Starting phenix.real_space_refine on Mon Nov 18 08:30:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hau_34609/11_2024/8hau_34609_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hau_34609/11_2024/8hau_34609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hau_34609/11_2024/8hau_34609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hau_34609/11_2024/8hau_34609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hau_34609/11_2024/8hau_34609_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hau_34609/11_2024/8hau_34609_trim.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.222 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 66 5.16 5 C 10184 2.51 5 N 2805 2.21 5 O 3084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16157 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2681 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 333} Chain breaks: 1 Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2689 Classifications: {'peptide': 350} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 334} Chain breaks: 1 Chain: "C" Number of atoms: 2631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2631 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 327} Chain breaks: 1 Chain: "D" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2649 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 329} Chain breaks: 1 Chain: "E" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2649 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 329} Chain breaks: 1 Chain: "F" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2672 Classifications: {'peptide': 348} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.32, per 1000 atoms: 0.58 Number of scatterers: 16157 At special positions: 0 Unit cell: (120.7, 119.28, 105.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 18 15.00 O 3084 8.00 N 2805 7.00 C 10184 6.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 2.2 seconds 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3704 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 19 sheets defined 17.8% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.535A pdb=" N LEU A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 111 removed outlier: 4.180A pdb=" N PHE A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.778A pdb=" N THR A 305 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 removed outlier: 4.253A pdb=" N LEU A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 440 Processing helix chain 'B' and resid 94 through 104 removed outlier: 4.274A pdb=" N THR B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ILE B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'C' and resid 93 through 104 removed outlier: 3.640A pdb=" N LEU C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 186 through 193 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.822A pdb=" N THR C 305 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 removed outlier: 4.184A pdb=" N LEU C 331 " --> pdb=" O PRO C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.630A pdb=" N LEU D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 111 removed outlier: 4.214A pdb=" N PHE D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'D' and resid 158 through 160 No H-bonds generated for 'chain 'D' and resid 158 through 160' Processing helix chain 'D' and resid 186 through 193 Processing helix chain 'D' and resid 272 through 277 Processing helix chain 'D' and resid 327 through 332 removed outlier: 4.164A pdb=" N LEU D 331 " --> pdb=" O PRO D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 440 Processing helix chain 'E' and resid 93 through 104 removed outlier: 3.509A pdb=" N LEU E 97 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 111 removed outlier: 4.421A pdb=" N PHE E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 145 Processing helix chain 'E' and resid 146 through 150 Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 186 through 193 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.552A pdb=" N THR E 305 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 331 Processing helix chain 'E' and resid 432 through 440 Processing helix chain 'F' and resid 93 through 104 Processing helix chain 'F' and resid 104 through 111 removed outlier: 4.191A pdb=" N PHE F 111 " --> pdb=" O ILE F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 146 through 150 removed outlier: 3.502A pdb=" N CYS F 150 " --> pdb=" O PRO F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 160 No H-bonds generated for 'chain 'F' and resid 158 through 160' Processing helix chain 'F' and resid 186 through 193 Processing helix chain 'F' and resid 232 through 237 Processing helix chain 'F' and resid 272 through 277 Processing helix chain 'F' and resid 302 through 306 removed outlier: 3.909A pdb=" N THR F 305 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 332 removed outlier: 4.189A pdb=" N LEU F 331 " --> pdb=" O PRO F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 440 Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 122 removed outlier: 3.635A pdb=" N GLY A 114 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE A 129 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ARG A 122 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR A 127 " --> pdb=" O ARG A 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 125 through 136 current: chain 'A' and resid 162 through 171 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 162 through 171 current: chain 'A' and resid 227 through 231 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 227 through 231 current: chain 'A' and resid 286 through 296 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 286 through 296 current: chain 'A' and resid 344 through 358 removed outlier: 5.463A pdb=" N THR A 349 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLY A 373 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET A 351 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL A 371 " --> pdb=" O MET A 351 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR A 353 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE A 369 " --> pdb=" O TYR A 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 364 through 373 current: chain 'A' and resid 400 through 407 Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 206 Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 249 removed outlier: 3.572A pdb=" N GLY A 261 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N HIS A 248 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N TYR A 259 " --> pdb=" O HIS