: 0.8447 (t) REVERT: B 225 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8922 (m-80) REVERT: B 359 ARG cc_start: 0.8331 (ttm170) cc_final: 0.7568 (ttp80) REVERT: C 105 TYR cc_start: 0.6276 (OUTLIER) cc_final: 0.5682 (p90) REVERT: C 285 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7346 (p) REVERT: C 343 LYS cc_start: 0.8768 (tttt) cc_final: 0.8566 (mmmt) REVERT: C 349 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6154 (tm-30) REVERT: C 351 HIS cc_start: 0.6534 (m-70) cc_final: 0.5964 (t-90) REVERT: C 355 ARG cc_start: 0.5548 (ptt180) cc_final: 0.5342 (ptm160) REVERT: C 357 GLU cc_start: 0.5427 (tm-30) cc_final: 0.5036 (mm-30) REVERT: D 221 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7989 (mt-10) REVERT: D 305 LYS cc_start: 0.9515 (mtpt) cc_final: 0.9217 (ptpp) REVERT: E 122 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7172 (mt) REVERT: E 204 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7941 (t0) REVERT: E 340 GLU cc_start: 0.8981 (tp30) cc_final: 0.8753 (tp30) REVERT: E 375 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: F 221 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8196 (mt-10) REVERT: F 348 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7598 (ptm) REVERT: F 351 HIS cc_start: 0.6368 (m-70) cc_final: 0.5616 (t-90) outliers start: 85 outliers final: 56 residues processed: 255 average time/residue: 0.3369 time to fit residues: 125.5804 Evaluate side-chains 228 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 164 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 385 HIS Chi-restraints excluded: chain F residue 396 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9980 chunk 188 optimal weight: 0.3980 chunk 41 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 173 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 17508 Z= 0.196 Angle : 0.690 8.885 23688 Z= 0.333 Chirality : 0.044 0.182 2718 Planarity : 0.006 0.117 3084 Dihedral : 9.318 131.559 2477 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.97 % Favored : 96.66 % Rotamer: Outliers : 4.50 % Allowed : 20.56 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 2154 helix: 0.16 (0.17), residues: 828 sheet: -0.30 (0.28), residues: 354 loop : -0.11 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 388 HIS 0.004 0.001 HIS E 351 PHE 0.011 0.001 PHE F 252 TYR 0.019 0.001 TYR C 98 ARG 0.010 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 178 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.9504 (mtpt) cc_final: 0.9198 (ptpp) REVERT: A 359 ARG cc_start: 0.8489 (ttt180) cc_final: 0.8275 (ttt180) REVERT: A 397 MET cc_start: 0.7787 (mtt) cc_final: 0.7350 (tpp) REVERT: A 405 MET cc_start: 0.5851 (ttp) cc_final: 0.5551 (tmm) REVERT: B 221 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7900 (pt0) REVERT: B 222 VAL cc_start: 0.8642 (t) cc_final: 0.8416 (t) REVERT: B 225 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8800 (m-80) REVERT: B 359 ARG cc_start: 0.8253 (ttm170) cc_final: 0.7668 (ttp-170) REVERT: B 397 MET cc_start: 0.6231 (mtm) cc_final: 0.6005 (ptp) REVERT: B 401 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6609 (pp20) REVERT: C 105 TYR cc_start: 0.6159 (OUTLIER) cc_final: 0.5274 (p90) REVERT: C 335 ASP cc_start: 0.6842 (OUTLIER) cc_final: 0.5444 (p0) REVERT: C 355 ARG cc_start: 0.5489 (ptt180) cc_final: 0.5284 (ptm160) REVERT: C 357 GLU cc_start: 0.5398 (tm-30) cc_final: 0.4972 (mm-30) REVERT: C 397 MET cc_start: 0.5986 (mtt) cc_final: 0.5697 (mtm) REVERT: C 405 MET cc_start: 0.5257 (ppp) cc_final: 0.5020 (tmm) REVERT: D 221 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7901 (mt-10) REVERT: D 305 LYS cc_start: 0.9520 (mtpt) cc_final: 0.9248 (ptpp) REVERT: E 375 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: E 405 MET cc_start: 0.3660 (tmm) cc_final: 0.3439 (tmm) REVERT: F 221 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8221 (mt-10) REVERT: