Starting phenix.real_space_refine on Fri Jun 27 21:55:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7utv_26790/06_2025/7utv_26790.cif Found real_map, /net/cci-nas-00/data/ceres_data/7utv_26790/06_2025/7utv_26790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7utv_26790/06_2025/7utv_26790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7utv_26790/06_2025/7utv_26790.map" model { file = "/net/cci-nas-00/data/ceres_data/7utv_26790/06_2025/7utv_26790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7utv_26790/06_2025/7utv_26790.cif" } resolution = 3.0 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 ------------------------------------------------------------------------------- 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= 0.011 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 122 5.16 5 C 20703 2.51 5 N 5570 2.21 5 O 6151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32546 Number of models: 1 Model: "" Number of chains: 10 Chain: "L" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 456 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'CIS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 91 Planarities with less than four sites: {'UNK:plan-1': 90} Unresolved non-hydrogen planarities: 90 Chain: "H" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 501 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'CIS': 1, 'TRANS': 98} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "A" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Chain: "B" Number of atoms: 3780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3780 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 437} Chain breaks: 3 Chain: "C" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3216 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 372} Chain breaks: 5 Chain: "D" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3449 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 398} Chain breaks: 4 Chain: "E" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Chain: "F" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Chain: "G" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Chain: "I" Number of atoms: 4192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4192 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 487} Chain breaks: 3 Time building chain proxies: 18.45, per 1000 atoms: 0.57 Number of scatterers: 32546 At special positions: 0 Unit cell: (182.6, 202.4, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 122 16.00 O 6151 8.00 N 5570 7.00 C 20703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 494 " distance=2.04 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 494 " distance=2.03 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 494 " distance=2.04 Simple disulfide: pdb=" SG CYS D 490 " - pdb=" SG CYS D 494 " distance=2.04 Simple disulfide: pdb=" SG CYS E 490 " - pdb=" SG CYS E 494 " distance=2.04 Simple disulfide: pdb=" SG CYS F 490 " - pdb=" SG CYS F 494 " distance=2.04 Simple disulfide: pdb=" SG CYS G 490 " - pdb=" SG CYS G 494 " distance=2.04 Simple disulfide: pdb=" SG CYS I 490 " - pdb=" SG CYS I 494 " distance=2.04 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: 7.47 Conformation dependent library (CDL) restraints added in 3.9 seconds 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7766 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 72 sheets defined 13.2% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'H' and resid 34 through 38 Processing helix chain 'A' and resid 86 through 92 removed outlier: 4.138A pdb=" N VAL A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.833A pdb=" N THR A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.668A pdb=" N MET A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.590A pdb=" N VAL A 241 " --> pdb=" O PRO A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.791A pdb=" N PHE A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 116 through 121 removed outlier: 4.098A pdb=" N TRP B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.504A pdb=" N MET B 190 " --> pdb=" O PRO B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.814A pdb=" N VAL B 241 " --> pdb=" O PRO B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.502A pdb=" N SER B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 443 through 448 removed outlier: 4.269A pdb=" N ILE B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 95 through 99 removed outlier: 3.817A pdb=" N ASP C 99 " --> pdb=" O MET C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 237 through 241 removed outlier: 3.737A pdb=" N VAL C 241 " --> pdb=" O PRO C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 557 through 562 removed outlier: 3.519A pdb=" N TYR C 561 " --> pdb=" O GLN C 558 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C 562 " --> pdb=" O PHE C 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 92 removed outlier: 3.964A pdb=" N VAL D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 237 through 241 removed outlier: 3.516A pdb=" N VAL D 241 " --> pdb=" O PRO D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 250 Processing helix chain 'D' and resid 557 through 561 Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.588A pdb=" N MET E 190 " --> pdb=" O PRO E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 241 removed outlier: 3.515A pdb=" N VAL E 241 " --> pdb=" O PRO E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 250 Processing helix chain 'E' and resid 281 through 285 Processing helix chain 'E' and resid 309 through 313 removed outlier: 3.779A pdb=" N ARG E 313 " --> pdb=" O GLN E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 413 Processing helix chain 'E' and resid 443 through 447 Processing helix chain 'E' and resid 557 through 561 Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 237 through 241 removed outlier: 3.561A pdb=" N VAL F 241 " --> pdb=" O PRO F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 250 Processing helix chain 'F' and resid 281 through 285 Processing helix chain 'F' and resid 309 through 313 removed outlier: 3.858A pdb=" N ARG F 313 " --> pdb=" O GLN F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 413 Processing helix chain 'F' and resid 425 through 427 No H-bonds generated for 'chain 'F' and resid 425 through 427' Processing helix chain 'F' and resid 443 through 448 removed outlier: 3.992A pdb=" N ILE F 447 " --> pdb=" O ASN F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 561 removed outlier: 3.601A pdb=" N TYR F 561 " --> pdb=" O GLN F 558 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 91 Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 116 through 120 Processing helix chain 'G' and resid 122 through 132 Processing helix chain 'G' and resid 187 through 192 removed outlier: 3.916A pdb=" N MET G 190 " --> pdb=" O PRO G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 241 removed outlier: 3.583A pdb=" N VAL G 241 " --> pdb=" O PRO G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 250 Processing helix chain 'G' and resid 281 through 285 Processing helix chain 'G' and resid 309 through 313 removed outlier: 4.091A pdb=" N ARG G 313 " --> pdb=" O GLN G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 385 removed outlier: 4.087A pdb=" N GLY G 385 " --> pdb=" O ARG G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 413 Processing helix chain 'G' and resid 425 through 427 No H-bonds generated for 'chain 'G' and resid 425 through 427' Processing helix chain 'G' and resid 443 through 448 Processing helix chain 'G' and resid 557 through 561 Processing helix chain 'I' and resid 86 through 91 Processing helix chain 'I' and resid 95 through 99 Processing helix chain 'I' and resid 116 through 120 Processing helix chain 'I' and resid 122 through 132 Processing helix chain 'I' and resid 187 through 192 removed outlier: 3.510A pdb=" N MET I 190 " --> pdb=" O PRO I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 241 Processing helix chain 'I' and resid 245 through 249 Processing helix chain 'I' and resid 281 through 285 Processing helix chain 'I' and resid 309 through 313 removed outlier: 4.088A pdb=" N ARG I 313 " --> pdb=" O GLN I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 413 Processing helix chain 'I' and resid 425 through 427 No H-bonds generated for 'chain 'I' and resid 425 through 427' Processing helix chain 'I' and resid 443 through 447 Processing helix chain 'I' and resid 557 through 561 removed outlier: 3.530A pdb=" N TYR I 561 " --> pdb=" O GLN I 558 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AA3, first strand: chain 'H' and resid 49 through 50 removed outlier: 6.429A pdb=" N UNK H 41 " --> pdb=" O UNK H 32 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N UNK H 32 " --> pdb=" O UNK H 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 44 through 45 current: chain 'B' and resid 102 through 112 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 72 current: chain 'A' and resid 164 through 167 Processing sheet with id=AA6, first strand: chain 'A' and resid 80 through 84 Processing sheet with id=AA7, first strand: chain 'A' and resid 216 through 218 Processing sheet with id=AA8, first strand: chain 'A' and resid 276 through 278 removed outlier: 6.018A pdb=" N HIS A 277 " --> pdb=" O ARG A 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 319 removed outlier: 4.190A pdb=" N MET A 319 " --> pdb=" O ASN G 375 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASN G 375 " --> pdb=" O MET A 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.866A pdb=" N GLU A 335 " --> pdb=" O ALA A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 351 through 354 removed outlier: 3.738A pdb=" N SER A 348 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 396 through 399 removed outlier: 7.036A pdb=" N ASN A 375 " --> pdb=" O MET F 319 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET F 319 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.628A pdb=" N SER G 348 " --> pdb=" O GLY G 351 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 463 through 464 removed outlier: 4.186A pdb=" N TYR A 464 " --> pdb=" O GLU A 574 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 574 " --> pdb=" O TYR A 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 470 through 472 removed outlier: 7.021A pdb=" N ASP A 471 " --> pdb=" O CYS A 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 44 through 45 current: chain 'C' and resid 102 through 112 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 72 current: chain 'B' and resid 164 through 167 Processing sheet with id=AB9, first strand: chain 'B' and resid 216 through 218 Processing sheet with id=AC1, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.034A pdb=" N HIS B 277 " --> pdb=" O ARG B 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 346 through 348 removed outlier: 3.557A pdb=" N SER B 348 " --> pdb=" O GLY B 351 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 396 through 399 removed outlier: 7.044A pdb=" N ASN B 375 " --> pdb=" O MET I 319 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N MET I 319 " --> pdb=" O ASN B 375 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 415 through 416 Processing sheet with id=AC5, first strand: chain 'B' and resid 463 through 464 removed outlier: 4.127A pdb=" N TYR B 464 " --> pdb=" O GLU B 574 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 574 " --> pdb=" O TYR B 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 470 through 472 removed outlier: 6.698A pdb=" N ASP B 471 " --> pdb=" O CYS B 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 44 through 45 current: chain 'D' and resid 102 through 112 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 72 current: chain 'C' and resid 261 through 262 Processing sheet with id=AC9, first strand: chain 'C' and resid 216 through 218 Processing sheet with id=AD1, first strand: chain 'C' and resid 345 through 347 Processing sheet with id=AD2, first strand: chain 'C' and resid 377 through 380 Processing sheet with id=AD3, first strand: chain 'C' and resid 470 through 472 removed outlier: 6.607A pdb=" N ASP C 471 " --> pdb=" O CYS C 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 49 through 54 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 58 through 72 current: chain 'D' and resid 164 through 167 Processing sheet with id=AD5, first strand: chain 'D' and resid 216 through 218 Processing sheet with id=AD6, first strand: chain 'D' and resid 276 through 278 removed outlier: 5.998A pdb=" N HIS D 277 " --> pdb=" O ARG D 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 345 through 348 removed outlier: 3.988A pdb=" N SER D 348 " --> pdb=" O GLY D 351 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 377 through 380 Processing sheet with id=AD9, first strand: chain 'D' and resid 463 through 464 removed outlier: 4.213A pdb=" N TYR D 464 " --> pdb=" O GLU D 574 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 470 through 472 removed outlier: 6.805A pdb=" N ASP D 471 " --> pdb=" O CYS D 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 58 through 72 current: chain 'E' and resid 164 through 167 Processing sheet with id=AE3, first strand: chain 'E' and resid 80 through 84 Processing sheet with id=AE4, first strand: chain 'E' and resid 215 through 218 removed outlier: 4.024A pdb=" N GLY E 235 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR E 217 " --> pdb=" O TYR E 233 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR E 233 " --> pdb=" O THR E 217 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 276 through 278 Processing sheet with id=AE6, first strand: chain 'E' and resid 335 through 