A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 122 removed outlier: 5.519A pdb=" N ILE B 129 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ARG B 122 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR B 127 " --> pdb=" O ARG B 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 125 through 136 current: chain 'B' and resid 162 through 171 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 162 through 171 current: chain 'B' and resid 227 through 231 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 227 through 231 current: chain 'B' and resid 286 through 296 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 286 through 296 current: chain 'B' and resid 344 through 358 removed outlier: 5.561A pdb=" N THR B 349 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLY B 373 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET B 351 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N VAL B 371 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TYR B 353 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE B 369 " --> pdb=" O TYR B 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 364 through 373 current: chain 'B' and resid 400 through 408 Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 200 removed outlier: 6.083A pdb=" N ILE B 199 " --> pdb=" O THR B 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 249 removed outlier: 6.577A pdb=" N MET B 246 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 122 removed outlier: 3.764A pdb=" N GLY C 114 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILE C 129 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ARG C 122 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR C 127 " --> pdb=" O ARG C 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 125 through 136 current: chain 'C' and resid 162 through 171 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 162 through 171 current: chain 'C' and resid 227 through 231 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 227 through 231 current: chain 'C' and resid 286 through 296 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 286 through 296 current: chain 'C' and resid 344 through 358 removed outlier: 6.694A pdb=" N LEU C 370 " --> pdb=" O MET C 351 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR C 353 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP C 368 " --> pdb=" O TYR C 353 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU C 355 " --> pdb=" O PHE C 366 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE C 366 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR C 357 " --> pdb=" O CYS C 364 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N CYS C 364 " --> pdb=" O TYR C 357 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 364 through 373 current: chain 'C' and resid 401 through 407 Processing sheet with id=AA9, first strand: chain 'C' and resid 211 through 213 removed outlier: 7.053A pdb=" N GLN C 204 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N MET C 246 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 122 removed outlier: 3.786A pdb=" N GLY D 114 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE D 129 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ARG D 122 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR D 127 " --> pdb=" O ARG D 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 125 through 136 current: chain 'D' and resid 162 through 171 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 162 through 171 current: chain 'D' and resid 227 through 231 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 227 through 231 current: chain 'D' and resid 286 through 296 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 286 through 296 current: chain 'D' and resid 344 through 358 removed outlier: 5.547A pdb=" N THR D 349 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLY D 373 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N MET D 351 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL D 371 " --> pdb=" O MET D 351 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR D 353 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE D 369 " --> pdb=" O TYR D 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 364 through 373 current: chain 'D' and resid 400 through 405 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 400 through 405 current: chain 'D' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'D' and resid 204 through 206 Processing sheet with id=AB3, first strand: chain 'D' and resid 245 through 249 removed outlier: 6.567A pdb=" N MET D 246 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 114 through 122 removed outlier: 6.936A pdb=" N GLY E 114 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU E 133 " --> pdb=" O GLY E 114 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ALA E 116 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA E 131 " --> pdb=" O ALA E 116 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY E 118 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE E 129 " --> pdb=" O GLY E 118 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ARG E 120 " --> pdb=" O THR E 127 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 125 through 136 current: chain 'E' and resid 162 through 171 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 162 through 171 current: chain 'E' and resid 227 through 231 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 227 through 231 current: chain 'E' and resid 287 through 296 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 287 through 296 current: chain 'E' and resid 344 through 358 removed outlier: 3.568A pdb=" N MET E 351 " --> pdb=" O LEU E 370 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU E 370 " --> pdb=" O MET E 351 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR E 353 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASP E 368 " --> pdb=" O TYR E 353 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU E 355 " --> pdb=" O PHE E 366 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE E 366 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR E 357 " --> pdb=" O CYS E 364 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N CYS E 364 " --> pdb=" O TYR E 357 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 364 through 373 current: chain 'E' and resid 401 through 408 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 401 through 408 current: chain 'E' and resid 423 through 424 Processing sheet with id=AB5, first strand: chain 'E' and resid 204 through 206 Processing sheet with id=AB6, first strand: chain 'E' and resid 245 through 249 removed outlier: 6.572A pdb=" N MET E 246 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 114 through 122 removed outlier: 5.624A pdb=" N ILE F 129 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ARG F 122 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR F 127 " --> pdb=" O ARG F 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 125 through 136 current: chain 'F' and resid 162 through 169 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 162 through 169 current: chain 'F' and resid 227 through 231 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 227 through 231 current: chain 'F' and resid 286 through 296 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 286 through 296 current: chain 'F' and resid 344 through 358 removed outlier: 7.105A pdb=" N LEU F 370 " --> pdb=" O MET F 351 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR F 353 " --> pdb=" O ASP F 368 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP F 368 " --> pdb=" O TYR F 353 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU F 355 " --> pdb=" O PHE F 366 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE F 366 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR F 357 " --> pdb=" O CYS F 364 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS F 364 " --> pdb=" O TYR F 357 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 364 through 373 current: chain 'F' and resid 400 through 407 removed outlier: 7.730A pdb=" N SER F 428 " --> pdb=" O TRP F 406 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 204 through 206 Processing sheet with id=AB9, first strand: chain 'F' and resid 245 through 249 removed outlier: 6.541A pdb=" N MET F 246 " --> pdb=" O LEU F 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 415 through 416 removed outlier: 3.501A pdb=" N LEU F 415 " --> pdb=" O GLU F 424 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 642 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: 5.13 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.22: 31 1.22 - 1.37: 5489 1.37 - 1.52: 4964 1.52 - 1.66: 5914 1.66 - 1.81: 90 Bond restraints: 16488 Sorted by residual: bond pdb=" C GLU F 285 " pdb=" O GLU F 285 " ideal model delta sigma weight residual 1.233 1.078 0.156 1.38e-02 5.25e+03 1.27e+02 bond pdb=" C GLU C 285 " pdb=" O GLU C 285 " ideal model delta sigma weight residual 1.231 1.092 0.138 1.24e-02 6.50e+03 1.25e+02 bond pdb=" CA GLU C 285 " pdb=" C GLU C 285 " ideal model delta sigma weight residual 1.531 1.420 0.112 1.12e-02 7.97e+03 9.93e+01 bond pdb=" C GLU E 285 " pdb=" O GLU E 285 " ideal model delta sigma weight residual 1.235 1.135 0.100 1.14e-02 7.69e+03 7.67e+01 bond pdb=" C GLU B 285 " pdb=" O GLU B 285 " ideal model delta sigma weight residual 1.234 1.135 0.098 1.19e-02 7.06e+03 6.84e+01 ... (remaining 16483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 22295 3.56 - 7.12: 94 7.12 - 10.68: 16 10.68 - 14.24: 5 14.24 - 17.80: 1 Bond angle restraints: 22411 Sorted by residual: angle pdb=" C GLU E 285 " pdb=" N THR E 286 " pdb=" CA THR E 286 " ideal model delta sigma weight residual 122.74 140.54 -17.80 1.54e+00 4.22e-01 1.34e+02 angle pdb=" C ASN D 283 " pdb=" N PRO D 284 " pdb=" CA PRO D 284 " ideal model delta sigma weight residual 119.47 132.63 -13.16 1.16e+00 7.43e-01 1.29e+02 angle pdb=" C ASN A 283 " pdb=" N PRO A 284 " pdb=" CA PRO A 284 " ideal model delta sigma weight residual 119.28 130.87 -11.59 1.10e+00 8.26e-01 1.11e+02 angle pdb=" N GLU F 285 " pdb=" CA GLU F 285 " pdb=" C GLU F 285 " ideal model delta sigma weight residual 113.20 100.49 12.71 1.36e+00 5.41e-01 8.73e+01 angle pdb=" C ASN F 283 " pdb=" N PRO F 284 " pdb=" CA PRO F 284 " ideal model delta sigma weight residual 119.84 129.99 -10.15 1.25e+00 6.40e-01 6.60e+01 ... (remaining 22406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8297 17.94 - 35.87: 1128 35.87 - 53.81: 313 53.81 - 71.74: 44 71.74 - 89.68: 19 Dihedral angle restraints: 9801 sinusoidal: 3992 harmonic: 5809 Sorted by residual: dihedral pdb=" C ASN B 283 " pdb=" N ASN B 283 " pdb=" CA ASN B 283 " pdb=" CB ASN B 283 " ideal model delta harmonic sigma weight residual -122.60 -109.66 -12.94 0 2.50e+00 1.60e-01 2.68e+01 dihedral pdb=" N ASN A 283 " pdb=" C ASN A 283 " pdb=" CA ASN A 283 " pdb=" CB ASN A 283 " ideal model delta harmonic sigma weight residual 122.80 110.37 12.43 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" N ASN D 283 " pdb=" C ASN D 283 " pdb=" CA ASN D 283 " pdb=" CB ASN D 283 " ideal model delta harmonic sigma weight residual 122.80 110.58 12.22 0 2.50e+00 1.60e-01 2.39e+01 ... (remaining 9798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2224 0.080 - 0.160: 291 0.160 - 0.239: 6 0.239 - 0.319: 19 0.319 - 0.399: 3 Chirality restraints: 2543 Sorted by residual: chirality pdb=" CA GLU B 285 " pdb=" N GLU B 285 " pdb=" C GLU B 285 " pdb=" CB GLU B 285 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CA PRO D 284 " pdb=" N PRO D 284 " pdb=" C PRO D 284 " pdb=" CB PRO D 284 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA PRO A 284 " pdb=" N PRO A 284 " pdb=" C PRO A 284 " pdb=" CB PRO A 284 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 2540 not shown) Planarity restraints: 2880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR F 282 " 0.050 2.00e-02 2.50e+03 9.90e-02 9.81e+01 pdb=" C THR F 282 " -0.171 2.00e-02 2.50e+03 pdb=" O THR F 282 " 0.064 2.00e-02 2.50e+03 pdb=" N ASN F 283 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 282 " -0.048 2.00e-02 2.50e+03 9.73e-02 9.47e+01 pdb=" C THR C 282 " 0.168 2.00e-02 2.50e+03 pdb=" O THR C 282 " -0.064 2.00e-02 2.50e+03 pdb=" N ASN C 283 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 282 " 0.040 2.00e-02 2.50e+03 7.69e-02 5.91e+01 pdb=" C THR A 282 " -0.133 2.00e-02 2.50e+03 pdb=" O THR A 282 " 0.048 2.00e-02 2.50e+03 pdb=" N ASN A 283 " 0.046 2.00e-02 2.50e+03 ... (remaining 2877 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 95 2.48 - 3.09: 11025 3.09 - 3.69: 23582 3.69 - 4.30: 34224 4.30 - 4.90: 59086 Nonbonded interactions: 128012 Sorted by model distance: nonbonded pdb=" O ASN C 283 " pdb=" OG1 THR C 286 " model vdw 1.876 3.040 nonbonded pdb=" OG1 THR E 409 " pdb=" O TRP E 426 " model vdw 1.972 3.040 nonbonded pdb=" OG1 THR C 409 " pdb=" O TRP C 426 " model vdw 1.980 3.040 nonbonded pdb=" OG1 THR A 409 " pdb=" O TRP A 426 " model vdw 1.983 3.040 nonbonded pdb=" OG1 THR B 409 " pdb=" O TRP B 426 " model vdw 2.014 3.040 ... (remaining 128007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 91 through 171 or resid 184 through 444 or resid 501)) selection = (chain 'B' and (resid 91 through 171 or resid 184 through 444 or resid 501)) selection = (chain 'C' and (resid 91 through 444 or resid 501)) selection = (chain 'D' and (resid 91 through 171 or resid 184 through 444 or resid 501)) selection = (chain 'E' and (resid 91 through 171 or resid 184 through 444 or resid 501)) selection = (chain 'F' and (resid 91 through 171 or resid 184 through 444 or resid 501)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.060 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.156 16488 Z= 0.430 Angle : 0.624 17.795 22411 Z= 0.375 Chirality : 0.050 0.399 2543 Planarity : 0.006 0.106 2880 Dihedral : 17.463 89.681 6097 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 23.