F 247 ILE cc_start: 0.9213 (pt) cc_final: 0.8960 (tp) REVERT: F 348 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7567 (ptm) REVERT: F 351 HIS cc_start: 0.6114 (m-70) cc_final: 0.5614 (t-90) REVERT: F 403 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7937 (ppp) outliers start: 82 outliers final: 58 residues processed: 236 average time/residue: 0.3207 time to fit residues: 110.9990 Evaluate side-chains 226 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 161 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 385 HIS Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 403 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 119 optimal weight: 0.0370 chunk 152 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 175 optimal weight: 0.0770 chunk 116 optimal weight: 0.1980 chunk 208 optimal weight: 0.0870 chunk 130 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 96 optimal weight: 0.0470 overall best weight: 0.0892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS E 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.6450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17508 Z= 0.186 Angle : 0.701 15.924 23688 Z= 0.334 Chirality : 0.044 0.178 2718 Planarity : 0.006 0.112 3084 Dihedral : 8.836 128.693 2477 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.06 % Favored : 96.56 % Rotamer: Outliers : 3.67 % Allowed : 21.11 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2154 helix: 0.18 (0.17), residues: 828 sheet: -0.10 (0.31), residues: 306 loop : -0.22 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 388 HIS 0.003 0.001 HIS E 351 PHE 0.014 0.001 PHE B 252 TYR 0.014 0.001 TYR C 98 ARG 0.006 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 190 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.9515 (mtpt) cc_final: 0.9211 (ptpp) REVERT: A 359 ARG cc_start: 0.8524 (ttt180) cc_final: 0.8309 (ttt180) REVERT: A 397 MET cc_start: 0.7711 (mtt) cc_final: 0.7498 (tpp) REVERT: A 405 MET cc_start: 0.5843 (ttp) cc_final: 0.5578 (tmm) REVERT: B 221 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7866 (pt0) REVERT: B 222 VAL cc_start: 0.8582 (t) cc_final: 0.8362 (t) REVERT: B 359 ARG cc_start: 0.8221 (ttm170) cc_final: 0.7654 (ttp-170) REVERT: B 397 MET cc_start: 0.6359 (mtm) cc_final: 0.6019 (ptp) REVERT: B 401 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6468 (pp20) REVERT: C 105 TYR cc_start: 0.6280 (OUTLIER) cc_final: 0.5373 (p90) REVERT: C 305 LYS cc_start: 0.9514 (mtpt) cc_final: 0.9303 (mtmm) REVERT: C 348 MET cc_start: 0.7920 (ppp) cc_final: 0.7063 (ppp) REVERT: C 349 GLU cc_start: 0.5906 (OUTLIER) cc_final: 0.5498 (tm-30) REVERT: C 355 ARG cc_start: 0.5550 (ptt180) cc_final: 0.5328 (ptm160) REVERT: C 357 GLU cc_start: 0.5363 (tm-30) cc_final: 0.5052 (mm-30) REVERT: D 221 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7949 (mt-10) REVERT: D 305 LYS cc_start: 0.9518 (mtpt) cc_final: 0.9248 (ptpp) REVERT: D 359 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7320 (ttt180) REVERT: E 355 ARG cc_start: 0.5278 (ptm160) cc_final: 0.5073 (ptm160) REVERT: F 247 ILE cc_start: 0.9188 (pt) cc_final: 0.8931 (tp) REVERT: F 348 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7492 (ptm) REVERT: F 405 MET cc_start: 0.5621 (ptt) cc_final: 0.4255 (ppp) outliers start: 67 outliers final: 50 residues processed: 238 average time/residue: 0.3364 time to fit residues: 117.4330 Evaluate side-chains 214 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 160 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 385 HIS Chi-restraints excluded: chain F residue 396 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 132 optimal weight: 0.0570 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 189 optimal weight: 0.9980 overall best weight: 1.2500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 ASN ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.6667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17508 