336 removed outlier: 6.648A pdb=" N GLU E 335 " --> pdb=" O ALA E 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 345 through 348 removed outlier: 3.972A pdb=" N SER E 348 " --> pdb=" O GLY E 351 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 377 through 380 Processing sheet with id=AE9, first strand: chain 'E' and resid 415 through 416 Processing sheet with id=AF1, first strand: chain 'E' and resid 463 through 464 removed outlier: 4.270A pdb=" N TYR E 464 " --> pdb=" O GLU E 574 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU E 574 " --> pdb=" O TYR E 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 470 through 472 removed outlier: 6.935A pdb=" N ASP E 471 " --> pdb=" O CYS E 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 58 through 72 current: chain 'F' and resid 164 through 167 Processing sheet with id=AF4, first strand: chain 'F' and resid 80 through 84 Processing sheet with id=AF5, first strand: chain 'F' and resid 215 through 218 removed outlier: 3.871A pdb=" N GLY F 235 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N THR F 217 " --> pdb=" O TYR F 233 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N TYR F 233 " --> pdb=" O THR F 217 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 276 through 278 removed outlier: 5.788A pdb=" N HIS F 277 " --> pdb=" O ARG F 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'F' and resid 335 through 336 removed outlier: 6.657A pdb=" N GLU F 335 " --> pdb=" O ALA F 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'F' and resid 351 through 354 removed outlier: 3.710A pdb=" N GLY F 351 " --> pdb=" O SER F 348 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 396 through 399 removed outlier: 7.226A pdb=" N ASN F 375 " --> pdb=" O MET G 319 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET G 319 " --> pdb=" O ASN F 375 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 463 through 464 removed outlier: 3.861A pdb=" N TYR F 464 " --> pdb=" O GLU F 574 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 470 through 472 removed outlier: 6.931A pdb=" N ASP F 471 " --> pdb=" O CYS F 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'G' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 58 through 72 current: chain 'G' and resid 164 through 167 Processing sheet with id=AG4, first strand: chain 'G' and resid 80 through 84 Processing sheet with id=AG5, first strand: chain 'G' and resid 215 through 218 removed outlier: 6.253A pdb=" N ASP G 215 " --> pdb=" O HIS G 234 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 276 through 278 removed outlier: 6.267A pdb=" N HIS G 277 " --> pdb=" O ARG G 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'G' and resid 335 through 336 removed outlier: 6.671A pdb=" N GLU G 335 " --> pdb=" O ALA G 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'G' and resid 470 through 472 removed outlier: 6.674A pdb=" N ASP G 471 " --> pdb=" O CYS G 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'I' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 58 through 72 current: chain 'I' and resid 164 through 167 Processing sheet with id=AH1, first strand: chain 'I' and resid 80 through 84 Processing sheet with id=AH2, first strand: chain 'I' and resid 215 through 218 removed outlier: 6.507A pdb=" N ASP I 215 " --> pdb=" O HIS I 234 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 276 through 278 removed outlier: 6.127A pdb=" N HIS I 277 " --> pdb=" O ARG I 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'I' and resid 335 through 336 removed outlier: 6.828A pdb=" N GLU I 335 " --> pdb=" O ALA I 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'I' and resid 345 through 347 Processing sheet with id=AH6, first strand: chain 'I' and resid 377 through 380 Processing sheet with id=AH7, first strand: chain 'I' and resid 415 through 416 Processing sheet with id=AH8, first strand: chain 'I' and resid 463 through 464 removed outlier: 4.044A pdb=" N TYR I 464 " --> pdb=" O GLU I 574 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 470 through 472 removed outlier: 6.816A pdb=" N ASP I 471 " --> pdb=" O CYS I 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 386 hydrogen bonds defined for protein. 702 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: 10.03 Time building geometry restraints manager: 8.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10686 1.35 - 1.47: 9169 1.47 - 1.60: 13411 1.60 - 1.73: 0 1.73 - 1.85: 212 Bond restraints: 33478 Sorted by residual: bond pdb=" N GLY F 37 " pdb=" CA GLY F 37 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.18e+00 bond pdb=" N GLY G 37 " pdb=" CA GLY G 37 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.10e+00 bond pdb=" N GLY A 37 " pdb=" CA GLY A 37 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.79e+00 bond pdb=" N GLY D 37 " pdb=" CA GLY D 37 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.63e+00 bond pdb=" N GLY B 37 " pdb=" CA GLY B 37 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.58e+00 ... (remaining 33473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 45029 2.85 - 5.70: 659 5.70 - 8.55: 96 8.55 - 11.40: 3 11.40 - 14.25: 1 Bond angle restraints: 45788 Sorted by residual: angle pdb=" CA UNK L 57 " pdb=" C UNK L 57 " pdb=" N UNK L 58 " ideal model delta sigma weight residual 116.20 127.29 -11.09 2.00e+00 2.50e-01 3.07e+01 angle pdb=" CA VAL I 562 " pdb=" C VAL I 562 " pdb=" N PRO I 563 " ideal model delta sigma weight residual 116.57 121.31 -4.74 9.80e-01 1.04e+00 2.34e+01 angle pdb=" N UNK L 57 " pdb=" CA UNK L 57 " pdb=" C UNK L 57 " ideal model delta sigma weight residual 110.74 124.99 -14.25 3.00e+00 1.11e-01 2.26e+01 angle pdb=" C UNK L 57 " pdb=" N UNK L 58 " pdb=" CA UNK L 58 " ideal model delta sigma weight residual 121.70 129.70 -8.00 1.80e+00 3.09e-01 1.97e+01 angle pdb=" N LEU A 255 " pdb=" CA LEU A 255 " pdb=" C LEU A 255 " ideal model delta sigma weight residual 111.28 116.10 -4.82 1.09e+00 8.42e-01 1.96e+01 ... (remaining 45783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18341 17.98 - 35.96: 955 35.96 - 53.94: 198 53.94 - 71.92: 60 71.92 - 89.90: 51 Dihedral angle restraints: 19605 sinusoidal: 7563 harmonic: 12042 Sorted by residual: dihedral pdb=" CA ASN G 421 " pdb=" C ASN G 421 " pdb=" N LEU G 422 " pdb=" CA LEU G 422 " ideal model delta harmonic sigma weight residual -180.00 -149.25 -30.75 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA GLU D 55 " pdb=" C GLU D 55 " pdb=" N ASN D 56 " pdb=" CA ASN D 56 " ideal model delta harmonic sigma weight residual -180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA PRO E 272 " pdb=" C PRO E 272 " pdb=" N CYS E 273 " pdb=" CA CYS E 273 " ideal model delta harmonic sigma weight residual 180.00 155.01 24.99 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 19602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3300 0.048 - 0.096: 1270 0.096 - 0.144: 381 0.144 - 0.192: 27 0.192 - 0.240: 2 Chirality restraints: 4980 Sorted by residual: chirality pdb=" CA UNK L 57 " pdb=" N UNK L 57 " pdb=" C UNK L 57 " pdb=" CB UNK L 57 " both_signs ideal model delta sigma weight residual False 2.52 2.28 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA LEU G 422 " pdb=" N LEU G 422 " pdb=" C LEU G 422 " pdb=" CB LEU G 422 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CA VAL I 562 " pdb=" N VAL I 562 " pdb=" C VAL I 562 " pdb=" CB VAL I 562 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 4977 not shown) Planarity restraints: 6021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 45 " 0.015 2.00e-02 2.50e+03 1.75e-02 5.33e+00 pdb=" CG PHE D 45 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE D 45 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE D 45 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE D 45 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 45 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 45 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 198 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 199 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 199 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 199 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 198 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 199 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 199 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 199 " -0.030 5.00e-02 4.00e+02 ... (remaining 6018 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5784 2.77 - 3.30: 30454 3.30 - 3.83: 53768 3.83 - 4.37: 66200 4.37 - 4.90: 113532 Nonbonded interactions: 269738 Sorted by model distance: nonbonded pdb=" OG SER F 339 " pdb=" OG1 THR F 450 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR D 278 " pdb=" OD1 ASN D 458 " model vdw 2.270 3.040 nonbonded pdb=" O SER B 192 " pdb=" OG SER B 192 " model vdw 2.305 3.040 nonbonded pdb=" OG1 THR G 152 " pdb=" OD2 ASP G 168 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR F 343 " pdb=" OD1 ASN G 321 " model vdw 2.321 3.040 ... (remaining 269733 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 37 through 284 or resid 345 through 509 or resid 516 throu \ gh 584)) selection = (chain 'B' and (resid 37 through 509 or resid 516 through 584)) selection = (chain 'E' and (resid 37 through 284 or resid 345 through 509 or resid 516 throu \ gh 584)) selection = (chain 'F' and (resid 37 through 284 or resid 345 through 509 or resid 516 throu \ gh 584)) selection = (chain 'G' and (resid 37 through 284 or resid 345 through 509 or resid 516 throu \ gh 584)) selection = (chain 'I' and (resid 37 through 284 or resid 345 through 584)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 37 through 277 or resid 341 through 361 or resid 373 throu \ gh 404 or resid 458 through 540 or resid 550 through 579)) } ncs_group { reference = (chain 'H' and resid 10 through 100) selection = chain 'L' } 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.320 Check model and map are aligned: 0.230 Set scattering table: 0.320 Process input model: 66.990 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.009 0.091 33486 Z= 0.368 Angle : 0.925 14.246 45804 Z= 0.493 Chirality : 0.053 0.240 4980 Planarity : 0.006 0.065 6021 Dihedral : 13.274 89.900 11815 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.54 % Rotamer: Outliers : 1.24 % Allowed : 3.43 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.60 (0.12), residues: 3895 helix: -1.05 (0.40), residues: 110 sheet: 0.07 (0.16), residues: 916 loop : -0.53 (0.11), residues: 2869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP G 545 HIS 0.009 0.002 HIS G 137 PHE 0.040 0.003 PHE D 45 TYR 0.034 0.003 TYR G 342 ARG 0.011 0.001 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.25940 ( 386) hydrogen bonds : angle 8.39753 ( 702) SS BOND : bond 0.00615 ( 8) SS BOND : angle 3.21566 ( 16) covalent geometry : bond 0.00929 (33478) covalent geometry : angle 0.92286 (45788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 1273 time to evaluate : 3.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8069 (t0) REVERT: A 48 GLN cc_start: 0.8257 (mt0) cc_final: 0.8020 (mt0) REVERT: A 60 GLU cc_start: 0.7810 (tt0) cc_final: 0.7509 (tt0) REVERT: A 87 MET cc_start: 0.7142 (ttm) cc_final: 0.6847 (ttm) REVERT: A 89 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7976 (ttmt) REVERT: A 100 ASP cc_start: 0.7745 (m-30) cc_final: 0.7446 (m-30) REVERT: A 128 LEU cc_start: 0.8654 (tp) cc_final: 0.8415 (tp) REVERT: A 131 ASN cc_start: 0.8448 (m-40) cc_final: 0.8215 (m-40) REVERT: A 144 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7459 (mt-10) REVERT: A 153 VAL cc_start: 0.8873 (t) cc_final: 0.8478 (m) REVERT: A 167 ASN cc_start: 0.8000 (m-40) cc_final: 0.7776 (m-40) REVERT: A 230 THR cc_start: 0.8518 (p) cc_final: 0.8303 (p) REVERT: A 239 ASP cc_start: 0.8053 (t0) cc_final: 0.7820 (t0) REVERT: A 249 SER cc_start: 0.8160 (p) cc_final: 0.7907 (p) REVERT: A 269 ASP cc_start: 0.7064 (p0) cc_final: 0.6643 (p0) REVERT: A 276 THR cc_start: 0.8823 (p) cc_final: 0.8609 (p) REVERT: A 296 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7695 (mm-40) REVERT: A 401 ILE cc_start: 0.8421 (mm) cc_final: 0.8182 (pp) REVERT: A 439 LYS cc_start: 0.8544 (mmtp) cc_final: 0.7951 (mmtt) REVERT: A 471 ASP cc_start: 0.7651 (t0) cc_final: 0.7439 (t0) REVERT: A 519 SER cc_start: 0.8481 (t) cc_final: 0.8257 (t) REVERT: A 536 LYS cc_start: 0.8325 (ttpp) cc_final: 0.8081 (ttpp) REVERT: A 556 ASP cc_start: 0.8015 (m-30) cc_final: 0.7790 (m-30) REVERT: A 575 LYS cc_start: 0.8625 (mttt) cc_final: 0.8349 (mttt) REVERT: B 47 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8379 (t160) REVERT: B 51 PHE cc_start: 0.8280 (m-80) cc_final: 0.8060 (m-80) REVERT: B 77 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 87 MET cc_start: 0.7536 (ptm) cc_final: 0.7329 (ptm) REVERT: B 109 TRP cc_start: 0.8693 (m100) cc_final: 0.8050 (m100) REVERT: B 113 ASP cc_start: 0.7803 (t0) cc_final: 0.7570 (t0) REVERT: B 145 ILE cc_start: 0.8739 (mt) cc_final: 0.8455 (mp) REVERT: B 180 ASN cc_start: 0.8169 (m-40) cc_final: 0.7940 (m-40) REVERT: B 219 ILE cc_start: 0.8733 (mt) cc_final: 0.8525 (OUTLIER) REVERT: B 221 SER cc_start: 0.8733 (p) cc_final: 0.8435 (p) REVERT: B 234 HIS cc_start: 0.8512 (m170) cc_final: 0.7927 (m-70) REVERT: B 248 ASN cc_start: 0.8436 (m-40) cc_final: 0.8201 (m-40) REVERT: B 271 LYS cc_start: 0.8225 (ptmt) cc_final: 0.7917 (ptmt) REVERT: B 384 HIS cc_start: 0.8683 (m90) cc_final: 0.8355 (m170) REVERT: B 408 ARG cc_start: 0.4888 (mtm110) cc_final: 0.4383 (mtm180) REVERT: B 409 TYR cc_start: 0.8110 (t80) cc_final: 0.7593 (t80) REVERT: B 411 GLU cc_start: 0.7945 (tt0) cc_final: 0.7195 (tt0) REVERT: B 468 GLN cc_start: 