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.99 % Favored : 97.96 % Rotamer: Outliers : 0.46 % Allowed : 24.11 % Favored : 75.43 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 6.67 % 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: 0.97 (0.19), residues: 2056 helix: 2.25 (0.42), residues: 208 sheet: -0.02 (0.22), residues: 501 loop : 0.81 (0.18), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 275 HIS 0.002 0.000 HIS D 345 PHE 0.006 0.000 PHE D 229 TYR 0.017 0.000 TYR E 241 ARG 0.002 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 265 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7229 (OUTLIER) cc_final: 0.5736 (t-90) REVERT: B 351 MET cc_start: 0.6233 (ptp) cc_final: 0.6027 (ptp) REVERT: F 285 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6199 (mt-10) outliers start: 8 outliers final: 4 residues processed: 268 average time/residue: 0.2864 time to fit residues: 114.6244 Evaluate side-chains 268 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 262 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain F residue 285 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 160 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 186 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 HIS C 375 ASN D 89 GLN ** D 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16488 Z= 0.347 Angle : 0.710 11.448 22411 Z= 0.372 Chirality : 0.050 0.214 2543 Planarity : 0.005 0.055 2880 Dihedral : 10.256 86.404 2444 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.06 % Rotamer: Outliers : 5.98 % Allowed : 19.74 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.04 (0.18), residues: 2056 helix: 0.43 (0.37), residues: 203 sheet: -0.52 (0.21), residues: 505 loop : 0.31 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 406 HIS 0.010 0.002 HIS E 248 PHE 0.030 0.003 PHE A 170 TYR 0.019 0.002 TYR A 259 ARG 0.008 0.001 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 324 time to evaluate : 1.926 Fit side-chains revert: symmetry clash REVERT: A 335 GLN cc_start: 0.8330 (tt0) cc_final: 0.7828 (tt0) REVERT: A 431 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7565 (t0) REVERT: A 436 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7047 (mp) REVERT: B 103 PHE cc_start: 0.6883 (t80) cc_final: 0.6659 (t80) REVERT: B 123 LYS cc_start: 0.7582 (mmmm) cc_final: 0.7154 (mtmm) REVERT: B 164 ASP cc_start: 0.7865 (m-30) cc_final: 0.7574 (m-30) REVERT: B 169 GLU cc_start: 0.7288 (tt0) cc_final: 0.7083 (tt0) REVERT: B 183 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: B 199 ILE cc_start: 0.7915 (tt) cc_final: 0.7572 (tt) REVERT: B 225 LYS cc_start: 0.7773 (mtmm) cc_final: 0.6900 (tmtt) REVERT: B 283 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7655 (m-40) REVERT: B 284 PRO cc_start: 0.8439 (Cg_exo) cc_final: 0.8120 (Cg_endo) REVERT: B 384 ASP cc_start: 0.8141 (m-30) cc_final: 0.7749 (m-30) REVERT: C 149 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: C 169 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7532 (tt0) REVERT: C 196 ASP cc_start: 0.7131 (t0) cc_final: 0.6623 (p0) REVERT: C 253 ASN cc_start: 0.8443 (p0) cc_final: 0.8188 (p0) REVERT: C 323 ASP cc_start: 0.6609 (m-30) cc_final: 0.6033 (t70) REVERT: C 431 ASP cc_start: 0.8201 (t0) cc_final: 0.7993 (t0) REVERT: D 320 LYS cc_start: 0.7753 (tptp) cc_final: 0.7500 (tptt) REVERT: E 253 ASN cc_start: 0.8324 (p0) cc_final: 0.8109 (p0) REVERT: F 133 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7606 (mt) REVERT: F 191 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7714 (mtpt) REVERT: F 245 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7946 (mtmt) REVERT: F 382 GLU cc_start: 0.7365 (pm20) cc_final: 0.6919 (pm20) REVERT: F 405 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7611 (mt) REVERT: F 438 ARG cc_start: 0.6936 (tpp-160) cc_final: 0.6537 (mmt-90) REVERT: F 443 ILE cc_start: 0.7363 (tt) cc_final: 0.7112 (tt) outliers start: 104 outliers final: 56 residues processed: 390 average time/residue: 0.2915 time to fit residues: 168.4930 Evaluate side-chains 344 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 281 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 409 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 166 optimal weight: 0.0570 chunk 184 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN D 208 HIS D 335 GLN F 183 GLN F 283 ASN ** F 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16488 Z= 0.204 Angle : 0.538 11.478 22411 Z= 0.280 Chirality : 0.045 0.166 2543 Planarity : 0.004 0.050 2880 Dihedral : 9.109 84.824 2429 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 4.09 % Allowed : 22.27 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.06 (0.18), residues: 2056 helix: 0.30 (0.38), residues: 209 sheet: -0.35 (0.21), residues: 500 loop : 0.28 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 406 HIS 0.005 0.001 HIS F 248 PHE 0.024 0.002 PHE C 170 TYR 0.014 0.001 TYR A 259 ARG 0.008 0.000 ARG F 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 324 time to evaluate : 1.845 Fit side-chains revert: symmetry clash REVERT: A 128 ASP cc_start: 0.6986 (p0) cc_final: 0.6703 (p0) REVERT: A 184 MET cc_start: 0.6750 (OUTLIER) cc_final: 0.6394 (mtp) REVERT: A 196 ASP cc_start: 0.7750 (t0) cc_final: 0.7410 (t0) REVERT: B 164 ASP cc_start: 0.7676 (m-30) cc_final: 0.7416 (m-30) REVERT: B 283 ASN cc_start: 0.8133 (m-40) cc_final: 0.7566 (t0) REVERT: B 284 PRO cc_start: 0.8735 (Cg_exo) cc_final: 0.8143 (Cg_endo) REVERT: B 285 GLU cc_start: 0.8139 (pt0) cc_final: 0.7870 (pt0) REVERT: B 414 ARG cc_start: 0.7188 (ttp-170) cc_final: 0.6928 (ttp-170) REVERT: C 225 LYS cc_start: 0.7690 (mttp) cc_final: 0.6696 (tmtt) REVERT: C 253 ASN cc_start: 0.8431 (p0) cc_final: 0.8199 (p0) REVERT: C 323 ASP cc_start: 0.6529 (m-30) cc_final: 0.5973 (t70) REVERT: D 156 