Z= 0.215 Angle : 0.698 13.061 23688 Z= 0.334 Chirality : 0.043 0.198 2718 Planarity : 0.006 0.107 3084 Dihedral : 8.716 125.191 2477 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.20 % Favored : 96.43 % Rotamer: Outliers : 3.51 % Allowed : 22.26 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.18), residues: 2154 helix: 0.21 (0.17), residues: 834 sheet: -0.25 (0.29), residues: 342 loop : -0.08 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 388 HIS 0.016 0.001 HIS B 351 PHE 0.012 0.001 PHE F 252 TYR 0.031 0.001 TYR C 98 ARG 0.009 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 162 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.9534 (mtpt) cc_final: 0.9219 (ptpp) REVERT: A 359 ARG cc_start: 0.8531 (ttt180) cc_final: 0.8202 (ttt180) REVERT: A 397 MET cc_start: 0.7732 (mtt) cc_final: 0.7373 (tpp) REVERT: A 405 MET cc_start: 0.5738 (ttp) cc_final: 0.5487 (tmm) REVERT: B 359 ARG cc_start: 0.8291 (ttm170) cc_final: 0.7599 (ttp-170) REVERT: C 105 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.5330 (p90) REVERT: C 305 LYS cc_start: 0.9535 (mtpt) cc_final: 0.9285 (mtmm) REVERT: C 355 ARG cc_start: 0.5565 (ptt180) cc_final: 0.5341 (ptm160) REVERT: C 357 GLU cc_start: 0.5610 (tm-30) cc_final: 0.4958 (mm-30) REVERT: D 221 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7951 (mt-10) REVERT: D 359 ARG cc_start: 0.8032 (ttm170) cc_final: 0.7066 (ttp-170) REVERT: F 348 MET cc_start: 0.7885 (ptm) cc_final: 0.7683 (ptm) outliers start: 64 outliers final: 57 residues processed: 207 average time/residue: 0.3323 time to fit residues: 101.2029 Evaluate side-chains 209 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 151 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 385 HIS Chi-restraints excluded: chain F residue 396 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 2.9990 chunk 181 optimal weight: 0.5980 chunk 194 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 84 optimal weight: 0.0870 chunk 152 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 183 optimal weight: 30.0000 chunk 193 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 17508 Z= 0.231 Angle : 0.713 12.330 23688 Z= 0.342 Chirality : 0.043 0.223 2718 Planarity : 0.006 0.102 3084 Dihedral : 8.590 121.916 2477 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 24.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.44 % Favored : 96.24 % Rotamer: Outliers : 3.95 % Allowed : 21.88 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2154 helix: 0.08 (0.17), residues: 876 sheet: -0.33 (0.29), residues: 342 loop : -0.27 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 388 HIS 0.012 0.001 HIS B 351 PHE 0.014 0.002 PHE D 252 TYR 0.025 0.001 TYR C 98 ARG 0.005 0.001 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 153 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ARG cc_start: 0.8528 (ttt180) cc_final: 0.8197 (ttt180) REVERT: A 397 MET cc_start: 0.7797 (mtt) cc_final: 0.7357 (tpp) REVERT: A 405 MET cc_start: 0.5642 (ttp) cc_final: 0.5408 (tmm) REVERT: B 359 ARG cc_start: 0.8395 (ttm170) cc_final: 0.7450 (ttp80) REVERT: B 401 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6606 (pp20) REVERT: C 105 TYR cc_start: 0.6213 (OUTLIER) cc_final: 0.5189 (p90) REVERT: C 305 LYS cc_start: 0.9537 (mtpt) cc_final: 0.9282 (mtmm) REVERT: C 335 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6788 (m-30) REVERT: C 355 ARG cc_start: 0.5497 (ptt180) cc_final: 0.5259 (ptm160) REVERT: D 111 ARG cc_start: 0.8092 (ttp-110) cc_final: 0.7860 (ttp80) REVERT: D 221 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8138 (mt-10) REVERT: D 359 ARG cc_start: 0.8051 (ttm170) cc_final: 0.7049 (ttp-170) REVERT: D 403 MET cc_start: 0.7760 (tpp) cc_final: 0.7274 (mtt) REVERT: E 375 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8213 (mp0) outliers start: 72 outliers final: 56 residues processed: 