0.8578 (mt0) cc_final: 0.7901 (mt0) REVERT: B 475 ASP cc_start: 0.7491 (t0) cc_final: 0.6891 (t0) REVERT: B 479 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8138 (mmtm) REVERT: B 549 GLN cc_start: 0.8069 (tt0) cc_final: 0.7813 (tt0) REVERT: B 569 MET cc_start: 0.8333 (mmm) cc_final: 0.7991 (mmm) REVERT: B 573 TYR cc_start: 0.8164 (p90) cc_final: 0.7525 (p90) REVERT: C 42 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7279 (t) REVERT: C 47 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7895 (t160) REVERT: C 52 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7865 (ttpt) REVERT: C 71 LEU cc_start: 0.8311 (tp) cc_final: 0.8039 (tm) REVERT: C 73 MET cc_start: 0.8129 (mtm) cc_final: 0.7913 (mtm) REVERT: C 77 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7302 (tm-30) REVERT: C 89 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8100 (ttmt) REVERT: C 96 MET cc_start: 0.6499 (ptm) cc_final: 0.5597 (ptm) REVERT: C 125 ASP cc_start: 0.7886 (m-30) cc_final: 0.7590 (m-30) REVERT: C 130 VAL cc_start: 0.8339 (m) cc_final: 0.8101 (t) REVERT: C 133 MET cc_start: 0.8214 (mmt) cc_final: 0.7994 (mmm) REVERT: C 151 LYS cc_start: 0.8335 (mttp) cc_final: 0.8039 (mtpp) REVERT: C 155 GLU cc_start: 0.6999 (pp20) cc_final: 0.6744 (pp20) REVERT: C 183 MET cc_start: 0.8394 (mmm) cc_final: 0.8115 (mmp) REVERT: C 193 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7230 (mt-10) REVERT: C 204 ILE cc_start: 0.8853 (pt) cc_final: 0.8637 (pp) REVERT: C 260 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6199 (mt-10) REVERT: C 271 LYS cc_start: 0.8116 (ptmt) cc_final: 0.7775 (ptmt) REVERT: C 344 SER cc_start: 0.8274 (t) cc_final: 0.7984 (t) REVERT: C 377 ARG cc_start: 0.8686 (ttt90) cc_final: 0.8463 (ttt180) REVERT: C 470 TRP cc_start: 0.8722 (p90) cc_final: 0.8224 (p90) REVERT: C 473 GLU cc_start: 0.7885 (tp30) cc_final: 0.7679 (tp30) REVERT: C 501 LYS cc_start: 0.8569 (tttt) cc_final: 0.8293 (tttt) REVERT: C 511 ASP cc_start: 0.7745 (t0) cc_final: 0.7438 (t0) REVERT: C 530 LYS cc_start: 0.8855 (ttmt) cc_final: 0.8652 (ttpp) REVERT: C 535 PHE cc_start: 0.8629 (m-80) cc_final: 0.8304 (m-80) REVERT: C 561 TYR cc_start: 0.8813 (m-80) cc_final: 0.8611 (m-80) REVERT: C 572 VAL cc_start: 0.8907 (m) cc_final: 0.8380 (p) REVERT: C 574 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7015 (mm-30) REVERT: D 60 GLU cc_start: 0.7852 (tt0) cc_final: 0.7600 (tt0) REVERT: D 77 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7133 (mm-30) REVERT: D 113 ASP cc_start: 0.7523 (t0) cc_final: 0.7304 (t0) REVERT: D 135 GLU cc_start: 0.7967 (pt0) cc_final: 0.7740 (pt0) REVERT: D 209 ARG cc_start: 0.8561 (pmt170) cc_final: 0.6214 (pmt-80) REVERT: D 246 ILE cc_start: 0.8454 (mm) cc_final: 0.8234 (mm) REVERT: D 260 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7128 (mt-10) REVERT: D 269 ASP cc_start: 0.7861 (p0) cc_final: 0.7306 (p0) REVERT: D 387 LYS cc_start: 0.8157 (tptm) cc_final: 0.7953 (tppp) REVERT: D 396 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7412 (mm-30) REVERT: D 400 TYR cc_start: 0.8548 (t80) cc_final: 0.8254 (t80) REVERT: D 472 LYS cc_start: 0.8229 (mmmm) cc_final: 0.8001 (mmmm) REVERT: D 511 ASP cc_start: 0.7956 (t0) cc_final: 0.7606 (t0) REVERT: D 513 ASP cc_start: 0.7796 (t0) cc_final: 0.7381 (t0) REVERT: D 538 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7689 (ttmm) REVERT: D 573 TYR cc_start: 0.7958 (p90) cc_final: 0.7157 (p90) REVERT: E 48 GLN cc_start: 0.8154 (mt0) cc_final: 0.7796 (mt0) REVERT: E 60 GLU cc_start: 0.7429 (tt0) cc_final: 0.7180 (tt0) REVERT: E 77 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7502 (mm-30) REVERT: E 95 ASN cc_start: 0.8024 (m110) cc_final: 0.7814 (m110) REVERT: E 122 ASN cc_start: 0.8221 (p0) cc_final: 0.7907 (p0) REVERT: E 125 ASP cc_start: 0.7706 (m-30) cc_final: 0.7494 (m-30) REVERT: E 144 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7486 (mt-10) REVERT: E 166 ASN cc_start: 0.7475 (m-40) cc_final: 0.7269 (m-40) REVERT: E 167 ASN cc_start: 0.7469 (m-40) cc_final: 0.7246 (m-40) REVERT: E 179 SER cc_start: 0.8404 (p) cc_final: 0.8186 (p) REVERT: E 193 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7309 (mt-10) REVERT: E 240 ASP cc_start: 0.7299 (m-30) cc_final: 0.6992 (m-30) REVERT: E 312 LYS cc_start: 0.5706 (tptp) cc_final: 0.4966 (mtpp) REVERT: E 314 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7333 (mtp180) REVERT: E 325 ILE cc_start: 0.8797 (mt) cc_final: 0.8504 (mp) REVERT: E 353 PHE cc_start: 0.8594 (p90) cc_final: 0.8228 (p90) REVERT: E 411 GLU cc_start: 0.7745 (mp0) cc_final: 0.7225 (mp0) REVERT: E 420 PHE cc_start: 0.8884 (t80) cc_final: 0.8643 (t80) REVERT: E 426 ASN cc_start: 0.8105 (t0) cc_final: 0.7681 (t0) REVERT: E 444 TYR cc_start: 0.8507 (p90) cc_final: 0.8300 (p90) REVERT: E 473 GLU cc_start: 0.7936 (tp30) cc_final: 0.7624 (tp30) REVERT: E 479 LYS cc_start: 0.8720 (mttm) cc_final: 0.8512 (mtpp) REVERT: E 557 ASN cc_start: 0.8320 (p0) cc_final: 0.8118 (p0) REVERT: E 570 LYS cc_start: 0.8667 (ptmt) cc_final: 0.8455 (ptmm) REVERT: E 575 LYS cc_start: 0.8545 (mttp) cc_final: 0.8327 (mttp) REVERT: F 42 THR cc_start: 0.8288 (p) cc_final: 0.7715 (t) REVERT: F 72 ASN cc_start: 0.8623 (m-40) cc_final: 0.8352 (m-40) REVERT: F 77 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7555 (mm-30) REVERT: F 78 ASN cc_start: 0.8511 (m-40) cc_final: 0.8286 (m-40) REVERT: F 135 GLU cc_start: 0.8004 (pt0) cc_final: 0.7722 (pt0) REVERT: F 144 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7692 (mt-10) REVERT: F 163 LYS cc_start: 0.8233 (mttt) cc_final: 0.7953 (mttt) REVERT: F 185 PHE cc_start: 0.8530 (t80) cc_final: 0.8245 (t80) REVERT: F 213 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7907 (tm-30) REVERT: F 239 ASP cc_start: 0.7885 (m-30) cc_final: 0.7589 (m-30) REVERT: F 244 TYR cc_start: 0.8477 (m-80) cc_final: 0.8253 (m-80) REVERT: F 302 ASN cc_start: 0.7749 (m110) cc_final: 0.7426 (m-40) REVERT: F 309 GLN cc_start: 0.7231 (mt0) cc_final: 0.6984 (mt0) REVERT: F 413 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7090 (t0) REVERT: F 434 ASP cc_start: 0.7795 (m-30) cc_final: 0.7407 (m-30) REVERT: F 444 TYR cc_start: 0.8373 (p90) cc_final: 0.8154 (p90) REVERT: F 473 GLU cc_start: 0.7648 (tp30) cc_final: 0.7363 (tp30) REVERT: F 479 LYS cc_start: 0.8592 (mttm) cc_final: 0.8147 (mttm) REVERT: F 481 ARG cc_start: 0.8546 (mmm-85) cc_final: 0.8345 (mmm-85) REVERT: F 570 LYS cc_start: 0.8747 (ptpt) cc_final: 0.8371 (ptmm) REVERT: G 60 GLU cc_start: 0.7876 (tt0) cc_final: 0.7576 (tt0) REVERT: G 87 MET cc_start: 0.6876 (ptm) cc_final: 0.6483 (ptm) REVERT: G 115 ASN cc_start: 0.8476 (t0) cc_final: 0.8253 (t0) REVERT: G 151 LYS cc_start: 0.8600 (mttm) cc_final: 0.8326 (mmmm) REVERT: G 177 LEU cc_start: 0.8346 (tp) cc_final: 0.8079 (tm) REVERT: G 204 ILE cc_start: 0.8863 (pt) cc_final: 0.8625 (OUTLIER) REVERT: G 237 ASP cc_start: 0.7747 (t0) cc_final: 0.7430 (t0) REVERT: G 259 ASP cc_start: 0.7236 (m-30) cc_final: 0.6915 (m-30) REVERT: G 274 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7559 (mtp-110) REVERT: G 275 LEU cc_start: 0.8398 (mt) cc_final: 0.8167 (mp) REVERT: G 319 MET cc_start: 0.8462 (mtp) cc_final: 0.8257 (mtp) REVERT: G 375 ASN cc_start: 0.7882 (m110) cc_final: 0.7616 (m110) REVERT: G 382 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8153 (mtm-85) REVERT: G 396 GLU cc_start: 0.7837 (tp30) cc_final: 0.7607 (tp30) REVERT: G 426 ASN cc_start: 0.8304 (t0) cc_final: 0.8057 (t0) REVERT: G 473 GLU cc_start: 0.7734 (tp30) cc_final: 0.7451 (tp30) REVERT: G 484 VAL cc_start: 0.8915 (m) cc_final: 0.8603 (t) REVERT: G 526 ASP cc_start: 0.7538 (p0) cc_final: 0.7333 (p0) REVERT: G 573 TYR cc_start: 0.8198 (p90) cc_final: 0.7406 (p90) REVERT: I 40 ILE cc_start: 0.8619 (mt) cc_final: 0.8304 (mp) REVERT: I 49 THR cc_start: 0.8310 (p) cc_final: 0.7946 (t) REVERT: I 88 ASP cc_start: 0.7692 (t0) cc_final: 0.7479 (t0) REVERT: I 125 ASP cc_start: 0.7518 (m-30) cc_final: 0.7318 (m-30) REVERT: I 133 MET cc_start: 0.8453 (mmt) cc_final: 0.8232 (mpm) REVERT: I 183 MET cc_start: 0.8330 (mmm) cc_final: 0.8109 (mmm) REVERT: I 193 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7316 (mt-10) REVERT: I 278 THR cc_start: 0.8855 (p) cc_final: 0.8648 (p) REVERT: I 303 PHE cc_start: 0.8310 (m-80) cc_final: 0.7951 (m-10) REVERT: I 311 ASP cc_start: 0.7682 (p0) cc_final: 0.7459 (p0) REVERT: I 312 LYS cc_start: 0.8623 (mttt) cc_final: 0.8291 (mttt) REVERT: I 342 TYR cc_start: 0.7978 (p90) cc_final: 0.7528 (p90) REVERT: I 350 GLN cc_start: 0.8783 (mt0) cc_final: 0.8534 (mt0) REVERT: I 387 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8154 (mmmm) REVERT: I 408 ARG cc_start: 0.8065 (mmt-90) cc_final: 0.7237 (mpt180) REVERT: I 414 TRP cc_start: 0.8717 (p90) cc_final: 0.8491 (p90) REVERT: I 439 LYS cc_start: 0.3149 (mmmt) cc_final: 0.2425 (mmmt) REVERT: I 457 LEU cc_start: 0.8293 (mt) cc_final: 0.8081 (OUTLIER) REVERT: I 501 LYS cc_start: 0.8408 (tttt) cc_final: 0.8111 (tttm) REVERT: I 518 MET cc_start: 0.6797 (ptp) cc_final: 0.6380 (ptp) outliers start: 43 outliers final: 16 residues processed: 1296 average time/residue: 1.2583 time to fit residues: 1972.7596 Evaluate side-chains 1155 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 1136 time to evaluate : 3.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 387 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 348 optimal weight: 0.8980 chunk 313 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 323 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 240 optimal weight: 0.7980 chunk 375 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 280 GLN ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 HIS A 468 GLN B 48 GLN B 85 ASN B 95 ASN B 122 ASN B 181 ASN B 280 GLN B 383 GLN B 404 GLN B 419 ASN C 383 GLN C 508 ASN D 383 GLN E 47 ASN E 102 HIS E 137 HIS E 180 ASN E 483 HIS E 497 GLN F 166 ASN F 180 ASN F 280 GLN ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 GLN F 493 ASN F 549 GLN F 554 ASN G 47 ASN G 234 HIS ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 419 ASN I 47 ASN I 147 ASN I 310 GLN I 404 GLN I 459 ASN ** I 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 549 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108700 restraints weight = 46918.603| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.14 r_work: 0.3243 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33486 Z= 0.127 Angle : 0.572 15.258 45804 Z= 0.291 Chirality : 0.043 0.189 4980 Planarity : 0.005 0.046 6021 Dihedral : 6.365 85.916 4468 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.31 % Allowed : 12.40 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 (0.13), residues: 3895 helix: -0.60 (0.40), residues: 116 sheet: 0.00 (0.16), residues: 1004 loop : -0.28 (0.11), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 414 HIS 0.008 0.001 HIS A 234 PHE 0.018 0.001 PHE E 448 TYR 0.027 0.001 TYR G 233 ARG 0.008 0.001 ARG I 361 Details of bonding type rmsd hydrogen bonds : bond 0.04544 ( 386) hydrogen bonds : angle 6.43841 ( 702) SS BOND : bond 0.00799 ( 8) SS BOND : angle 1.33776 ( 16) covalent geometry : bond 0.00283 (33478) covalent geometry : angle 0.57184 (45788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 1161 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8292 (t0) REVERT: A 48 GLN cc_start: 0.8226 (mt0) cc_final: 0.8014 (mt0) REVERT: A 60 GLU cc_start: 0.7909 (tt0) cc_final: 0.7700 (tt0) REVERT: A 77 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7683 (mm-30) REVERT: A 100 ASP cc_start: 0.7874 (m-30) cc_final: 0.7636 (m-30) REVERT: A 125 ASP cc_start: 0.7761 (m-30) cc_final: 0.7537 (m-30) REVERT: A 131 ASN cc_start: 0.8479 (m-40) cc_final: 0.8106 (m-40) REVERT: A 144 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7655 (mt-10) REVERT: A 239 ASP cc_start: 0.7899 (t0) cc_final: 0.7673 (t0) REVERT: A 296 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7759 (mm-40) REVERT: A 302 ASN cc_start: 0.7381 (m110) cc_final: 0.6925 (m110) REVERT: A 327 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7728 (mm-30) REVERT: A 380 PHE cc_start: 0.8399 (p90) cc_final: 0.8183 (p90) REVERT: A 439 LYS cc_start: 0.8481 (mmtp) cc_final: 0.8199 (mttm) REVERT: A 460 VAL cc_start: 0.8755 (OUTLIER) cc_final: 0.8470 (p) REVERT: A 471 ASP cc_start: 0.7835 (t0) cc_final: 0.7517 (t0) REVERT: A 519 SER cc_start: 0.8602 (t) cc_final: 0.8385 (t) REVERT: A 536 LYS cc_start: 0.8372 (ttpp) cc_final: 0.8138 (ttpp) REVERT: B 51 PHE cc_start: 0.8398 (m-80) cc_final: 0.8193 (m-80) REVERT: B 77 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7469 (tm-30) REVERT: B 82 VAL cc_start: 0.8851 (t) cc_final: 0.8589 (p) REVERT: B 87 MET cc_start: 0.7986 (ptm) cc_final: 0.7734 (ptm) REVERT: B 101 ILE cc_start: 0.8647 (mt) cc_final: 0.8321 (mt) REVERT: B 109 TRP cc_start: 0.8662 (m100) cc_final: 0.8004 (m100) REVERT: B 216 ARG cc_start: 0.8221 (ttt90) cc_final: 0.7866 (ttt90) REVERT: B 217 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7958 (p) REVERT: B 219 ILE cc_start: 0.8762 (mt) cc_final: 0.8556 (OUTLIER) REVERT: B 221 SER cc_start: 0.8869 (p) cc_final: 0.8602 (p) REVERT: B 232 ILE cc_start: 0.8622 (pt) cc_final: 0.8415 (pp) REVERT: B 271 LYS cc_start: 0.8279 (ptmt) cc_final: 0.7990 (ptmt) REVERT: B 357 ILE cc_start: 0.8205 (mm) cc_final: 0.7961 (mp) REVERT: B 384 HIS cc_start: 0.8710 (m90) cc_final: 0.8507 (m170) REVERT: B 408 ARG cc_start: 0.5338 (mtm110) cc_final: 0.3924 (mtm180) REVERT: B 409 TYR cc_start: 0.7934 (t80) cc_final: 0.7483 (t80) REVERT: B 411 GLU cc_start: 0.8313 (tt0) cc_final: 0.7670 (tt0) REVERT: B 436 ILE cc_start: 0.8246 (tt) cc_final: 0.7957 (OUTLIER) REVERT: B 479 LYS cc_start: 0.8733 (mmtm) cc_final: 0.8216 (mmtm) REVERT: B 549 GLN cc_start: 0.8408 (tt0) cc_final: 0.8182 (tt0) REVERT: B 559 PHE cc_start: 0.8761 (m-80) cc_final: 0.8526 (m-80) REVERT: B 573 TYR cc_start: 0.8197 (p90) cc_final: 0.7816 (p90) REVERT: B 576 SER cc_start: 0.8485 (t) cc_final: 0.8007 (p) REVERT: C 52 LYS cc_start: 0.8486 (ttpt) cc_final: 0.8057 (ttpt) REVERT: C 71 LEU cc_start: 0.8482 (tp) cc_final: 0.8170 (tm) REVERT: C 73 MET cc_start: 0.8182 (mtm) cc_final: 0.7979 (mtm) REVERT: C 77 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7397 (tm-30) REVERT: C 89 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8328 (ttmt) REVERT: C 96 MET cc_start: 0.6058 (ptm) cc_final: 0.5715 (ptm) REVERT: C 133 MET cc_start: 0.8275 (mmt) cc_final: 0.7995 (mmm) REVERT: C 155 GLU cc_start: 0.7592 (pp20) cc_final: 0.7245 (pp20) REVERT: C 193 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7546 (mt-10) REVERT: C 204 ILE cc_start: 0.9003 (pt) cc_final: 0.8756 (pp) REVERT: C 209 ARG cc_start: 0.8432 (pmt170) cc_final: 0.5166 (pmt-80) REVERT: C 232 ILE cc_start: 0.8458 (pt) cc_final: 0.8252 (pp) REVERT: C 271 LYS cc_start: 0.8096 (ptmt) cc_final: 0.7879 (ptmt) REVERT: C 344 SER cc_start: 0.8234 (t) cc_final: 0.7960 (t) REVERT: C 377 ARG cc_start: 0.8690 (ttt90) cc_final: 0.8452 (ttt180) REVERT: C 470 TRP cc_start: 0.8691 (p90) cc_final: 0.8211 (p90) REVERT: C 479 LYS cc_start: 0.8638 (mttm) cc_final: 0.8426 (mttm) REVERT: C 501 LYS cc_start: 0.8632 (tttt) cc_final: 0.8410 (tttp) REVERT: C 511 ASP cc_start: 0.7849 (t0) cc_final: 0.7483 (t0) REVERT: C 525 SER cc_start: 0.8690 (t) cc_final: 0.8476 (t) REVERT: C 535 PHE cc_start: 0.8547 (m-80) cc_final: 0.8340 (m-80) REVERT: C 550 GLN cc_start: 0.6333 (mm-40) cc_final: 0.6049 (mp-120) REVERT: C 561 TYR cc_start: 0.8835 (m-80) cc_final: 0.8590 (m-80) REVERT: C 574 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7208 (mm-30) REVERT: D 40 ILE cc_start: 0.8194 (mt) cc_final: 0.7968 (pp) REVERT: D 47 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8318 (t160) REVERT: D 60 GLU cc_start: 0.8138 (tt0) cc_final: 0.7923 (tt0) REVERT: D 77 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7303 (mm-30) REVERT: D 80 ARG cc_start: 0.8616 (mtp-110) cc_final: 0.8326 (mtp85) REVERT: D 101 ILE cc_start: 0.8724 (mt) cc_final: 0.8460 (mp) REVERT: D 135 GLU cc_start: 0.8188 (pt0) cc_final: 0.7952 (pt0) REVERT: D 260 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7427 (mt-10) REVERT: D 387 LYS cc_start: 0.8320 (tptm) cc_final: 0.8090 (tppp) REVERT: D 396 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7641 (mm-30) REVERT: D 400 TYR cc_start: 0.8604 (t80) cc_final: 0.8285 (t80) REVERT: D 511 ASP cc_start: 0.7952 (t0) cc_final: 0.7601 (t0) REVERT: D 513 ASP cc_start: 0.7921 (t0) cc_final: 0.7547 (t0) REVERT: D 532 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8619 (ttpt) REVERT: D 581 ARG cc_start: 0.8389 (ttp80) cc_final: 0.8141 (ttp80) REVERT: E 42 THR cc_start: 0.8217 (m) cc_final: 0.7877 (p) REVERT: E 53 PHE cc_start: 0.8245 (m-80) cc_final: 0.8027 (m-80) REVERT: E 60 GLU cc_start: 0.7746 (tt0) cc_final: 0.7513 (tt0) REVERT: E 77 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7644 (mm-30) REVERT: E 101 ILE cc_start: 0.8354 (mt) cc_final: 0.8074 (mt) REVERT: E 122 ASN cc_start: 0.8221 (p0) cc_final: 0.7909 (p0) REVERT: E 167 ASN cc_start: 0.7690 (m-40) cc_final: 0.7464 (m-40) REVERT: E 179 SER cc_start: 0.8439 (p) cc_final: 0.8201 (p) REVERT: E 193 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7461 (mt-10) REVERT: E 240 ASP cc_start: 0.7342 (m-30) cc_final: 0.7041 (m-30) REVERT: E 266 PHE cc_start: 0.8201 (t80) cc_final: 0.7806 (t80) REVERT: E 314 ARG cc_start: 0.8536 (mtt90) cc_final: 0.7405 (mtp180) REVERT: E 325 ILE cc_start: 0.8707 (mt) cc_final: 0.8388 (mp) REVERT: E 342 TYR cc_start: 0.7952 (p90) cc_final: 0.7567 (p90) REVERT: E 397 ARG cc_start: 0.7600 (mtt180) cc_final: 0.7060 (mtt90) REVERT: E 411 GLU cc_start: 0.8036 (mp0) cc_final: 0.7555 (mp0) REVERT: E 426 ASN cc_start: 0.8113 (t0) cc_final: 0.7647 (t0) REVERT: E 460 VAL cc_start: 0.8567 (p) cc_final: 0.8322 (m) REVERT: E 473 GLU cc_start: 0.7911 (tp30) cc_final: 0.7588 (tp30) REVERT: E 557 ASN cc_start: 0.8499 (p0) cc_final: 0.8188 (p0) REVERT: E 570 LYS cc_start: 0.8773 (ptmt) cc_final: 0.8569 (ptmm) REVERT: F 40 ILE cc_start: 0.8513 (mt) cc_final: 0.8145 (tp) REVERT: F 42 THR cc_start: 0.8285 (p) cc_final: 0.7691 (t) REVERT: F 72 ASN cc_start: 0.8616 (m-40) cc_final: 0.8363 (m-40) REVERT: F 77 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7758 (mm-30) REVERT: F 81 ARG cc_start: 0.8593 (ttp80) cc_final: 0.6778 (pmt-80) REVERT: F 89 LYS cc_start: 0.8344 (tppt) cc_final: 0.7980 (tppt) REVERT: F 163 LYS cc_start: 0.8225 (mttt) cc_final: 0.7918 (mttt) REVERT: F 185 PHE cc_start: 0.8569 (t80) cc_final: 0.8241 (t80) REVERT: F 192 SER cc_start: 0.8310 (t) cc_final: 0.7881 (p) REVERT: F 213 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8010 (tm-30) REVERT: F 239 ASP cc_start: 0.7948 (m-30) cc_final: 0.7622 (m-30) REVERT: F 244 TYR cc_start: 0.8493 (m-80) cc_final: 0.8257 (m-80) REVERT: F 411 GLU cc_start: 0.7950 (mp0) cc_final: 0.7687 (mp0) REVERT: F 413 ASP cc_start: 0.7662 (t70) cc_final: 0.7286 (t0) REVERT: F 472 LYS cc_start: 0.8571 (ttpp) cc_final: 0.8186 (ttpp) REVERT: F 473 GLU cc_start: 0.7616 (tp30) cc_final: 0.7346 (tp30) REVERT: F 475 ASP cc_start: 0.7894 (t70) cc_final: 0.7663 (t70) REVERT: F 479 LYS cc_start: 0.8503 (mttm) cc_final: 0.8123 (mttm) REVERT: F 481 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8320 (mmm-85) REVERT: F 570 LYS cc_start: 0.8792 (ptpt) cc_final: 0.8444 (ptmm) REVERT: G 49 THR cc_start: 0.8399 (m) cc_final: 0.8069 (p) REVERT: G 87 MET cc_start: 0.7368 (ptm) cc_final: 0.7101 (ptm) REVERT: G 89 LYS cc_start: 0.8503 (tttt) cc_final: 0.8253 (ttmm) REVERT: G 115 ASN cc_start: 0.8416 (t0) cc_final: 0.8128 (t0) REVERT: G 151 LYS cc_start: 0.8574 (mttm) cc_final: 0.8293 (mmmm) REVERT: G 177 LEU cc_start: 0.8414 (tp) cc_final: 0.8192 (tm) REVERT: G 204 ILE cc_start: 0.8804 (pt) cc_final: 0.8592 (OUTLIER) REVERT: G 237 ASP cc_start: 0.7465 (t0) cc_final: 0.7144 (t0) REVERT: G 274 ARG cc_start: 0.8352 (ttm110) cc_final: 0.8148 (mtp-110) REVERT: G 275 LEU cc_start: 0.8368 (mt) cc_final: 0.8156 (mp) REVERT: G 335 GLU cc_start: 0.7780 (tt0) cc_final: 0.7382 (tt0) REVERT: G 349 THR cc_start: 0.8752 (p) cc_final: 0.8525 (p) REVERT: G 375 ASN cc_start: 0.7891 (m110) cc_final: 0.7686 (m110) REVERT: G 382 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8297 (mtm-85) REVERT: G 387 LYS cc_start: 0.8518 (tttt) cc_final: 0.8166 (ttmm) REVERT: G 396 GLU cc_start: 0.8009 (tp30) cc_final: 0.7790 (tp30) REVERT: G 426 ASN cc_start: 0.8428 (t0) cc_final: 0.8152 (t0) REVERT: G 473 GLU cc_start: 0.7835 (tp30) cc_final: 0.7609 (tp30) REVERT: G 475 ASP cc_start: 0.7597 (t70) cc_final: 0.7262 (t70) REVERT: G 511 ASP cc_start: 0.7882 (t0) cc_final: 0.7654 (t0) REVERT: G 549 GLN cc_start: 0.8272 (tp-100) cc_final: 0.7837 (tp40) REVERT: G 558 GLN cc_start: 0.8512 (tt0) cc_final: 0.8283 (tt0) REVERT: I 40 ILE cc_start: 0.8578 (mt) cc_final: 0.8360 (mp) REVERT: I 88 ASP cc_start: 0.8070 (t0) cc_final: 0.7834 (t0) REVERT: I 151 LYS cc_start: 0.8381 (mtpp) cc_final: 0.8095 (mttp) REVERT: I 183 MET cc_start: 0.8311 (mmm) cc_final: 0.8057 (mmm) REVERT: I 193 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7642 (mt-10) REVERT: I 303 PHE cc_start: 0.8380 (m-80) cc_final: 0.8011 (m-10) REVERT: I 312 LYS cc_start: 0.8642 (mttt) cc_final: 0.8353 (mttt) REVERT: I 339 SER cc_start: 0.8446 (m) cc_final: 0.7995 (p) REVERT: I 387 LYS cc_start: 0.8523 (mmmm) cc_final: 0.8173 (mmmm) REVERT: I 439 LYS cc_start: 0.3828 (mmmt) cc_final: 0.2688 (mmmt) REVERT: I 501 LYS cc_start: 0.8700 (tttt) cc_final: 0.8414 (tttm) REVERT: I 518 MET cc_start: 0.6846 (ptp) cc_final: 0.6409 (ptp) outliers start: 80 outliers final: 43 residues processed: 1190 average time/residue: 1.3414 time to fit residues: 1919.0471 Evaluate side-chains 1152 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 1108 time to evaluate : 3.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 383 GLN Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 583 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 555 VAL Chi-restraints excluded: chain I residue 569 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 286 optimal weight: 2.9990 chunk 280 optimal weight: 10.0000 chunk 378 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 410 optimal weight: 0.0020 chunk 195 optimal weight: 5.9990 chunk 189 optimal weight: 0.0000 chunk 277 optimal weight: 6.9990 chunk 5 optimal weight: 50.0000 chunk 65 optimal weight: 10.0000 chunk 383 optimal weight: 7.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 HIS A 404 GLN A 468 GLN A 554 ASN B 48 GLN B 383 GLN B 419 ASN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 GLN D 508 ASN E 47 ASN E 48 GLN E 95 ASN E 102 HIS E 137 HIS E 180 ASN E 181 ASN E 483 HIS E 497 GLN F 180 ASN F 222 HIS ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 ASN F 549 GLN G 47 ASN G 550 GLN G 577 GLN I 47 ASN I 72 ASN I 147 ASN I 234 HIS I 302 ASN I 318 GLN I 404 GLN I 416 GLN I 459 ASN ** I 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 549 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.123059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106961 restraints weight = 47517.123| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.14 r_work: 0.3218 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 33486 Z= 0.224 Angle : 0.590 16.110 45804 Z= 0.297 Chirality : 0.045 0.186 4980 Planarity : 0.005 0.048 6021 Dihedral : 5.820 87.823 4445 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.97 % Allowed : 15.34 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.42 (0.13), residues: 3895 helix: -0.27 (0.42), residues: 116 sheet: -0.11 (0.16), residues: 998 loop : -0.30 (0.11), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 545 HIS 0.011 0.001 HIS A 234 PHE 0.022 0.002 PHE F 45 TYR 0.024 0.002 TYR G 233 ARG 0.009 0.001 ARG F 314 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 386) hydrogen bonds : angle 6.07962 ( 702) SS BOND : bond 0.00420 ( 8) SS BOND : angle 1.29572 ( 16) covalent geometry : bond 0.00512 (33478) covalent geometry : angle 0.58957 (45788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1135 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 SER cc_start: 0.8538 (t) cc_final: 0.8324 (t) REVERT: A 47 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8215 (t0) REVERT: A 77 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7675 (mm-30) REVERT: A 87 MET cc_start: 0.7901 (ttm) cc_final: 0.7609 (ttm) REVERT: A 89 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8221 (ttmt) REVERT: A 131 ASN cc_start: 0.8447 (m-40) cc_final: 0.8049 (m-40) REVERT: A 144 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7638 (mt-10) REVERT: A 221 SER cc_start: 0.8842 (m) cc_final: 0.8602 (t) REVERT: A 239 ASP cc_start: 0.7956 (t0) cc_final: 0.7671 (t0) REVERT: A 296 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7777 (mm-40) REVERT: A 302 ASN cc_start: 0.7419 (m110) cc_final: 0.6953 (m110) REVERT: A 311 ASP cc_start: 0.7789 (p0) cc_final: 0.7562 (p0) REVERT: A 327 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 380 PHE cc_start: 0.8398 (p90) cc_final: 0.8169 (p90) REVERT: A 460 VAL cc_start: 0.8749 (m) cc_final: 0.8462 (p) REVERT: A 471 ASP cc_start: 0.7816 (t0) cc_final: 0.7588 (t0) REVERT: A 536 LYS cc_start: 0.8408 (ttpp) cc_final: 0.8146 (ttpp) REVERT: B 51 PHE cc_start: 0.8480 (m-80) cc_final: 0.8217 (m-80) REVERT: B 77 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7411 (tm-30) REVERT: B 87 MET cc_start: 0.8091 (ptm) cc_final: 0.7799 (ptm) REVERT: B 89 LYS cc_start: 0.8849 (tppp) cc_final: 0.8641 (tppp) REVERT: B 96 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8129 (ptp) REVERT: B 101 ILE cc_start: 0.8631 (mt) cc_final: 0.8246 (mt) REVERT: B 216 ARG cc_start: 0.8322 (ttt90) cc_final: 0.7921 (ttt90) REVERT: B 217 THR cc_start: 0.8214 (p) cc_final: 0.8001 (p) REVERT: B 221 SER cc_start: 0.8854 (p) cc_final: 0.8376 (p) REVERT: B 271 LYS cc_start: 0.8314 (ptmt) cc_final: 0.8008 (ptmt) REVERT: B 382 ARG cc_start: 0.8617 (mtm-85) cc_final: 0.8332 (mtm-85) REVERT: B 408 ARG cc_start: 0.5393 (mtm110) cc_final: 0.4615 (mtm180) REVERT: B 409 TYR cc_start: 0.8034 (t80) cc_final: 0.7662 (t80) REVERT: B 411 GLU cc_start: 0.8327 (tt0) cc_final: 0.7672 (tt0) REVERT: B 479 LYS cc_start: 0.8673 (mmtm) cc_final: 0.8154 (mmtm) REVERT: B 553 ILE cc_start: 0.6520 (mp) cc_final: 0.6011 (tt) REVERT: B 556 ASP cc_start: 0.8019 (m-30) cc_final: 0.7789 (m-30) REVERT: B 573 TYR cc_start: 0.8170 (p90) cc_final: 0.7786 (p90) REVERT: B 576 SER cc_start: 0.8477 (t) cc_final: 0.8015 (p) REVERT: B 582 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8061 (mtmm) REVERT: C 52 LYS cc_start: 0.8513 (ttpt) cc_final: 0.8079 (ttpt) REVERT: C 71 LEU cc_start: 0.8499 (tp) cc_final: 0.8177 (tm) REVERT: C 77 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7420 (tm-30) REVERT: C 89 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8371 (ttmt) REVERT: C 100 ASP cc_start: 0.7338 (m-30) cc_final: 0.7068 (m-30) REVERT: C 133 MET cc_start: 0.8254 (mmt) cc_final: 0.8003 (mmm) REVERT: C 155 GLU cc_start: 0.7397 (pp20) cc_final: 0.7082 (pp20) REVERT: C 186 THR cc_start: 0.8282 (m) cc_final: 0.8005 (p) REVERT: C 193 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7467 (mt-10) REVERT: C 204 ILE cc_start: 0.9038 (pt) cc_final: 0.8789 (pp) REVERT: C 209 ARG cc_start: 0.8468 (pmt170) cc_final: 0.8109 (pmt170) REVERT: C 271 LYS cc_start: 0.8120 (ptmt) cc_final: 0.7767 (ptmt) REVERT: C 344 SER cc_start: 