GLU cc_start: 0.5510 (tm-30) cc_final: 0.5296 (tp30) REVERT: D 219 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7456 (ptmm) REVERT: D 282 THR cc_start: 0.8790 (m) cc_final: 0.8555 (p) REVERT: D 351 MET cc_start: 0.8035 (ptp) cc_final: 0.7642 (ptp) REVERT: D 442 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6755 (t0) REVERT: E 253 ASN cc_start: 0.8514 (p0) cc_final: 0.8256 (p0) REVERT: E 283 ASN cc_start: 0.7836 (m110) cc_final: 0.7600 (m-40) REVERT: E 338 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7979 (pttp) REVERT: E 438 ARG cc_start: 0.7129 (mmt-90) cc_final: 0.6858 (mmt180) REVERT: F 144 TRP cc_start: 0.7378 (m-90) cc_final: 0.6999 (m-90) REVERT: F 169 GLU cc_start: 0.7438 (tt0) cc_final: 0.7190 (tt0) REVERT: F 191 LYS cc_start: 0.8174 (mmtp) cc_final: 0.7790 (mtpt) REVERT: F 198 CYS cc_start: 0.7315 (p) cc_final: 0.6465 (m) REVERT: F 245 LYS cc_start: 0.8401 (mtmm) cc_final: 0.8103 (mtmt) REVERT: F 246 MET cc_start: 0.8261 (mmm) cc_final: 0.7931 (mmm) REVERT: F 265 ARG cc_start: 0.5856 (tpt170) cc_final: 0.4421 (tpt170) REVERT: F 405 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7596 (mt) REVERT: F 409 THR cc_start: 0.2539 (OUTLIER) cc_final: 0.2319 (m) REVERT: F 443 ILE cc_start: 0.7627 (tt) cc_final: 0.7399 (tt) outliers start: 71 outliers final: 47 residues processed: 370 average time/residue: 0.2854 time to fit residues: 156.7006 Evaluate side-chains 343 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 290 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 244 GLN Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 445 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 198 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 177 optimal weight: 0.0170 chunk 53 optimal weight: 5.9990 overall best weight: 1.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN E 244 GLN F 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16488 Z= 0.205 Angle : 0.542 11.930 22411 Z= 0.282 Chirality : 0.045 0.167 2543 Planarity : 0.004 0.045 2880 Dihedral : 8.792 77.354 2429 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 4.32 % Allowed : 21.92 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.03 (0.18), residues: 2056 helix: 0.32 (0.38), residues: 208 sheet: -0.46 (0.22), residues: 467 loop : 0.19 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 406 HIS 0.004 0.001 HIS F 248 PHE 0.025 0.002 PHE C 170 TYR 0.025 0.002 TYR E 241 ARG 0.006 0.000 ARG E 438 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 302 time to evaluate : 1.814 Fit side-chains REVERT: A 122 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7439 (ttm170) REVERT: A 128 ASP cc_start: 0.7008 (p0) cc_final: 0.6730 (p0) REVERT: A 156 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.5486 (mm-30) REVERT: A 184 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6515 (mtp) REVERT: A 199 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8202 (mt) REVERT: A 282 THR cc_start: 0.8729 (m) cc_final: 0.8310 (p) REVERT: B 104 HIS cc_start: 0.7744 (m90) cc_final: 0.7354 (m-70) REVERT: B 156 GLU cc_start: 0.6904 (tp30) cc_final: 0.6502 (mm-30) REVERT: B 164 ASP cc_start: 0.7716 (m-30) cc_final: 0.7425 (m-30) REVERT: B 209 GLU cc_start: 0.6533 (pm20) cc_final: 0.6175 (pm20) REVERT: B 283 ASN cc_start: 0.8115 (m-40) cc_final: 0.7651 (t0) REVERT: B 284 PRO cc_start: 0.8418 (Cg_exo) cc_final: 0.7774 (Cg_endo) REVERT: B 285 GLU cc_start: 0.7999 (pt0) cc_final: 0.7642 (pt0) REVERT: C 185 PHE cc_start: 0.8462 (m-80) cc_final: 0.8240 (m-80) REVERT: C 225 LYS cc_start: 0.7579 (mttp) cc_final: 0.6408 (tmtt) REVERT: C 246 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7373 (mtp) REVERT: C 253 ASN cc_start: 0.8396 (p0) cc_final: 0.8179 (p0) REVERT: C 323 ASP cc_start: 0.6484 (m-30) cc_final: 0.5988 (t70) REVERT: D 219 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7483 (ptmm) REVERT: D 245 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8422 (mtmt) REVERT: D 282 THR cc_start: 0.8860 (m) cc_final: 0.8635 (p) REVERT: D 351 MET cc_start: 0.8041 (ptp) cc_final: 0.7643 (ptp) REVERT: D 356 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: D 442 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6764 (t0) REVERT: E 253 ASN cc_start: 0.8607 (p0) cc_final: 0.8170 (p0) REVERT: E 341 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7669 (ppt170) REVERT: F 191 LYS cc_start: 0.8096 (mmtp) cc_final: 0.7824 (mtpt) REVERT: F 198 CYS cc_start: 0.7545 (p) cc_final: 0.6578 (m) REVERT: F 245 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7965 (mtmt) REVERT: F 246 MET cc_start: 0.8300 (mmm) cc_final: 0.8059 (mmm) REVERT: F 265 ARG cc_start: 0.6438 (tpt170) cc_final: 0.5976 (tpt170) REVERT: F 405 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7666 (mt) outliers start: 75 outliers final: 46 residues processed: 351 average time/residue: 0.2890 time to fit residues: 150.9316 Evaluate side-chains 351 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 295 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 81 optimal weight: 0.0770 chunk 169 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.0980 chunk 177 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN E 90 GLN E 224 ASN F 283 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16488 Z= 0.143 Angle : 0.479 7.963 22411 Z= 0.251 Chirality : 0.043 0.151 2543 Planarity : 0.003 0.043 2880 Dihedral : 8.270 79.193 2429 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.39 % Allowed : 22.50 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.09 (0.19), residues: 2056 helix: 0.59 (0.40), residues: 203 sheet: -0.42 (0.22), residues: 519 loop : 0.30 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 275 HIS 0.005 0.001 HIS C 248 PHE 0.017 0.001 PHE C 170 TYR 0.011 0.001 TYR E 241 ARG 0.006 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 298 time to evaluate : 1.710 Fit side-chains revert: symmetry clash REVERT: A 103 PHE cc_start: 0.7054 (t80) cc_final: 0.6809 (t80) REVERT: A 128 ASP cc_start: 0.6959 (p0) cc_final: 0.6672 (p0) REVERT: A 156 GLU cc_start: 0.5838 (OUTLIER) cc_final: 0.5458 (mm-30) REVERT: A 184 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.6500 (mtp) REVERT: A 282 THR cc_start: 0.8719 (m) cc_final: 0.8282 (p) REVERT: A 335 GLN cc_start: 0.8216 (tt0) cc_final: 0.7947 (tt0) REVERT: A 431 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7976 (t0) REVERT: B 104 HIS cc_start: 0.7708 (m90) cc_final: 0.7344 (m-70) REVERT: B 156 GLU cc_start: 0.6898 (tp30) cc_final: 0.6391 (mm-30) REVERT: B 209 GLU cc_start: 0.6414 (pm20) cc_final: 0.6052 (pm20) REVERT: B 244 GLN cc_start: 0.7305 (mp10) cc_final: 0.6816 (mp10) REVERT: B 272 ASP cc_start: 0.7659 (p0) cc_final: 0.7436 (p0) REVERT: B 283 ASN cc_start: 0.8061 (m-40) cc_final: 0.7614 (t0) REVERT: B 284 PRO cc_start: 0.8610 (Cg_exo) cc_final: 0.7944 (Cg_endo) REVERT: B 285 GLU cc_start: 0.7954 (pt0) cc_final: 0.7560 (pt0) REVERT: B 376 ARG cc_start: 0.7048 (mtp-110) cc_final: 0.6841 (mtp-110) REVERT: C 149 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: C 196 ASP cc_start: 0.7892 (t0) cc_final: 0.7657 (t0) REVERT: C 197 GLU cc_start: 0.7529 (mp0) cc_final: 0.7205 (mp0) REVERT: C 211 PHE cc_start: 0.8317 (p90) cc_final: 0.8001 (p90) REVERT: C 225 LYS cc_start: 0.7580 (mttp) cc_final: 0.6424 (tmtt) REVERT: C 253 ASN cc_start: 0.8385 (p0) cc_final: 0.8145 (p0) REVERT: C 285 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7372 (mt-10) REVERT: C 323 ASP cc_start: 0.6332 (m-30) cc_final: 0.5869 (t70) REVERT: D 144 TRP cc_start: 0.7646 (m-10) cc_final: 0.7343 (m100) REVERT: D 245 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8394 (mtmt) REVERT: D 282 THR cc_start: 0.8870 (m) cc_final: 0.8571 (p) REVERT: D 351 MET cc_start: 0.7936 (ptp) cc_final: 0.7505 (ptp) REVERT: D 356 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: D 442 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6774 (t0) REVERT: F 191 LYS cc_start: 0.8059 (mmtp) cc_final: 0.7823 (mtpt) REVERT: F 198 CYS cc_start: 0.7545 (p) cc_final: 0.6627 (m) REVERT: F 245 LYS cc_start: 0.8252 (mtmm) cc_final: 0.7932 (mtmt) REVERT: F 246 MET cc_start: 0.8260 (mmm) cc_final: 0.8059 (mmm) REVERT: F 265 ARG cc_start: 0.6408 (tpt170) cc_final: 0.5727 (ttt90) REVERT: F 374 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7633 (mt-10) outliers start: 59 outliers final: 40 residues processed: 339 average time/residue: 0.2918 time to fit residues: 146.8687 Evaluate side-chains 330 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 284 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 244 GLN Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN B 224 ASN D 335 GLN E 234 HIS F 183 GLN F 283 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.6505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16488 Z= 0.339 Angle : 0.621 8.195 22411 Z= 0.324 Chirality : 0.048 0.198 2543 Planarity : 0.005 0.043 2880 Dihedral : 9.572 74.645 2429 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.12 % Allowed : 21.29 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.39 (0.18), residues: 2056 helix: 0.12 (0.38), residues: 203 sheet: -0.73 (0.22), residues: 488 loop : -0.04 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 144 HIS 0.008 0.001 HIS C 248 PHE 0.027 0.002 PHE C 170 TYR 0.018 0.002 TYR B 172 ARG 0.007 0.001 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 294 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7483 (ttm170) REVERT: A 128 ASP cc_start: 0.6987 (p0) cc_final: 0.6718 (p0) REVERT: A 156 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.5981 (mm-30) REVERT: A 169 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7859 (tt0) REVERT: A 184 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6682 (mtp) REVERT: A 282 THR cc_start: 0.8656 (m) cc_final: 0.8345 (p) REVERT: A 431 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.7950 (t0) REVERT: A 436 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7200 (mt) REVERT: B 156 GLU cc_start: 0.7170 (tp30) cc_final: 0.6669 (mm-30) REVERT: B 272 ASP cc_start: 0.7324 (p0) cc_final: 0.7055 (p0) REVERT: B 283 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7664 (m-40) REVERT: B 284 PRO cc_start: 0.8601 (Cg_exo) cc_final: 0.8335 (Cg_endo) REVERT: B 285 GLU cc_start: 0.7987 (pt0) cc_final: 0.7541 (pt0) REVERT: B 438 ARG cc_start: 0.7629 (mmt-90) cc_final: 0.7327 (mmt-90) REVERT: C 149 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: C 196 ASP cc_start: 0.7882 (t0) cc_final: 0.7459 (t0) REVERT: C 253 ASN cc_start: 0.8442 (p0) cc_final: 0.8237 (p0) REVERT: C 323 ASP cc_start: 0.6410 (m-30) cc_final: 0.5995 (t70) REVERT: D 90 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: D 282 THR cc_start: 0.8694 (m) cc_final: 0.8429 (p) REVERT: D 335 GLN cc_start: 0.8224 (tt0) cc_final: 0.7976 (tt0) REVERT: D 351 MET cc_start: 0.8122 (ptp) cc_final: 0.7902 (ptp) REVERT: D 442 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6730 (t0) REVERT: E 198 CYS cc_start: 0.7711 (p) cc_final: 0.7433 (m) REVERT: E 220 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6747 (ttm170) REVERT: F 98 MET cc_start: 0.8473 (mtt) cc_final: 0.8235 (mtt) REVERT: F 191 LYS cc_start: 0.8152 (mmtp) cc_final: 0.7741 (mtpt) REVERT: F 196 ASP cc_start: 0.6861 (t0) cc_final: 0.6613 (p0) REVERT: F 265 ARG cc_start: 0.6442 (tpt170) cc_final: 0.6001 (ttt90) REVERT: F 374 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7871 (mt-10) outliers start: 89 outliers final: 65 residues processed: 349 average time/residue: 0.2877 time to fit residues: 148.9641 Evaluate side-chains 358 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 283 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 244 GLN Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 120 optimal weight: 0.0050 chunk 91 optimal weight: 8.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN D 183 GLN F 283 ASN F 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.6863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16488 Z= 0.300 Angle : 0.595 7.401 22411 Z= 0.310 Chirality : 0.047 0.179 2543 Planarity : 0.005 0.044 2880 Dihedral : 9.405 75.021 2429 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.52 % Allowed : 20.94 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.55 (0.18), residues: 2056 helix: 0.15 (0.39), residues: 203 sheet: -0.89 (0.22), residues: 497 loop : -0.15 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 144 HIS 0.004 0.001 HIS E 208 PHE 0.022 0.002 PHE C 170 TYR 0.021 0.002 TYR B 172 ARG 0.008 0.001 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 286 time to evaluate : 1.824 Fit side-chains REVERT: A 122 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7504 (ttm170) REVERT: A 128 ASP cc_start: 0.6973 (p0) cc_final: 0.6709 (p0) REVERT: A 156 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6419 (mm-30) REVERT: A 169 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7440 (tt0) REVERT: A 184 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6893 (mtt) REVERT: A 282 THR cc_start: 0.8642 (m) cc_final: 0.8386 (p) REVERT: A 431 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8044 (t0) REVERT: A 436 