209 average time/residue: 0.3212 time to fit residues: 99.6345 Evaluate side-chains 212 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 152 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 385 HIS Chi-restraints excluded: chain F residue 396 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.0970 chunk 125 optimal weight: 5.9990 chunk 97 optimal weight: 0.0270 chunk 142 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 198 optimal weight: 0.1980 chunk 171 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 132 optimal weight: 0.6980 chunk 105 optimal weight: 0.0870 chunk 136 optimal weight: 2.9990 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 HIS ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.7182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 17508 Z= 0.181 Angle : 0.702 12.192 23688 Z= 0.331 Chirality : 0.044 0.237 2718 Planarity : 0.006 0.099 3084 Dihedral : 8.096 123.309 2476 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.11 % Favored : 96.56 % Rotamer: Outliers : 2.85 % Allowed : 22.86 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2154 helix: 0.13 (0.17), residues: 876 sheet: -0.04 (0.30), residues: 306 loop : -0.37 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 388 HIS 0.007 0.001 HIS D 81 PHE 0.011 0.001 PHE C 225 TYR 0.023 0.001 TYR C 98 ARG 0.007 0.000 ARG D 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 168 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.9499 (mtpt) cc_final: 0.9206 (ptpp) REVERT: A 343 LYS cc_start: 0.8878 (mtpp) cc_final: 0.8598 (mtpt) REVERT: A 359 ARG cc_start: 0.8486 (ttt180) cc_final: 0.8040 (ttt180) REVERT: A 405 MET cc_start: 0.5669 (ttp) cc_final: 0.5443 (tmm) REVERT: B 276 ARG cc_start: 0.8712 (mtp85) cc_final: 0.8447 (ptp-110) REVERT: B 359 ARG cc_start: 0.8143 (ttm170) cc_final: 0.7586 (ttp-170) REVERT: C 105 TYR cc_start: 0.6291 (OUTLIER) cc_final: 0.5269 (p90) REVERT: C 335 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.5828 (p0) REVERT: C 355 ARG cc_start: 0.5704 (ptt180) cc_final: 0.5444 (ptm160) REVERT: D 221 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8021 (mt-10) REVERT: D 359 ARG cc_start: 0.7915 (ttm170) cc_final: 0.6935 (ttp-170) REVERT: D 403 MET cc_start: 0.7617 (tpp) cc_final: 0.7179 (mtt) REVERT: F 247 ILE cc_start: 0.9158 (pt) cc_final: 0.8887 (tp) REVERT: F 405 MET cc_start: 0.5944 (ptt) cc_final: 0.4310 (ppp) outliers start: 52 outliers final: 49 residues processed: 207 average time/residue: 0.3200 time to fit residues: 98.6204 Evaluate side-chains 208 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 157 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 385 HIS Chi-restraints excluded: chain F residue 396 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 158 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.118001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.093053 restraints weight = 71271.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.095178 restraints weight = 48815.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.096652 restraints weight = 38083.672| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.7316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 17508 Z= 0.235 Angle : 0.721 11.823 23688 Z= 0.343 Chirality : 0.044 0.225 2718 Planarity : 0.006 0.095 3084 Dihedral : 8.104 115.847 2476 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.11 % Favored : 96.56 % Rotamer: Outliers : 3.23 % Allowed : 22.86 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.18), residues: 2154 helix: 0.04 (0.17), residues: 882 sheet: -0.46 (0.26), residues: 426 loop : -0.42 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 388 HIS 0.008 0.001 HIS B 351 PHE 0.013 0.001 PHE F 252 TYR 0.019 0.001 TYR C 98 ARG 0.008 0.001 ARG D 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3666.74 seconds wall clock time: 68 minutes 9.91 seconds (4089.91 seconds total)