0.8327 (t) cc_final: 0.8060 (t) REVERT: C 353 PHE cc_start: 0.8258 (p90) cc_final: 0.7973 (p90) REVERT: C 377 ARG cc_start: 0.8694 (ttt90) cc_final: 0.8430 (ttt180) REVERT: C 470 TRP cc_start: 0.8706 (p90) cc_final: 0.8294 (p90) REVERT: C 479 LYS cc_start: 0.8717 (mttm) cc_final: 0.8494 (mttm) REVERT: C 509 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7007 (mm-30) REVERT: C 511 ASP cc_start: 0.7799 (t0) cc_final: 0.7457 (t0) REVERT: C 550 GLN cc_start: 0.6353 (mm-40) cc_final: 0.5621 (tp40) REVERT: C 561 TYR cc_start: 0.8831 (m-80) cc_final: 0.8610 (m-80) REVERT: C 574 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7145 (mm-30) REVERT: D 51 PHE cc_start: 0.8313 (m-80) cc_final: 0.7880 (m-80) REVERT: D 77 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7370 (mm-30) REVERT: D 101 ILE cc_start: 0.8713 (mt) cc_final: 0.8449 (mp) REVERT: D 135 GLU cc_start: 0.8198 (pt0) cc_final: 0.7982 (pt0) REVERT: D 178 ASP cc_start: 0.7870 (t0) cc_final: 0.7420 (t0) REVERT: D 182 THR cc_start: 0.8200 (m) cc_final: 0.7997 (p) REVERT: D 260 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7433 (mt-10) REVERT: D 387 LYS cc_start: 0.8358 (tptm) cc_final: 0.8128 (tppp) REVERT: D 396 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7613 (mm-30) REVERT: D 400 TYR cc_start: 0.8636 (t80) cc_final: 0.8344 (t80) REVERT: D 501 LYS cc_start: 0.8454 (tttt) cc_final: 0.8244 (tttm) REVERT: D 511 ASP cc_start: 0.7970 (t0) cc_final: 0.7640 (t0) REVERT: D 513 ASP cc_start: 0.7979 (t0) cc_final: 0.7669 (t0) REVERT: D 581 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8182 (ttp80) REVERT: E 42 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7804 (p) REVERT: E 60 GLU cc_start: 0.7698 (tt0) cc_final: 0.7479 (tt0) REVERT: E 77 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7618 (mm-30) REVERT: E 101 ILE cc_start: 0.8512 (mt) cc_final: 0.8196 (mt) REVERT: E 125 ASP cc_start: 0.7798 (m-30) cc_final: 0.7591 (m-30) REVERT: E 135 GLU cc_start: 0.8107 (pt0) cc_final: 0.7832 (pt0) REVERT: E 149 VAL cc_start: 0.8854 (t) cc_final: 0.8337 (p) REVERT: E 179 SER cc_start: 0.8494 (p) cc_final: 0.8255 (p) REVERT: E 193 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7480 (mt-10) REVERT: E 266 PHE cc_start: 0.8305 (t80) cc_final: 0.7854 (t80) REVERT: E 296 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8190 (mm-40) REVERT: E 303 PHE cc_start: 0.8388 (m-10) cc_final: 0.8187 (m-10) REVERT: E 305 ASP cc_start: 0.8398 (m-30) cc_final: 0.5879 (m-30) REVERT: E 314 ARG cc_start: 0.8504 (mtt90) cc_final: 0.7228 (mtt-85) REVERT: E 325 ILE cc_start: 0.8695 (mt) cc_final: 0.8412 (mp) REVERT: E 342 TYR cc_start: 0.8009 (p90) cc_final: 0.7663 (p90) REVERT: E 411 GLU cc_start: 0.8021 (mp0) cc_final: 0.7537 (mp0) REVERT: E 426 ASN cc_start: 0.8127 (t0) cc_final: 0.7654 (t0) REVERT: E 460 VAL cc_start: 0.8560 (p) cc_final: 0.8347 (m) REVERT: E 557 ASN cc_start: 0.8510 (p0) cc_final: 0.7990 (p0) REVERT: E 570 LYS cc_start: 0.8791 (ptmt) cc_final: 0.8566 (ptmm) REVERT: F 40 ILE cc_start: 0.8508 (mt) cc_final: 0.8134 (tp) REVERT: F 42 THR cc_start: 0.8259 (p) cc_final: 0.7656 (t) REVERT: F 77 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7660 (mm-30) REVERT: F 89 LYS cc_start: 0.8387 (tppt) cc_final: 0.7949 (tppt) REVERT: F 163 LYS cc_start: 0.8243 (mttt) cc_final: 0.7981 (mttt) REVERT: F 173 LEU cc_start: 0.8574 (tp) cc_final: 0.8293 (tt) REVERT: F 185 PHE cc_start: 0.8544 (t80) cc_final: 0.8288 (t80) REVERT: F 192 SER cc_start: 0.8352 (t) cc_final: 0.7890 (p) REVERT: F 213 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7898 (tm-30) REVERT: F 215 ASP cc_start: 0.7845 (m-30) cc_final: 0.7449 (m-30) REVERT: F 222 HIS cc_start: 0.8733 (p90) cc_final: 0.8301 (p-80) REVERT: F 239 ASP cc_start: 0.8003 (m-30) cc_final: 0.7696 (m-30) REVERT: F 244 TYR cc_start: 0.8548 (m-80) cc_final: 0.8319 (m-80) REVERT: F 265 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8128 (p) REVERT: F 297 SER cc_start: 0.8496 (m) cc_final: 0.8188 (p) REVERT: F 411 GLU cc_start: 0.7881 (mp0) cc_final: 0.7593 (mp0) REVERT: F 472 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8173 (ttpp) REVERT: F 475 ASP cc_start: 0.7847 (t70) cc_final: 0.7501 (t70) REVERT: F 479 LYS cc_start: 0.8582 (mttm) cc_final: 0.8364 (mttm) REVERT: F 570 LYS cc_start: 0.8792 (ptpt) cc_final: 0.8428 (ptmm) REVERT: G 49 THR cc_start: 0.8436 (m) cc_final: 0.8064 (p) REVERT: G 77 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7438 (mm-30) REVERT: G 87 MET cc_start: 0.7452 (ptm) cc_final: 0.7098 (ptm) REVERT: G 89 LYS cc_start: 0.8621 (tttt) cc_final: 0.8349 (ttmm) REVERT: G 90 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8519 (t) REVERT: G 101 ILE cc_start: 0.8225 (mt) cc_final: 0.7542 (mt) REVERT: G 115 ASN cc_start: 0.8378 (t0) cc_final: 0.8080 (t0) REVERT: G 151 LYS cc_start: 0.8580 (mttm) cc_final: 0.8376 (mttm) REVERT: G 204 ILE cc_start: 0.8878 (pt) cc_final: 0.8661 (pp) REVERT: G 216 ARG cc_start: 0.8073 (tmt-80) cc_final: 0.7472 (tmt90) REVERT: G 275 LEU cc_start: 0.8449 (mt) cc_final: 0.8245 (mp) REVERT: G 335 GLU cc_start: 0.7812 (tt0) cc_final: 0.7365 (tt0) REVERT: G 375 ASN cc_start: 0.7878 (m110) cc_final: 0.7561 (m110) REVERT: G 387 LYS cc_start: 0.8452 (tttt) cc_final: 0.8102 (ttmm) REVERT: G 396 GLU cc_start: 0.8025 (tp30) cc_final: 0.7806 (tp30) REVERT: G 426 ASN cc_start: 0.8532 (t0) cc_final: 0.8251 (t0) REVERT: G 473 GLU cc_start: 0.7841 (tp30) cc_final: 0.7559 (tp30) REVERT: G 475 ASP cc_start: 0.7736 (t70) cc_final: 0.7037 (t70) REVERT: G 511 ASP cc_start: 0.8011 (t0) cc_final: 0.7779 (t0) REVERT: G 513 ASP cc_start: 0.7605 (m-30) cc_final: 0.7325 (m-30) REVERT: G 524 TYR cc_start: 0.8772 (p90) cc_final: 0.8568 (p90) REVERT: G 532 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8486 (ttpp) REVERT: G 549 GLN cc_start: 0.8310 (tp-100) cc_final: 0.7837 (tp40) REVERT: I 40 ILE cc_start: 0.8606 (mt) cc_final: 0.8386 (mp) REVERT: I 41 SER cc_start: 0.8465 (t) cc_final: 0.8151 (p) REVERT: I 88 ASP cc_start: 0.8078 (t0) cc_final: 0.7853 (t0) REVERT: I 163 LYS cc_start: 0.8110 (mttp) cc_final: 0.7845 (mttp) REVERT: I 183 MET cc_start: 0.8358 (mmm) cc_final: 0.8069 (mmm) REVERT: I 193 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7568 (mt-10) REVERT: I 303 PHE cc_start: 0.8382 (m-80) cc_final: 0.8030 (m-10) REVERT: I 312 LYS cc_start: 0.8629 (mttt) cc_final: 0.8382 (mttt) REVERT: I 375 ASN cc_start: 0.7702 (m110) cc_final: 0.7403 (m110) REVERT: I 387 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8348 (mtpp) REVERT: I 475 ASP cc_start: 0.8091 (m-30) cc_final: 0.7841 (t0) REVERT: I 501 LYS cc_start: 0.8758 (tttt) cc_final: 0.8462 (tttm) REVERT: I 518 MET cc_start: 0.6883 (ptp) cc_final: 0.6449 (ptp) REVERT: I 546 ASN cc_start: 0.8313 (p0) cc_final: 0.8019 (p0) outliers start: 103 outliers final: 59 residues processed: 1173 average time/residue: 1.3383 time to fit residues: 1881.7296 Evaluate side-chains 1155 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 1090 time to evaluate : 3.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 271 LYS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 569 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 365 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 391 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 306 optimal weight: 6.9990 chunk 213 optimal weight: 8.9990 chunk 281 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 333 optimal weight: 3.9990 chunk 339 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 280 GLN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 HIS A 446 ASN A 468 GLN A 554 ASN B 48 GLN B 166 ASN B 181 ASN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN B 565 ASN C 47 ASN C 70 HIS C 181 ASN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 HIS C 383 GLN D 47 ASN D 350 GLN D 383 GLN D 459 ASN D 508 ASN E 47 ASN E 95 ASN E 102 HIS E 137 HIS E 180 ASN E 383 GLN E 417 ASN E 419 ASN E 483 HIS E 497 GLN F 180 ASN F 505 ASN G 47 ASN G 166 ASN G 577 GLN I 47 ASN I 72 ASN ** I 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 234 HIS I 302 ASN I 310 GLN ** I 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 404 GLN I 459 ASN ** I 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 549 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105064 restraints weight = 47381.460| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.13 r_work: 0.3192 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 33486 Z= 0.365 Angle : 0.647 16.583 45804 Z= 0.328 Chirality : 0.048 0.187 4980 Planarity : 0.005 0.055 6021 Dihedral : 5.958 88.611 4445 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.86 % Allowed : 16.69 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.65 (0.13), residues: 3895 helix: -0.23 (0.43), residues: 116 sheet: -0.30 (0.16), residues: 998 loop : -0.47 (0.11), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 545 HIS 0.013 0.001 HIS B 234 PHE 0.032 0.002 PHE I 266 TYR 0.026 0.002 TYR B 524 ARG 0.012 0.001 ARG C 382 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 386) hydrogen bonds : angle 6.10508 ( 702) SS BOND : bond 0.00582 ( 8) SS BOND : angle 1.36226 ( 16) covalent geometry : bond 0.00830 (33478) covalent geometry : angle 0.64664 (45788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1138 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8227 (t0) REVERT: A 77 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7701 (mm-30) REVERT: A 87 MET cc_start: 0.7776 (ttm) cc_final: 0.7538 (ttm) REVERT: A 131 ASN cc_start: 0.8470 (m-40) cc_final: 0.8006 (m-40) REVERT: A 140 SER cc_start: 0.8725 (p) cc_final: 0.8339 (t) REVERT: A 144 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7667 (mt-10) REVERT: A 174 MET cc_start: 0.8592 (mtm) cc_final: 0.8368 (mtm) REVERT: A 239 ASP cc_start: 0.7988 (t0) cc_final: 0.7705 (t0) REVERT: A 296 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7713 (mm-40) REVERT: A 302 ASN cc_start: 0.7443 (m110) cc_final: 0.6876 (m110) REVERT: A 327 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7687 (mm-30) REVERT: A 344 SER cc_start: 0.8977 (t) cc_final: 0.8742 (p) REVERT: A 380 PHE cc_start: 0.8409 (p90) cc_final: 0.8202 (p90) REVERT: A 460 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8511 (p) REVERT: A 471 ASP cc_start: 0.7861 (t0) cc_final: 0.7493 (t0) REVERT: A 530 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8382 (ttmt) REVERT: A 536 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8218 (ttpp) REVERT: B 51 PHE cc_start: 0.8503 (m-80) cc_final: 0.8277 (m-80) REVERT: B 77 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7296 (tm-30) REVERT: B 87 MET cc_start: 0.8094 (ptm) cc_final: 0.7794 (ptm) REVERT: B 101 ILE cc_start: 0.8639 (mt) cc_final: 0.8221 (mt) REVERT: B 166 ASN cc_start: 0.8231 (m-40) cc_final: 0.7928 (m-40) REVERT: B 178 ASP cc_start: 0.7614 (t0) cc_final: 0.7393 (t0) REVERT: B 216 ARG cc_start: 0.8341 (ttt90) cc_final: 0.7876 (ttt90) REVERT: B 219 ILE cc_start: 0.8768 (mt) cc_final: 0.8550 (mm) REVERT: B 221 SER cc_start: 0.8792 (p) cc_final: 0.8532 (p) REVERT: B 271 LYS cc_start: 0.8306 (ptmt) cc_final: 0.7991 (ptmt) REVERT: B 408 ARG cc_start: 0.5430 (mtm180) cc_final: 0.4682 (mtm180) REVERT: B 409 TYR cc_start: 0.8074 (t80) cc_final: 0.7729 (t80) REVERT: B 411 GLU cc_start: 0.8362 (tt0) cc_final: 0.7722 (tt0) REVERT: B 479 LYS cc_start: 0.8681 (mmtm) cc_final: 0.8143 (mmtm) REVERT: B 553 ILE cc_start: 0.6401 (mp) cc_final: 0.5916 (tt) REVERT: B 556 ASP cc_start: 0.8022 (m-30) cc_final: 0.7773 (m-30) REVERT: B 573 TYR cc_start: 0.8136 (p90) cc_final: 0.7757 (p90) REVERT: B 576 SER cc_start: 0.8450 (t) cc_final: 0.8005 (p) REVERT: B 582 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8025 (mtmm) REVERT: C 52 LYS cc_start: 0.8444 (ttpt) cc_final: 0.7958 (ttpt) REVERT: C 71 LEU cc_start: 0.8480 (tp) cc_final: 0.8166 (tm) REVERT: C 77 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7350 (tm-30) REVERT: C 130 VAL cc_start: 0.8347 (t) cc_final: 0.8096 (m) REVERT: C 133 MET cc_start: 0.8233 (mmt) cc_final: 0.7748 (mmm) REVERT: C 155 GLU cc_start: 0.7644 (pp20) cc_final: 0.7270 (pp20) REVERT: C 186 THR cc_start: 0.8255 (m) cc_final: 0.8007 (p) REVERT: C 193 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7444 (mt-10) REVERT: C 204 ILE cc_start: 0.9046 (pt) cc_final: 0.8779 (pp) REVERT: C 260 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7405 (mt-10) REVERT: C 271 LYS cc_start: 0.8201 (ptmt) cc_final: 0.7839 (ptmt) REVERT: C 344 SER cc_start: 0.8366 (t) cc_final: 0.8122 (t) REVERT: C 377 ARG cc_start: 0.8661 (ttt90) cc_final: 0.8414 (ttt-90) REVERT: C 404 GLN cc_start: 0.7914 (pp30) cc_final: 0.7483 (pp30) REVERT: C 470 TRP cc_start: 0.8712 (p90) cc_final: 0.8279 (p90) REVERT: C 509 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7116 (mm-30) REVERT: C 511 ASP cc_start: 0.7841 (t0) cc_final: 0.7487 (t0) REVERT: C 520 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8499 (mtm110) REVERT: C 550 GLN cc_start: 0.5675 (mm-40) cc_final: 0.5068 (tp40) REVERT: C 574 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7185 (mm-30) REVERT: D 51 PHE cc_start: 0.8349 (m-80) cc_final: 0.7882 (m-80) REVERT: D 101 ILE cc_start: 0.8694 (mt) cc_final: 0.8442 (mp) REVERT: D 178 ASP cc_start: 0.7928 (t0) cc_final: 0.7477 (t0) REVERT: D 257 THR cc_start: 0.8022 (t) cc_final: 0.7603 (m) REVERT: D 396 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7615 (tm-30) REVERT: D 400 TYR cc_start: 0.8696 (t80) cc_final: 0.8335 (t80) REVERT: D 511 ASP cc_start: 0.7980 (t0) cc_final: 0.7636 (t0) REVERT: D 513 ASP cc_start: 0.7959 (t0) cc_final: 0.7723 (t0) REVERT: D 558 GLN cc_start: 0.8449 (tt0) cc_final: 0.8242 (pt0) REVERT: D 581 