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7186 (mt) REVERT: B 156 GLU cc_start: 0.7268 (tp30) cc_final: 0.6699 (mm-30) REVERT: B 283 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7729 (m-40) REVERT: B 284 PRO cc_start: 0.8676 (Cg_exo) cc_final: 0.8434 (Cg_endo) REVERT: B 438 ARG cc_start: 0.7597 (mmt-90) cc_final: 0.7360 (mmt-90) REVERT: C 253 ASN cc_start: 0.8517 (p0) cc_final: 0.8314 (p0) REVERT: C 264 GLU cc_start: 0.7689 (tt0) cc_final: 0.7341 (tt0) REVERT: C 282 THR cc_start: 0.8457 (m) cc_final: 0.8148 (p) REVERT: C 323 ASP cc_start: 0.6418 (m-30) cc_final: 0.6118 (t70) REVERT: D 133 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7501 (mt) REVERT: D 282 THR cc_start: 0.8812 (m) cc_final: 0.8573 (p) REVERT: D 351 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7916 (ptp) REVERT: D 442 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6784 (t0) REVERT: E 149 GLN cc_start: 0.8315 (mt0) cc_final: 0.7987 (mt0) REVERT: E 198 CYS cc_start: 0.7920 (p) cc_final: 0.7382 (m) REVERT: F 149 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.6971 (tp40) REVERT: F 191 LYS cc_start: 0.8139 (mmtp) cc_final: 0.7621 (mtpt) REVERT: F 196 ASP cc_start: 0.7360 (t0) cc_final: 0.6987 (p0) REVERT: F 245 LYS cc_start: 0.8329 (mtmm) cc_final: 0.8073 (mtmt) REVERT: F 265 ARG cc_start: 0.6445 (tpt170) cc_final: 0.6054 (ttt90) REVERT: F 361 LYS cc_start: 0.5986 (mttt) cc_final: 0.5532 (mmtt) REVERT: F 374 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7959 (mt-10) outliers start: 96 outliers final: 69 residues processed: 352 average time/residue: 0.2874 time to fit residues: 149.8159 Evaluate side-chains 358 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 279 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 134 optimal weight: 0.0470 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN E 141 HIS F 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16488 Z= 0.200 Angle : 0.531 9.092 22411 Z= 0.278 Chirality : 0.045 0.164 2543 Planarity : 0.004 0.041 2880 Dihedral : 8.808 77.906 2429 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.60 % Allowed : 21.46 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.41 (0.18), residues: 2056 helix: 0.29 (0.39), residues: 207 sheet: -0.81 (0.22), residues: 487 loop : -0.06 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 144 HIS 0.004 0.001 HIS D 104 PHE 0.018 0.002 PHE C 170 TYR 0.013 0.001 TYR D 241 ARG 0.004 0.000 ARG C 438 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 295 time to evaluate : 1.953 Fit side-chains revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7516 (ttm170) REVERT: A 128 ASP cc_start: 0.6842 (p0) cc_final: 0.6564 (p0) REVERT: A 149 GLN cc_start: 0.8544 (mt0) cc_final: 0.8303 (mt0) REVERT: A 169 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7354 (tt0) REVERT: A 184 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6907 (mtp) REVERT: A 199 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8078 (mt) REVERT: A 282 THR cc_start: 0.8643 (m) cc_final: 0.8366 (p) REVERT: A 341 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6953 (ppt90) REVERT: A 431 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.7960 (t0) REVERT: A 436 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7272 (mt) REVERT: B 156 GLU cc_start: 0.7215 (tp30) cc_final: 0.6679 (mm-30) REVERT: B 209 GLU cc_start: 0.6602 (pm20) cc_final: 0.6306 (pm20) REVERT: B 283 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7520 (t0) REVERT: B 284 PRO cc_start: 0.8435 (Cg_exo) cc_final: 0.7889 (Cg_endo) REVERT: B 285 GLU cc_start: 0.7788 (pt0) cc_final: 0.7580 (pt0) REVERT: B 416 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8160 (ttpt) REVERT: B 438 ARG cc_start: 0.7431 (mmt-90) cc_final: 0.7181 (mmt-90) REVERT: C 253 ASN cc_start: 0.8382 (p0) cc_final: 0.8166 (p0) REVERT: C 282 THR cc_start: 0.8439 (m) cc_final: 0.8131 (p) REVERT: C 323 ASP cc_start: 0.6456 (m-30) cc_final: 0.6180 (t70) REVERT: D 133 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7421 (mt) REVERT: D 184 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.6988 (ptp) REVERT: D 282 THR cc_start: 0.8621 (m) cc_final: 0.8342 (p) REVERT: D 318 ASP cc_start: 0.7195 (t0) cc_final: 0.6926 (p0) REVERT: D 442 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6743 (t0) REVERT: E 149 GLN cc_start: 0.8300 (mt0) cc_final: 0.8012 (mt0) REVERT: E 198 CYS cc_start: 0.7931 (p) cc_final: 0.7418 (m) REVERT: F 144 TRP cc_start: 0.8072 (m-90) cc_final: 0.7771 (m-90) REVERT: F 191 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7614 (mtpt) REVERT: F 196 ASP cc_start: 0.7153 (t0) cc_final: 0.6890 (p0) REVERT: F 245 LYS cc_start: 0.8320 (mtmm) cc_final: 0.8034 (mtmt) REVERT: F 265 ARG cc_start: 0.6796 (tpt170) cc_final: 0.6301 (ttt90) REVERT: F 361 LYS cc_start: 0.6030 (mttt) cc_final: 0.5626 (mmtt) REVERT: F 374 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7934 (mt-10) REVERT: F 424 GLU cc_start: 0.6406 (mt-10) cc_final: 0.6178 (mt-10) outliers start: 80 outliers final: 62 residues processed: 345 average time/residue: 0.2817 time to fit residues: 144.5438 Evaluate side-chains 363 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 291 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 335 GLN F 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.7054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16488 Z= 0.201 Angle : 0.530 7.648 22411 Z= 0.276 Chirality : 0.045 0.166 2543 Planarity : 0.004 0.041 2880 Dihedral : 8.695 79.383 2429 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.49 % Allowed : 21.63 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.41 (0.18), residues: 2056 helix: 0.29 (0.39), residues: 207 sheet: -0.79 (0.23), residues: 478 loop : -0.08 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 144 HIS 0.005 0.001 HIS D 104 PHE 0.018 0.001 PHE C 170 TYR 0.014 0.002 TYR E 241 ARG 0.004 0.000 ARG C 438 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 300 time to evaluate : 1.838 Fit side-chains revert: symmetry clash REVERT: A 128 ASP cc_start: 0.6851 (p0) cc_final: 0.6576 (p0) REVERT: A 169 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7342 (tt0) REVERT: A 184 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6972 (mtt) REVERT: A 199 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8094 (mt) REVERT: A 282 THR cc_start: 0.8630 (m) cc_final: 0.8353 (p) REVERT: A 341 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6966 (ppt90) REVERT: A 424 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5844 (pt0) REVERT: A 431 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.7970 (t0) REVERT: B 156 GLU cc_start: 0.7247 (tp30) cc_final: 0.6705 (mm-30) REVERT: B 209 GLU cc_start: 0.6616 (pm20) cc_final: 0.6330 (pm20) REVERT: B 245 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8398 (mtmm) REVERT: B 283 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7644 (t0) REVERT: B 284 PRO cc_start: 0.8484 (Cg_exo) cc_final: 0.7951 (Cg_endo) REVERT: B 416 LYS cc_start: 0.8669 (ttmt) cc_final: 0.8201 (ttpt) REVERT: B 438 ARG cc_start: 0.7470 (mmt-90) cc_final: 0.7240 (mmt-90) REVERT: C 253 ASN cc_start: 0.8369 (p0) cc_final: 0.8148 (p0) REVERT: C 282 THR cc_start: 0.8488 (m) cc_final: 0.8180 (p) REVERT: C 323 ASP cc_start: 0.6477 (m-30) cc_final: 0.6202 (t70) REVERT: C 347 THR cc_start: 0.8509 (p) cc_final: 0.8186 (p) REVERT: D 92 ASN cc_start: 0.7349 (t0) cc_final: 0.7032 (p0) REVERT: D 133 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7398 (mt) REVERT: D 184 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.6968 (ptp) REVERT: D 282 THR cc_start: 0.8612 (m) cc_final: 0.8318 (p) REVERT: D 356 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7608 (tt0) REVERT: D 442 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6755 (t0) REVERT: E 103 PHE cc_start: 0.7247 (t80) cc_final: 0.6998 (t80) REVERT: E 149 GLN cc_start: 0.8255 (mt0) cc_final: 0.7981 (mt0) REVERT: E 198 CYS cc_start: 0.7993 (p) cc_final: 0.7365 (m) REVERT: F 144 TRP cc_start: 0.8090 (m-90) cc_final: 0.7806 (m-90) REVERT: F 191 LYS cc_start: 0.8108 (mmtp) cc_final: 0.7656 (mtpt) REVERT: F 196 ASP cc_start: 0.7251 (t0) cc_final: 0.6912 (p0) REVERT: F 265 ARG cc_start: 0.6725 (tpt170) cc_final: 0.6303 (ttt90) REVERT: F 361 LYS cc_start: 0.6002 (mttt) cc_final: 0.5737 (mmtt) REVERT: F 374 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7936 (mt-10) REVERT: F 424 GLU cc_start: 0.6382 (mt-10) cc_final: 0.6175 (mt-10) outliers start: 78 outliers final: 63 residues processed: 352 average time/residue: 0.2832 time to fit residues: 148.1505 Evaluate side-chains 365 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 293 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 99 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 335 GLN F 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.7139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16488 Z= 0.197 Angle : 0.526 7.760 22411 Z= 0.273 Chirality : 0.045 0.163 2543 Planarity : 0.004 0.040 2880 Dihedral : 8.514 80.417 2429 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.32 % Allowed : 21.81 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.36 (0.18), residues: 2056 helix: 0.35 (0.39), residues: 207 sheet: -0.85 (0.23), residues: 456 loop : -0.03 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 144 HIS 0.005 0.001 HIS D 104 PHE 0.018 0.001 PHE C 170 TYR 0.014 0.002 TYR D 241 ARG 0.004 0.000 ARG E 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 299 time to evaluate : 1.862 Fit side-chains revert: symmetry clash REVERT: A 128 ASP cc_start: 0.6848 (p0) cc_final: 0.6581 (p0) REVERT: A 169 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7320 (tt0) REVERT: A 184 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.7082 (mtt) REVERT: A 199 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7971 (mt) REVERT: A 282 THR cc_start: 0.8622 (m) cc_final: 0.8345 (p) REVERT: A 341 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6984 (ppt90) REVERT: A 431 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8005 (t0) REVERT: B 156 GLU cc_start: 0.7266 (tp30) cc_final: 0.6723 (mm-30) REVERT: B 209 GLU cc_start: 0.6609 (pm20) cc_final: 0.6325 (pm20) REVERT: B 283 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7486 (t0) REVERT: B 284 PRO cc_start: 0.8313 (Cg_exo) cc_final: 0.7865 (Cg_endo) REVERT: B 438 ARG cc_start: 0.7273 (mmt-90) cc_final: 0.6883 (mmp80) REVERT: C 282 THR cc_start: 0.8487 (m) cc_final: 0.8181 (p) REVERT: C 323 ASP cc_start: 0.6483 (m-30) cc_final: 0.6150 (t70) REVERT: C 347 THR cc_start: 0.8514 (p) cc_final: 0.8200 (p) REVERT: D 92 ASN cc_start: 0.7220 (t0) cc_final: 0.6889 (p0) REVERT: D 133 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7406 (mt) REVERT: D 184 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6975 (ptp) REVERT: D 282 THR cc_start: 0.8616 (m) cc_final: 0.8338 (p) REVERT: D 356 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: D 442 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6725 (t0) REVERT: E 103 PHE cc_start: 0.7336 (t80) cc_final: 0.7090 (t80) REVERT: E 149 GLN cc_start: 0.8263 (mt0) cc_final: 0.7972 (mt0) REVERT: E 198 CYS cc_start: 0.7993 (p) cc_final: 0.7318 (m) REVERT: E 253 ASN cc_start: 0.8607 (p0) cc_final: 0.8246 (p0) REVERT: E 341 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7580 (ppt170) REVERT: E 438 ARG cc_start: 0.7115 (mmt-90) cc_final: 0.6734 (mmt180) REVERT: F 191 LYS cc_start: 0.8082 (mmtp) cc_final: 0.7631 (mtpt) REVERT: F 196 ASP cc_start: 0.7843 (t0) cc_final: 0.7374 (p0) REVERT: F 245 LYS cc_start: 0.8378 (mtmm) cc_final: 0.8091 (mtmt) REVERT: F 265 ARG cc_start: 0.6421 (tpt170) cc_final: 0.6189 (ttt90) REVERT: F 361 LYS cc_start: 0.6025 (mttt) cc_final: 0.5758 (mmtt) REVERT: F 424 GLU cc_start: 0.6381 (mt-10) cc_final: 0.6174 (mt-10) outliers start: 75 outliers final: 61 residues processed: 346 average time/residue: 0.2888 time to fit residues: 148.6386 Evaluate side-chains 364 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 293 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.6980 chunk 49 optimal weight: 0.0170 chunk 149 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 335 GLN D 375 ASN F 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.171592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.139996 restraints weight = 17281.163| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.28 r_work: 0.3303 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.7123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16488 Z= 0.141 Angle : 0.482 7.249 22411 Z= 0.253 Chirality : 0.044 0.149 2543 Planarity : 0.003 0.040 2880 Dihedral : 7.812 84.903 2429 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.93 % Allowed : 23.53 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.21 (0.19), residues: 2056 helix: 0.56 (0.40), residues: 208 sheet: -0.73 (0.23), residues: 490 loop : 0.08 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 144 HIS 0.005 0.000 HIS D 104 PHE 0.014 0.001 PHE C 170 TYR 0.011 0.001 TYR E 241 ARG 0.003 0.000 ARG C 438 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3777.48 seconds wall clock time: 69 minutes 30.53 seconds (4170.53 seconds total)