ARG cc_start: 0.8480 (ttp80) cc_final: 0.8201 (ttp80) REVERT: D 583 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7710 (mt) REVERT: E 42 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.8037 (m) REVERT: E 60 GLU cc_start: 0.7730 (tt0) cc_final: 0.7525 (tt0) REVERT: E 77 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7626 (mm-30) REVERT: E 101 ILE cc_start: 0.8534 (mt) cc_final: 0.8231 (mt) REVERT: E 135 GLU cc_start: 0.8129 (pt0) cc_final: 0.7868 (pt0) REVERT: E 149 VAL cc_start: 0.8899 (t) cc_final: 0.8407 (p) REVERT: E 179 SER cc_start: 0.8542 (p) cc_final: 0.8319 (p) REVERT: E 193 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7495 (mt-10) REVERT: E 255 LEU cc_start: 0.8371 (mp) cc_final: 0.8105 (mm) REVERT: E 266 PHE cc_start: 0.8372 (t80) cc_final: 0.7919 (t80) REVERT: E 296 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8179 (mm-40) REVERT: E 305 ASP cc_start: 0.8427 (m-30) cc_final: 0.5872 (m-30) REVERT: E 312 LYS cc_start: 0.5665 (tttp) cc_final: 0.4833 (tptp) REVERT: E 314 ARG cc_start: 0.8502 (mtt90) cc_final: 0.7245 (mtt-85) REVERT: E 325 ILE cc_start: 0.8720 (mt) cc_final: 0.8396 (mp) REVERT: E 411 GLU cc_start: 0.7960 (mp0) cc_final: 0.7492 (mp0) REVERT: E 460 VAL cc_start: 0.8561 (p) cc_final: 0.8358 (m) REVERT: E 549 GLN cc_start: 0.8319 (tp40) cc_final: 0.8075 (tt0) REVERT: F 40 ILE cc_start: 0.8498 (mt) cc_final: 0.8085 (tp) REVERT: F 77 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7600 (mm-30) REVERT: F 89 LYS cc_start: 0.8397 (tppt) cc_final: 0.8015 (tppt) REVERT: F 163 LYS cc_start: 0.8248 (mttt) cc_final: 0.7980 (mttt) REVERT: F 173 LEU cc_start: 0.8697 (tp) cc_final: 0.8416 (tt) REVERT: F 185 PHE cc_start: 0.8568 (t80) cc_final: 0.8310 (t80) REVERT: F 215 ASP cc_start: 0.7863 (m-30) cc_final: 0.7571 (m-30) REVERT: F 222 HIS cc_start: 0.8835 (p90) cc_final: 0.8252 (p-80) REVERT: F 239 ASP cc_start: 0.8092 (m-30) cc_final: 0.7791 (m-30) REVERT: F 244 TYR cc_start: 0.8553 (m-80) cc_final: 0.8317 (m-80) REVERT: F 265 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8247 (p) REVERT: F 293 SER cc_start: 0.8427 (t) cc_final: 0.8059 (p) REVERT: F 297 SER cc_start: 0.8412 (m) cc_final: 0.8083 (p) REVERT: F 411 GLU cc_start: 0.7864 (mp0) cc_final: 0.7575 (mp0) REVERT: F 472 LYS cc_start: 0.8618 (ttpp) cc_final: 0.8201 (ttpp) REVERT: F 566 ILE cc_start: 0.9183 (pt) cc_final: 0.8935 (OUTLIER) REVERT: F 570 LYS cc_start: 0.8805 (ptpt) cc_final: 0.8435 (ptmm) REVERT: G 49 THR cc_start: 0.8448 (m) cc_final: 0.8070 (p) REVERT: G 87 MET cc_start: 0.7466 (ptm) cc_final: 0.7167 (ptm) REVERT: G 89 LYS cc_start: 0.8678 (tttt) cc_final: 0.8368 (ttmm) REVERT: G 115 ASN cc_start: 0.8343 (t0) cc_final: 0.8136 (t160) REVERT: G 177 LEU cc_start: 0.8542 (tm) cc_final: 0.8331 (tm) REVERT: G 204 ILE cc_start: 0.8908 (pt) cc_final: 0.8689 (pp) REVERT: G 215 ASP cc_start: 0.7741 (m-30) cc_final: 0.7541 (t0) REVERT: G 335 GLU cc_start: 0.7828 (tt0) cc_final: 0.7411 (tt0) REVERT: G 349 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8504 (p) REVERT: G 375 ASN cc_start: 0.7885 (m110) cc_final: 0.7589 (m110) REVERT: G 396 GLU cc_start: 0.8037 (tp30) cc_final: 0.7803 (tp30) REVERT: G 401 ILE cc_start: 0.8535 (mm) cc_final: 0.8275 (mp) REVERT: G 426 ASN cc_start: 0.8621 (t0) cc_final: 0.8380 (t0) REVERT: G 473 GLU cc_start: 0.7865 (tp30) cc_final: 0.7595 (tp30) REVERT: G 475 ASP cc_start: 0.7726 (t70) cc_final: 0.7247 (t70) REVERT: G 511 ASP cc_start: 0.7986 (t0) cc_final: 0.7715 (t0) REVERT: G 524 TYR cc_start: 0.8783 (p90) cc_final: 0.8538 (p90) REVERT: G 530 LYS cc_start: 0.8905 (ttpt) cc_final: 0.8703 (ttpt) REVERT: G 532 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8505 (ttpp) REVERT: G 536 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7934 (ttpp) REVERT: G 549 GLN cc_start: 0.8332 (tp40) cc_final: 0.7887 (tp40) REVERT: I 40 ILE cc_start: 0.8630 (mt) cc_final: 0.8383 (mp) REVERT: I 41 SER cc_start: 0.8488 (t) cc_final: 0.8128 (p) REVERT: I 88 ASP cc_start: 0.8069 (t0) cc_final: 0.7842 (t0) REVERT: I 89 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8270 (ttmt) REVERT: I 96 MET cc_start: 0.7931 (mpp) cc_final: 0.6548 (ppp) REVERT: I 163 LYS cc_start: 0.8117 (mttp) cc_final: 0.7909 (mttp) REVERT: I 193 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7560 (mt-10) REVERT: I 303 PHE cc_start: 0.8421 (m-80) cc_final: 0.8083 (m-10) REVERT: I 312 LYS cc_start: 0.8671 (mttt) cc_final: 0.8458 (mttt) REVERT: I 380 PHE cc_start: 0.8571 (p90) cc_final: 0.8367 (p90) REVERT: I 387 LYS cc_start: 0.8785 (mmmm) cc_final: 0.8506 (mtpp) REVERT: I 439 LYS cc_start: 0.4627 (mmtt) cc_final: 0.2942 (mmmt) REVERT: I 501 LYS cc_start: 0.8832 (tttt) cc_final: 0.8618 (tttm) REVERT: I 518 MET cc_start: 0.6990 (ptp) cc_final: 0.6573 (ptp) REVERT: I 546 ASN cc_start: 0.8413 (p0) cc_final: 0.8161 (p0) outliers start: 134 outliers final: 87 residues processed: 1185 average time/residue: 1.3356 time to fit residues: 1900.8707 Evaluate side-chains 1187 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 1093 time to evaluate : 3.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 448 PHE Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 577 GLN Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 553 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 263 optimal weight: 1.9990 chunk 368 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 291 optimal weight: 0.9980 chunk 344 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 15 optimal weight: 50.0000 chunk 402 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 388 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 HIS A 468 GLN A 558 GLN B 48 GLN B 95 ASN B 147 ASN B 383 GLN B 404 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN B 558 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN C 248 ASN C 383 GLN D 47 ASN D 72 ASN D 167 ASN D 350 GLN D 383 GLN D 508 ASN E 47 ASN E 95 ASN E 102 HIS E 137 HIS E 180 ASN E 483 HIS E 497 GLN F 180 ASN F 350 GLN F 505 ASN F 554 ASN G 47 ASN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 419 ASN I 72 ASN I 147 ASN I 234 HIS I 302 ASN I 310 GLN I 404 GLN I 459 ASN ** I 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 549 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.107384 restraints weight = 46968.205| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.14 r_work: 0.3233 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33486 Z= 0.123 Angle : 0.547 15.833 45804 Z= 0.273 Chirality : 0.042 0.185 4980 Planarity : 0.004 0.050 6021 Dihedral : 5.494 87.861 4445 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.17 % Allowed : 19.20 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 3895 helix: -0.11 (0.42), residues: 116 sheet: -0.20 (0.16), residues: 979 loop : -0.31 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 414 HIS 0.007 0.001 HIS B 234 PHE 0.019 0.001 PHE I 266 TYR 0.021 0.001 TYR B 524 ARG 0.010 0.001 ARG G 408 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 386) hydrogen bonds : angle 5.91718 ( 702) SS BOND : bond 0.00422 ( 8) SS BOND : angle 1.01491 ( 16) covalent geometry : bond 0.00281 (33478) covalent geometry : angle 0.54687 (45788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1122 time to evaluate : 3.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8234 (t0) REVERT: A 77 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7556 (mm-30) REVERT: A 87 MET cc_start: 0.7781 (ttm) cc_final: 0.7533 (ttm) REVERT: A 131 ASN cc_start: 0.8458 (m-40) cc_final: 0.8100 (m-40) REVERT: A 144 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7570 (mt-10) REVERT: A 221 SER cc_start: 0.8877 (m) cc_final: 0.8551 (t) REVERT: A 239 ASP cc_start: 0.7941 (t0) cc_final: 0.7627 (t0) REVERT: A 296 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7721 (mm-40) REVERT: A 302 ASN cc_start: 0.7460 (m110) cc_final: 0.6924 (m110) REVERT: A 327 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7617 (mm-30) REVERT: A 460 VAL cc_start: 0.8820 (m) cc_final: 0.8523 (p) REVERT: A 471 ASP cc_start: 0.7875 (t0) cc_final: 0.7636 (t0) REVERT: B 51 PHE cc_start: 0.8448 (m-80) cc_final: 0.8139 (m-80) REVERT: B 53 PHE cc_start: 0.8603 (m-80) cc_final: 0.8312 (m-80) REVERT: B 77 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7179 (tm-30) REVERT: B 87 MET cc_start: 0.8111 (ptm) cc_final: 0.7818 (ptm) REVERT: B 96 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8147 (ptp) REVERT: B 101 ILE cc_start: 0.8572 (mt) cc_final: 0.8094 (mt) REVERT: B 135 GLU cc_start: 0.8259 (pt0) cc_final: 0.7991 (pt0) REVERT: B 154 SER cc_start: 0.8742 (m) cc_final: 0.8205 (t) REVERT: B 166 ASN cc_start: 0.8191 (m-40) cc_final: 0.7903 (m-40) REVERT: B 178 ASP cc_start: 0.7633 (t0) cc_final: 0.7376 (t0) REVERT: B 216 ARG cc_start: 0.8286 (ttt90) cc_final: 0.7778 (ttt90) REVERT: B 221 SER cc_start: 0.8729 (p) cc_final: 0.8214 (p) REVERT: B 271 LYS cc_start: 0.8311 (ptmt) cc_final: 0.8008 (ptmt) REVERT: B 405 ASP cc_start: 0.6710 (m-30) cc_final: 0.6494 (m-30) REVERT: B 408 ARG cc_start: 0.5327 (mtm180) cc_final: 0.4509 (mtm180) REVERT: B 409 TYR cc_start: 0.8000 (t80) cc_final: 0.7650 (t80) REVERT: B 411 GLU cc_start: 0.8372 (tt0) cc_final: 0.7745 (tt0) REVERT: B 439 LYS cc_start: 0.8536 (mmtm) cc_final: 0.8202 (mmtt) REVERT: B 479 LYS cc_start: 0.8678 (mmtm) cc_final: 0.8132 (mmtm) REVERT: B 553 ILE cc_start: 0.6442 (mp) cc_final: 0.5932 (tt) REVERT: B 554 ASN cc_start: 0.8051 (p0) cc_final: 0.7813 (p0) REVERT: B 556 ASP cc_start: 0.7975 (m-30) cc_final: 0.7661 (m-30) REVERT: B 576 SER cc_start: 0.8427 (t) cc_final: 0.7975 (p) REVERT: C 52 LYS cc_start: 0.8344 (ttpt) cc_final: 0.7865 (ttpt) REVERT: C 71 LEU cc_start: 0.8476 (tp) cc_final: 0.8131 (tm) REVERT: C 77 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7305 (tm-30) REVERT: C 130 VAL cc_start: 0.8255 (t) cc_final: 0.8006 (m) REVERT: C 133 MET cc_start: 0.8120 (mmt) cc_final: 0.7544 (mmm) REVERT: C 155 GLU cc_start: 0.7594 (pp20) cc_final: 0.7203 (pp20) REVERT: C 168 ASP cc_start: 0.7043 (t0) cc_final: 0.6550 (t0) REVERT: C 186 THR cc_start: 0.8222 (m) cc_final: 0.8015 (p) REVERT: C 193 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7463 (mt-10) REVERT: C 204 ILE cc_start: 0.9025 (pt) cc_final: 0.8780 (pp) REVERT: C 209 ARG cc_start: 0.8414 (pmt170) cc_final: 0.8067 (pmt170) REVERT: C 260 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7374 (mt-10) REVERT: C 344 SER cc_start: 0.8318 (t) cc_final: 0.8090 (t) REVERT: C 377 ARG cc_start: 0.8643 (ttt90) cc_final: 0.8389 (ttt-90) REVERT: C 397 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7410 (mtm-85) REVERT: C 404 GLN cc_start: 0.7825 (pp30) cc_final: 0.7395 (pp30) REVERT: C 470 TRP cc_start: 0.8666 (p90) cc_final: 0.8317 (p90) REVERT: C 509 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7050 (mm-30) REVERT: C 511 ASP cc_start: 0.7800 (t0) cc_final: 0.7462 (t0) REVERT: C 550 GLN cc_start: 0.5515 (mm-40) cc_final: 0.4991 (tp40) REVERT: C 569 MET cc_start: 0.8177 (tpp) cc_final: 0.7967 (ttp) REVERT: D 51 PHE cc_start: 0.8344 (m-80) cc_final: 0.7903 (m-80) REVERT: D 101 ILE cc_start: 0.8633 (mt) cc_final: 0.8359 (mp) REVERT: D 178 ASP cc_start: 0.7924 (t0) cc_final: 0.7449 (t0) REVERT: D 232 ILE cc_start: 0.8583 (pt) cc_final: 0.8357 (pp) REVERT: D 257 THR cc_start: 0.7644 (t) cc_final: 0.7236 (m) REVERT: D 345 PHE cc_start: 0.8473 (m-80) cc_final: 0.7917 (m-80) REVERT: D 387 LYS cc_start: 0.8347 (tptm) cc_final: 0.7918 (tppp) REVERT: D 396 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7600 (mm-30) REVERT: D 400 TYR cc_start: 0.8652 (t80) cc_final: 0.8348 (t80) REVERT: D 511 ASP cc_start: 0.7883 (t0) cc_final: 0.7529 (t0) REVERT: D 513 ASP cc_start: 0.7961 (t0) cc_final: 0.7602 (t0) REVERT: D 570 LYS cc_start: 0.8642 (ptmt) cc_final: 0.8404 (ptmt) REVERT: D 581 ARG cc_start: 0.8433 (ttp80) cc_final: 0.8158 (ttp80) REVERT: D 583 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7753 (mt) REVERT: E 42 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7867 (m) REVERT: E 60 GLU cc_start: 0.7692 (tt0) cc_final: 0.7485 (tt0) REVERT: E 77 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7578 (mm-30) REVERT: E 96 MET cc_start: 0.8069 (pmm) cc_final: 0.6467 (ptt) REVERT: E 101 ILE cc_start: 0.8500 (mt) cc_final: 0.8103 (mt) REVERT: E 135 GLU cc_start: 0.8052 (pt0) cc_final: 0.7795 (pt0) REVERT: E 149 VAL cc_start: 0.8907 (t) cc_final: 0.8460 (p) REVERT: E 179 SER cc_start: 0.8515 (p) cc_final: 0.8271 (p) REVERT: E 193 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7447 (mt-10) REVERT: E 255 LEU cc_start: 0.8245 (mp) cc_final: 0.7963 (mm) REVERT: E 296 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8179 (mm-40) REVERT: E 305 ASP cc_start: 0.8419 (m-30) cc_final: 0.5854 (m-30) REVERT: E 314 ARG cc_start: 0.8512 (mtt90) cc_final: 0.7365 (mtp180) REVERT: E 325 ILE cc_start: 0.8646 (mt) cc_final: 0.8324 (mp) REVERT: E 342 TYR cc_start: 0.7897 (p90) cc_final: 0.7632 (p90) REVERT: E 411 GLU cc_start: 0.8003 (mp0) cc_final: 0.7526 (mp0) REVERT: E 426 ASN cc_start: 0.8119 (t0) cc_final: 0.7663 (t0) REVERT: E 549 GLN cc_start: 0.8320 (tp40) cc_final: 0.8046 (tt0) REVERT: F 40 ILE cc_start: 0.8426 (mt) cc_final: 0.8014 (tp) REVERT: F 77 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7584 (mm-30) REVERT: F 89 LYS cc_start: 0.8427 (tppt) cc_final: 0.8047 (tppt) REVERT: F 163 LYS cc_start: 0.8251 (mttt) cc_final: 0.7991 (mttt) REVERT: F 173 LEU cc_start: 0.8545 (tp) cc_final: 0.8241 (tt) REVERT: F 192 SER cc_start: 0.8397 (t) cc_final: 0.7934 (p) REVERT: F 219 ILE cc_start: 0.8957 (mm) cc_final: 0.8757 (mp) REVERT: F 222 HIS cc_start: 0.8857 (p90) cc_final: 0.8237 (p-80) REVERT: F 239 ASP cc_start: 0.8041 (m-30) cc_final: 0.7656 (m-30) REVERT: F 244 TYR cc_start: 0.8541 (m-80) cc_final: 0.8313 (m-80) REVERT: F 249 SER cc_start: 0.8861 (OUTLIER) cc_final: 0.8439 (t) REVERT: F 265 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8171 (p) REVERT: F 293 SER cc_start: 0.8382 (t) cc_final: 0.8035 (p) REVERT: F 297 SER cc_start: 0.8452 (m) cc_final: 0.8126 (p) REVERT: F 411 GLU cc_start: 0.7850 (mp0) cc_final: 0.7557 (mp0) REVERT: F 472 LYS cc_start: 0.8524 (ttpp) cc_final: 0.8248 (ttpp) REVERT: F 566 ILE cc_start: 0.9164 (pt) cc_final: 0.8911 (pp) REVERT: F 570 LYS cc_start: 0.8829 (ptpt) cc_final: 0.8462 (ptmm) REVERT: G 49 THR cc_start: 0.8444 (m) cc_final: 0.8050 (p) REVERT: G 87 MET cc_start: 0.7409 (ptm) cc_final: 0.7093 (ptm) REVERT: G 89 LYS cc_start: 0.8671 (tttt) cc_final: 0.8336 (ttmm) REVERT: G 115 ASN cc_start: 0.8332 (t0) cc_final: 0.8111 (t160) REVERT: G 177 LEU cc_start: 0.8538 (tm) cc_final: 0.8296 (tm) REVERT: G 187 PRO cc_start: 0.8792 (Cg_endo) cc_final: 0.8442 (Cg_exo) REVERT: G 204 ILE cc_start: 0.8819 (pt) cc_final: 0.8604 (pp) REVERT: G 216 ARG cc_start: 0.8014 (tmt-80) cc_final: 0.7762 (tmt90) REVERT: G 335 GLU cc_start: 0.7783 (tt0) cc_final: 0.7376 (tt0) REVERT: G 375 ASN cc_start: 0.7933 (m110) cc_final: 0.7633 (m110) REVERT: G 393 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7824 (mt-10) REVERT: G 396 GLU cc_start: 0.8039 (tp30) cc_final: 0.7810 (tp30) REVERT: G 400 TYR cc_start: 0.8294 (t80) cc_final: 0.7904 (t80) REVERT: G 401 ILE cc_start: 0.8540 (mm) cc_final: 0.8274 (mp) REVERT: G 426 ASN cc_start: 0.8559 (t0) cc_final: 0.8291 (t0) REVERT: G 473 GLU cc_start: 0.7877 (tp30) cc_final: 0.7611 (tp30) REVERT: G 475 ASP cc_start: 0.7681 (t70) cc_final: 0.7195 (t70) REVERT: G 501 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8225 (tttm) REVERT: G 511 ASP cc_start: 0.7929 (t0) cc_final: 0.7691 (t0) REVERT: G 524 TYR cc_start: 0.8768 (p90) cc_final: 0.8493 (p90) REVERT: G 532 LYS cc_start: 0.8845 (ttmt) cc_final: 0.8494 (ttpp) REVERT: G 536 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7843 (ttpp) REVERT: G 549 GLN cc_start: 0.8323 (tp40) cc_final: 0.7913 (tp40) REVERT: I 40 ILE cc_start: 0.8604 (mt) cc_final: 0.8381 (mp) REVERT: I 41 SER cc_start: 0.8430 (t) cc_final: 0.8144 (p) REVERT: I 76 SER cc_start: 0.8379 (p) cc_final: 0.8147 (t) REVERT: I 88 ASP cc_start: 0.8095 (t0) cc_final: 0.7838 (t0) REVERT: I 96 MET cc_start: 0.8051 (mpp) cc_final: 0.6538 (ppp) REVERT: I 163 LYS cc_start: 0.8070 (mttp) cc_final: 0.7851 (mttp) REVERT: I 183 MET cc_start: 0.8270 (mmm) cc_final: 0.8022 (mmm) REVERT: I 193 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7576 (mt-10) REVERT: I 233 TYR cc_start: 0.8151 (t80) cc_final: 0.7561 (t80) REVERT: I 302 ASN cc_start: 0.8231 (m-40) cc_final: 0.7918 (m-40) REVERT: I 303 PHE cc_start: 0.8373 (m-80) cc_final: 0.8027 (m-10) REVERT: I 312 LYS cc_start: 0.8687 (mttt) cc_final: 0.8426 (mttt) REVERT: I 439 LYS cc_start: 0.4501 (mmtt) cc_final: 0.2773 (mmmt) REVERT: I 501 LYS cc_start: 0.8793 (tttt) cc_final: 0.8477 (tttm) REVERT: I 518 MET cc_start: 0.7002 (ptp) cc_final: 0.6581 (ptp) REVERT: I 546 ASN cc_start: 0.8386 (p0) cc_final: 0.8151 (p0) outliers start: 110 outliers final: 64 residues processed: 1152 average time/residue: 1.3244 time to fit residues: 1826.6556 Evaluate side-chains 1160 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1088 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 583 LEU Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 354 LYS Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 501 LYS Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 478 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 401 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 358 optimal weight: 0.0370 chunk 87 optimal weight: 6.9990 chunk 296 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 131 optimal weight: 0.0980 chunk 145 optimal weight: 6.9990 chunk 338 optimal weight: 7.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 403 HIS A 468 GLN B 48 GLN B 95 ASN B 280 GLN B 383 GLN B 404 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN C 47 ASN C 383 GLN C 459 ASN D 47 ASN D 350 GLN D 383 GLN E 47 ASN E 102 HIS E 137 HIS E 180 ASN E 483 HIS E 497 GLN E 558 GLN F 180 ASN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 ASN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 318 GLN G 383 GLN G 577 GLN I 72 ASN I 147 ASN I 310 GLN I 404 GLN I 459 ASN I 546 ASN I 549 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.124577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108560 restraints weight = 47088.025| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.14 r_work: 0.3241 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33486 Z= 0.114 Angle : 0.529 15.935 45804 Z= 0.262 Chirality : 0.042 0.183 4980 Planarity : 0.004 0.050 6021 Dihedral : 5.210 85.967 4445 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.23 % Allowed : 19.80 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.29 (0.13), residues: 3895 helix: -0.14 (0.43), residues: 111 sheet: -0.10 (0.17), residues: 920 loop : -0.19 (0.11), residues: 2864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 414 HIS 0.008 0.001 HIS B 70 PHE 0.019 0.001 PHE G 303 TYR 0.027 0.001 TYR A 444 ARG 0.011 0.001 ARG B 382 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 386) hydrogen bonds : angle 5.78513 ( 702) SS BOND : bond 0.00390 ( 8) SS BOND : angle 0.94387 ( 16) covalent geometry : bond 0.00262 (33478) covalent geometry : angle 0.52928 (45788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 1120 time to evaluate : 3.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8274 (t0) REVERT: A 77 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7640 (mm-30) REVERT: A 87 MET cc_start: 0.7878 (ttm) cc_final: 0.7649 (ttm) REVERT: A 98 LEU cc_start: 0.8567 (mt) cc_final: 0.8334 (mm) REVERT: A 144 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7521 (mt-10) REVERT: A 221 SER cc_start: 0.8896 (m) cc_final: 0.8555 (t) REVERT: A 239 ASP cc_start: 0.7927 (t0) cc_final: 0.7626 (t0) REVERT: A 296 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7710 (mm-40) REVERT: A 302 ASN cc_start: 0.7505 (m110) cc_final: 0.6978 (m110) REVERT: A 327 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7624 (mm-30) REVERT: A 339 SER cc_start: 0.8646 (m) cc_final: 0.8250 (p) REVERT: A 460 VAL cc_start: 0.8822 (m) cc_final: 0.8520 (p) REVERT: A 471 ASP cc_start: 0.7855 (t0) cc_final: 0.7651 (t0) REVERT: B 51 PHE cc_start: 0.8437 (m-80) cc_final: 0.8140 (m-80) REVERT: B 53 PHE cc_start: 0.8571 (m-80) cc_final: 0.8240 (m-80) REVERT: B 77 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7164 (tm-30) REVERT: B 87 MET cc_start: 0.8072 (ptm) cc_final: 0.7782 (ptm) REVERT: B 101 ILE cc_start: 0.8501 (mt) cc_final: 0.8088 (mt) REVERT: B 135 GLU cc_start: 0.8247 (pt0) cc_final: 0.7986 (pt0) REVERT: B 154 SER cc_start: 0.8744 (m) cc_final: 0.8219 (t) REVERT: B 178 ASP cc_start: 0.7570 (t0) cc_final: 0.7355 (t0) REVERT: B 216 ARG cc_start: 0.8295 (ttt90) cc_final: 0.7836 (ttt90) REVERT: B 221 SER cc_start: 0.8772 (p) cc_final: 0.8402 (p) REVERT: B 271 LYS cc_start: 0.8299 (ptmt) cc_final: 0.7981 (ptmt) REVERT: B 408 ARG cc_start: 0.5380 (mtm180) cc_final: 0.4286 (mtm180) REVERT: B 411 GLU cc_start: 0.8383 (tt0) cc_final: 0.7897 (tt0) REVERT: B 439 LYS cc_start: 0.8553 (mmtm) cc_final: 0.8276 (mmtt) REVERT: B 468 GLN cc_start: 0.8491 (mt0) cc_final: 0.7945 (mt0) REVERT: B 479 LYS cc_start: 0.8663 (mmtm) cc_final: 0.8130 (mmtm) REVERT: B 553 ILE cc_start: 0.6465 (mp) cc_final: 0.5955 (tt) REVERT: B 554 ASN cc_start: 0.8057 (p0) cc_final: 0.7830 (p0) REVERT: B 556 ASP cc_start: 0.7903 (m-30) cc_final: 0.7603 (m-30) REVERT: B 576 SER cc_start: 0.8365 (t) cc_final: 0.7996 (p) REVERT: C 52 LYS cc_start: 0.8339 (ttpt) cc_final: 0.7928 (ttpt) REVERT: C 71 LEU cc_start: 0.8518 (tp) cc_final: 0.8189 (tm) REVERT: C 77 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7232 (tm-30) REVERT: C 133 MET cc_start: 0.8119 (mmt) cc_final: 0.7616 (mmm) REVERT: C 155 GLU cc_start: 0.7555 (pp20) cc_final: 0.7163 (pp20) REVERT: C 193 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7293 (mt-10) REVERT: C 204 ILE cc_start: 0.9013 (pt) cc_final: 0.8779 (pp) REVERT: C 209 ARG cc_start: 0.8405 (pmt170) cc_final: 0.8046 (pmt170) REVERT: C 260 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7293 (mt-10) REVERT: C 344 SER cc_start: 0.8339 (t) cc_final: 0.8121 (t) REVERT: C 377 ARG cc_start: 0.8654 (ttt90) cc_final: 0.8415 (ttt-90) REVERT: C 397 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7386 (mtm-85) REVERT: C 404 GLN cc_start: 0.7781 (pp30) cc_final: 0.7368 (pp30) REVERT: C 470 TRP cc_start: 0.8663 (p90) cc_final: 0.8364 (p90) REVERT: C 509 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7023 (mm-30) REVERT: C 511 ASP cc_start: 0.7805 (t0) cc_final: 0.7479 (t0) REVERT: C 550 GLN cc_start: 0.4603 (mm-40) cc_final: 0.4367 (tp40) REVERT: C 569 MET cc_start: 0.8210 (tpp) cc_final: 0.7994 (ttp) REVERT: C 574 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7094 (mm-30) REVERT: D 51 PHE cc_start: 0.8353 (m-80) cc_final: 0.7916 (m-80) REVERT: D 82 VAL cc_start: 0.8368 (t) cc_final: 0.8108 (m) REVERT: D 101 ILE cc_start: 0.8626 (mt) cc_final: 0.8348 (mp) REVERT: D 167 ASN cc_start: 0.8163 (m110) cc_final: 0.7842 (m-40) REVERT: D 190 MET cc_start: 0.7663 (pmm) cc_final: 0.7379 (pmm) REVERT: D 232 ILE cc_start: 0.8586 (pt) cc_final: 0.8362 (pp) REVERT: D 257 THR cc_start: 0.7504 (t) cc_final: 0.7074 (m) REVERT: D 345 PHE cc_start: 0.8506 (m-80) cc_final: 0.7966 (m-80) REVERT: D 396 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7639 (tm-30) REVERT: D 400 TYR cc_start: 0.8634 (t80) cc_final: 0.8303 (t80) REVERT: D 511 ASP cc_start: 0.7860 (t0) cc_final: 0.7502 (t0) REVERT: D 513 ASP cc_start: 0.7932 (t0) cc_final: 0.7685 (t0) REVERT: D 581 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8236 (ttp80) REVERT: D 583 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7799 (mt) REVERT: E 60 GLU cc_start: 0.7659 (tt0) cc_final: 0.7456 (tt0) REVERT: E 77 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7542 (mm-30) REVERT: E 96 MET cc_start: 0.8009 (pmm) cc_final: 0.6511 (ptt) REVERT: E 101 ILE cc_start: 0.8483 (mt) cc_final: 0.8188 (mt) REVERT: E 125 ASP cc_start: 0.7630 (m-30) cc_final: 0.7417 (m-30) REVERT: E 135 GLU cc_start: 0.8099 (pt0) cc_final: 0.7858 (pt0) REVERT: E 149 VAL cc_start: 0.8923 (t) cc_final: 0.8482 (p) REVERT: E 179 SER cc_start: 0.8494 (p) cc_final: 0.8270 (p) REVERT: E 193 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7460 (mt-10) REVERT: E 255 LEU cc_start: 0.8256 (mp) cc_final: 0.7977 (mm) REVERT: E 296 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8168 (mm-40) REVERT: E 305 ASP cc_start: 0.8435 (m-30) cc_final: 0.5878 (m-30) REVERT: E 314 ARG cc_start: 0.8498 (mtt90) cc_final: 0.7361 (mtt-85) REVERT: E 325 ILE cc_start: 0.8576 (mt) cc_final: 0.8273 (mp) REVERT: E 332 ARG cc_start: 0.8612 (mmt180) cc_final: 0.8322 (mpt180) REVERT: E 411 GLU cc_start: 0.7971 (mp0) cc_final: 0.7507 (mp0) REVERT: E 426 ASN cc_start: 0.8141 (t0) cc_final: 0.7680 (t0) REVERT: F 40 ILE cc_start: 0.8404 (mt) cc_final: 0.8011 (tp) REVERT: F 42 THR cc_start: 0.8235 (p) cc_final: 0.7624 (t) REVERT: F 77 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7556 (mm-30) REVERT: F 89 LYS cc_start: 0.8432 (tppt) cc_final: 0.8054 (tppt) REVERT: F 163 LYS cc_start: 0.8235 (mttt) cc_final: 0.7969 (mttt) REVERT: F 192 SER cc_start: 0.8371 (t) cc_final: 0.7919 (p) REVERT: F 239 ASP cc_start: 0.8000 (m-30) cc_final: 0.7702 (m-30) REVERT: F 244 TYR cc_start: 0.8554 (m-80) cc_final: 0.8315 (m-80) REVERT: F 249 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8492 (t) REVERT: F 411 GLU cc_start: 0.7887 (mp0) cc_final: 0.7590 (mp0) REVERT: F 472 LYS cc_start: 0.8519 (ttpp) cc_final: 0.8283 (ttpp) REVERT: F 475 ASP cc_start: 0.7821 (t70) cc_final: 0.7580 (t70) REVERT: F 566 ILE cc_start: 0.9174 (pt) cc_final: 0.8931 (pp) REVERT: G 77 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7291 (mm-30) REVERT: G 81 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8293 (ttp80) REVERT: G 87 MET cc_start: 0.7377 (ptm) cc_final: 0.7152 (ptm) REVERT: G 89 LYS cc_start: 0.8655 (tttt) cc_final: 0.8328 (ttmm) REVERT: G 115 ASN cc_start: 0.8330 (t0) cc_final: 0.8113 (t160) REVERT: G 177 LEU cc_start: 0.8532 (tm) cc_final: 0.8265 (tm) REVERT: G 187 PRO cc_start: 0.8760 (Cg_endo) cc_final: 0.8464 (Cg_exo) REVERT: G 204 ILE cc_start: 0.8883 (pt) cc_final: 0.8642 (pp) REVERT: G 335 GLU cc_start: 0.7765 (tt0) cc_final: 0.7387 (tt0) REVERT: G 375 ASN cc_start: 0.7942 (m110) cc_final: 0.7642 (m110) REVERT: G 393 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7711 (mt-10) REVERT: G 396 GLU cc_start: 0.8014 (tp30) cc_final: 0.7798 (tp30) REVERT: G 400 TYR cc_start: 0.8313 (t80) cc_final: 0.7907 (t80) REVERT: G 401 ILE cc_start: 0.8568 (mm) cc_final: 0.8301 (mp) REVERT: G 426 ASN cc_start: 0.8510 (t0) cc_final: 0.8262 (t0) REVERT: G 473 GLU cc_start: 0.7880 (tp30) cc_final: 0.7636 (tp30) REVERT: G 475 ASP cc_start: 0.7667 (t70) cc_final: 0.7198 (t70) REVERT: G 511 ASP cc_start: 0.7916 (t0) cc_final: 0.7697 (t0) REVERT: G 532 LYS cc_start: 0.8841 (ttmt) cc_final: 0.8491 (ttpp) REVERT: G 536 LYS cc_start: 0.8118 (ttpp) cc_final: 0.7834 (ttpp) REVERT: G 549 GLN cc_start: 0.8322 (tp40) cc_final: 0.7925 (tp-100) REVERT: I 40 ILE cc_start: 0.8587 (mt) cc_final: 0.8357 (mp) REVERT: I 41 SER cc_start: 0.8444 (t) cc_final: 0.8164 (p) REVERT: I 89 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8265 (ttmt) REVERT: I 96 MET cc_start: 0.8082 (mpp) cc_final: 0.6580 (ppp) REVERT: I 163 LYS cc_start: 0.8089 (mttp) cc_final: 0.7836 (mttp) REVERT: I 193 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7587 (mt-10) REVERT: I 233 TYR cc_start: 0.8073 (t80) cc_final: 0.7620 (t80) REVERT: I 302 ASN cc_start: 0.8241 (m-40) cc_final: 0.7881 (m-40) REVERT: I 303 PHE cc_start: 0.8330 (m-80) cc_final: 0.7997 (m-10) REVERT: I 312 LYS cc_start: 0.8658 (mttt) cc_final: 0.8414 (mttt) REVERT: I 387 LYS cc_start: 0.8697 (mmmm) cc_final: 0.8434 (mtpp) REVERT: I 439 LYS cc_start: 0.4553 (mmtt) cc_final: 0.2907 (mmmt) REVERT: I 501 LYS cc_start: 0.8787 (tttt) cc_final: 0.8473 (tttm) REVERT: I 518 MET cc_start: 0.7017 (ptp) cc_final: 0.6593 (ptp) outliers start: 112 outliers final: 65 residues processed: 1158 average time/residue: 1.5846 time to fit residues: 2233.1379 Evaluate side-chains 1144 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 1075 time to evaluate : 5.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 HIS Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 403 HIS Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain G residue 271 LYS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 569 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 164 optimal weight: 7.9990 chunk 372 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 388 optimal weight: 7.9990 chunk 312 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 266 optimal weight: 8.9990 chunk 378 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 chunk 321 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 242 GLN A 403 HIS A 468 GLN B 48 GLN B 95 ASN B 383 GLN B 404 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN C 47 ASN C 95 ASN C 248 ASN C 383 GLN D 47 ASN D 383 GLN E 47 ASN E 102 HIS E 137 HIS E 180 ASN E 483 HIS E 558 GLN F 180 ASN F 213 GLN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 ASN F 505 ASN F 549 GLN F 554 ASN G 577 GLN I 48 GLN I 72 ASN I 147 ASN I 404 GLN I 459 ASN I 549 GLN ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106200 restraints weight = 47277.242| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.13 r_work: 0.3205 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 33486 Z= 0.259 Angle : 0.600 16.379 45804 Z= 0.299 Chirality : 0.045 0.192 4980 Planarity : 0.005 0.070 6021 Dihedral : 5.441 86.208 4445 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.23 % Allowed : 20.73 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.48 (0.13), residues: 3895 helix: -0.24 (0.42), residues: 117 sheet: -0.26 (0.16), residues: 986 loop : -0.31 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 58 HIS 0.009 0.001 HIS B 70 PHE 0.030 0.002 PHE I 266 TYR 0.029 0.002 TYR A 444 ARG 0.014 0.001 ARG G 408 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 386) hydrogen bonds : angle 5.86580 ( 702) SS BOND : bond 0.00679 ( 8) SS BOND : angle 1.32038 ( 16) covalent geometry : bond 0.00592 (33478) covalent geometry : angle 0.59913 (45788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1216 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 1104 time to evaluate : 3.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8253 (t0) REVERT: A 77 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7602 (mm-30) REVERT: A 86 ASN cc_start: 0.7992 (p0) cc_final: 0.7384 (p0) REVERT: A 87 MET cc_start: 0.7851 (ttm) cc_final: 0.7583 (ttm) REVERT: A 142 GLU cc_start: 0.8022 (pt0) cc_final: 0.7821 (pt0) REVERT: A 144 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 221 SER cc_start: 0.8882 (m) cc_final: 0.8558 (t) REVERT: A 239 ASP cc_start: 0.7938 (t0) cc_final: 0.7664 (t0) REVERT: A 245 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7826 (m) REVERT: A 268 PHE cc_start: 0.8679 (m-80) cc_final: 0.8191 (m-80) REVERT: A 296 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7707 (mm-40) REVERT: A 302 ASN cc_start: 0.7508 (m110) cc_final: 0.6988 (m110) REVERT: A 339 SER cc_start: 0.8701 (m) cc_final: 0.8253 (p) REVERT: A 471 ASP cc_start: 0.7892 (t0) cc_final: 0.7571 (t0) REVERT: A 530 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8408 (ttmt) REVERT: B 51 PHE cc_start: 0.8463 (m-80) cc_final: 0.8222 (m-80) REVERT: B 77 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7140 (tm-30) REVERT: B 87 MET cc_start: 0.8090 (ptm) cc_final: 0.7807 (ptm) REVERT: B 96 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8050 (ptp) REVERT: B 101 ILE cc_start: 0.8527 (mt) cc_final: 0.8158 (mt) REVERT: B 135 GLU cc_start: 0.8221 (pt0) cc_final: 0.7990 (pt0) REVERT: B 154 SER cc_start: 0.8755 (m) cc_final: 0.8308 (t) REVERT: B 166 ASN cc_start: 0.8182 (m-40) cc_final: 0.7893 (m-40) REVERT: B 172 SER cc_start: 0.8556 (p) cc_final: 0.8283 (p) REVERT: B 178 ASP cc_start: 0.7603 (t0) cc_final: 0.7389 (t0) REVERT: B 216 ARG cc_start: 0.8325 (ttt90) cc_final: 0.7885 (ttt90) REVERT: B 271 LYS cc_start: 0.8332 (ptmt) cc_final: 0.8012 (ptmt) REVERT: B 408 ARG cc_start: 0.5401 (mtm180) cc_final: 0.4180 (mtm180) REVERT: B 411 GLU cc_start: 0.8408 (tt0) cc_final: 0.7894 (tt0) REVERT: B 439 LYS cc_start: 0.8559 (mmtm) cc_final: 0.8292 (mmtt) REVERT: B 479 LYS cc_start: 0.8652 (mmtm) cc_final: 0.8113 (mmtm) REVERT: B 485 ASN cc_start: 0.8455 (p0) cc_final: 0.8178 (p0) REVERT: B 553 ILE cc_start: 0.6486 (mp) cc_final: 0.5977 (tt) REVERT: B 556 ASP cc_start: 0.7940 (m-30) cc_final: 0.7636 (m-30) REVERT: B 576 SER cc_start: 0.8400 (t) cc_final: 0.7935 (p) REVERT: C 52 LYS cc_start: 0.8325 (ttpt) cc_final: 0.7897 (ttpt) REVERT: C 71 LEU cc_start: 0.8500 (tp) cc_final: 0.8220 (tm) REVERT: C 77 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7275 (tm-30) REVERT: C 99 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7122 (t0) REVERT: C 133 MET cc_start: 0.8149 (mmt) cc_final: 0.7896 (mmm) REVERT: C 140 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8712 (t) REVERT: C 155 GLU cc_start: 0.7573 (pp20) cc_final: 0.7177 (pp20) REVERT: C 193 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7244 (mt-10) REVERT: C 204 ILE cc_start: 0.9020 (pt) cc_final: 0.8781 (pp) REVERT: C 209 ARG cc_start: 0.8484 (pmt170) cc_final: 0.8063 (pmt170) REVERT: C 221 SER cc_start: 0.8806 (p) cc_final: 0.8520 (t) REVERT: C 260 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7492 (mt-10) REVERT: C 397 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7440 (mtm-85) REVERT: C 404 GLN cc_start: 0.7878 (pp30) cc_final: 0.7525 (pp30) REVERT: C 470 TRP cc_start: 0.8688 (p90) cc_final: 0.8414 (p90) REVERT: C 509 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7123 (mm-30) REVERT: C 511 ASP cc_start: 0.7830 (t0) cc_final: 0.7514 (t0) REVERT: C 569 MET cc_start: 0.8262 (tpp) cc_final: 0.8047 (ttp) REVERT: C 574 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7179 (mm-30) REVERT: D 51 PHE cc_start: 0.8380 (m-80) cc_final: 0.7906 (m-80) REVERT: D 82 VAL cc_start: 0.8396 (t) cc_final: 0.8089 (m) REVERT: D 98 LEU cc_start: 0.8365 (mm) cc_final: 0.8158 (mp) REVERT: D 101 ILE cc_start: 0.8658 (mt) cc_final: 0.8392 (mp) REVERT: D 167 ASN cc_start: 0.8171 (m110) cc_final: 0.7859 (m-40) REVERT: D 178 ASP cc_start: 0.7945 (t0) cc_final: 0.7464 (t0) REVERT: D 232 ILE cc_start: 0.8585 (pt) cc_final: 0.8360 (pp) REVERT: D 257 THR cc_start: 0.7789 (t) cc_final: 0.7336 (m) REVERT: D 345 PHE cc_start: 0.8542 (m-80) cc_final: 0.8131 (m-80) REVERT: D 396 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7621 (mm-30) REVERT: D 400 TYR cc_start: 0.8685 (t80) cc_final: 0.8377 (t80) REVERT: D 511 ASP cc_start: 0.7878 (t0) cc_final: 0.7505 (t0) REVERT: D 513 ASP cc_start: 0.7982 (t0) cc_final: 0.7682 (t0) REVERT: D 532 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8511 (ttpp) REVERT: D 581 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8245 (ttp80) REVERT: D 583 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7852 (mt) REVERT: E 44 THR cc_start: 0.8152 (t) cc_final: 0.7773 (t) REVERT: E 60 GLU cc_start: 0.7676 (tt0) cc_final: 0.7476 (tt0) REVERT: E 77 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7560 (mm-30) REVERT: E 96 MET cc_start: 0.8106 (pmm) cc_final: 0.6490 (ptt) REVERT: E 101 ILE cc_start: 0.8545 (mt) cc_final: 0.8202 (mt) REVERT: E 125 ASP cc_start: 0.7617 (m-30) cc_final: 0.7362 (m-30) REVERT: E 135 GLU cc_start: 0.8093 (pt0) cc_final: 0.7852 (pt0) REVERT: E 149 VAL cc_start: 0.8908 (t) cc_final: 0.8479 (p) REVERT: E 179 SER cc_start: 0.8522 (p) cc_final: 0.8296 (p) REVERT: E 193 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7464 (mt-10) REVERT: E 255 LEU cc_start: 0.8266 (mp) cc_final: 0.7956 (mm) REVERT: E 260 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: E 296 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8209 (mm-40) REVERT: E 305 ASP cc_start: 0.8456 (m-30) cc_final: 0.5988 (m-30) REVERT: E 314 ARG cc_start: 0.8483 (mtt90) cc_final: 0.7301 (mtt-85) REVERT: E 411 GLU cc_start: 0.7942 (mp0) cc_final: 0.7490 (mp0) REVERT: E 473 GLU cc_start: 0.7964 (tp30) cc_final: 0.7717 (tp30) REVERT: E 549 GLN cc_start: 0.8268 (tp40) cc_final: 0.8016 (tt0) REVERT: F 40 ILE cc_start: 0.8404 (mt) cc_final: 0.7980 (tp) REVERT: F 77 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7634 (mm-30) REVERT: F 89 LYS cc_start: 0.8438 (tppt) cc_final: 0.8080 (tppt) REVERT: F 163 LYS cc_start: 0.8256 (mttt) cc_final: 0.7986 (mttt) REVERT: F 173 LEU cc_start: 0.8580 (tp) cc_final: 0.8275 (tt) REVERT: F 222 HIS cc_start: 0.8951 (p90) cc_final: 0.8436 (p-80) REVERT: F 239 ASP cc_start: 0.8039 (m-30) cc_final: 0.7711 (m-30) REVERT: F 244 TYR cc_start: 0.8572 (m-80) cc_final: 0.8324 (m-80) REVERT: F 265 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8173 (p) REVERT: F 266 PHE cc_start: 0.8639 (t80) cc_final: 0.8381 (t80) REVERT: F 293 SER cc_start: 0.8372 (t) cc_final: 0.8013 (p) REVERT: F 411 GLU cc_start: 0.7878 (mp0) cc_final: 0.7609 (mp0) REVERT: F 472 LYS cc_start: 0.8528 (ttpp) cc_final: 0.8139 (ttpp) REVERT: F 566 ILE cc_start: 0.9218 (pt) cc_final: 0.8944 (pp) REVERT: G 49 THR cc_start: 0.8540 (m) cc_final: 0.8167 (t) REVERT: G 77 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7397 (mm-30) REVERT: G 87 MET cc_start: 0.7403 (ptm) cc_final: 0.7195 (ptm) REVERT: G 89 LYS cc_start: 0.8696 (tttt) cc_final: 0.8367 (ttmm) REVERT: G 115 ASN cc_start: 0.8366 (t0) cc_final: 0.8163 (t160) REVERT: G 177 LEU cc_start: 0.8522 (tm) cc_final: 0.8259 (tm) REVERT: G 187 PRO cc_start: 0.8855 (Cg_endo) cc_final: 0.8550 (Cg_exo) REVERT: G 204 ILE cc_start: 0.8902 (pt) cc_final: 0.8674 (pp) REVERT: G 335 GLU cc_start: 0.7742 (tt0) cc_final: 0.7357 (tt0) REVERT: G 375 ASN cc_start: 0.7950 (m110) cc_final: 0.7656 (m110) REVERT: G 393 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7726 (mt-10) REVERT: G 396 GLU cc_start: 0.7998 (tp30) cc_final: 0.7774 (tp30) REVERT: G 426 ASN cc_start: 0.8611 (t0) cc_final: 0.8344 (t0) REVERT: G 439 LYS cc_start: 0.8797 (mmmm) cc_final: 0.8535 (mmtp) REVERT: G 473 GLU cc_start: 0.7848 (tp30) cc_final: 0.7588 (tp30) REVERT: G 475 ASP cc_start: 0.7703 (t70) cc_final: 0.7294 (t70) REVERT: G 501 LYS cc_start: 0.8645 (tttp) cc_final: 0.8343 (ptmm) REVERT: G 511 ASP cc_start: 0.7928 (t0) cc_final: 0.7706 (t0) REVERT: G 536 LYS cc_start: 0.8182 (ttpp) cc_final: 0.7897 (ttpp) REVERT: G 549 GLN cc_start: 0.8234 (tp40) cc_final: 0.7762 (tp40) REVERT: G 552 SER cc_start: 0.8587 (p) cc_final: 0.8269 (t) REVERT: I 40 ILE cc_start: 0.8619 (mt) cc_final: 0.8403 (mp) REVERT: I 41 SER cc_start: 0.8465 (t) cc_final: 0.8128 (p) REVERT: I 89 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8260 (ttmt) REVERT: I 96 MET cc_start: 0.8120 (mpp) cc_final: 0.6606 (ppp) REVERT: I 163 LYS cc_start: 0.8075 (mttp) cc_final: 0.7851 (mttp) REVERT: I 193 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7580 (mt-10) REVERT: I 233 TYR cc_start: 0.8225 (t80) cc_final: 0.7545 (t80) REVERT: I 249 SER cc_start: 0.8591 (t) cc_final: 0.8220 (p) REVERT: I 303 PHE cc_start: 0.8393 (m-80) cc_final: 0.8081 (m-10) REVERT: I 312 LYS cc_start: 0.8678 (mttt) cc_final: 0.8435 (mttt) REVERT: I 387 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8393 (mtpp) REVERT: I 436 ILE cc_start: 0.8688 (mm) cc_final: 0.8458 (mp) REVERT: I 439 LYS cc_start: 0.4842 (mmtt) cc_final: 0.3176 (mmmt) REVERT: I 501 LYS cc_start: 0.8827 (tttt) cc_final: 0.8619 (tttp) REVERT: I 518 MET cc_start: 0.7086 (ptp) cc_final: 0.6664 (ptp) outliers start: 112 outliers final: 71 residues processed: 1143 average time/residue: 1.3182 time to fit residues: 1804.0258 Evaluate side-chains 1166 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 1084 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 403 HIS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 271 LYS Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 411 GLU Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 387 LYS Chi-restraints excluded: chain I residue 472 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 376 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 chunk 339 optimal weight: 2.9990 chunk 357 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 286 optimal weight: 3.9990 chunk 321 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 5 optimal weight: 50.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 242 GLN A 309 GLN ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 HIS A 468 GLN B 48 GLN B 95 ASN B 383 GLN B 404 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN B 565 ASN C 383 GLN C 550 GLN D 47 ASN D 383 GLN E 47 ASN E 102 HIS E 137 HIS E 180 ASN E 483 HIS F 180 ASN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 ASN F 505 ASN F 549 GLN G 242 GLN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 577 GLN ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 ASN ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN I 302 ASN I 310 GLN I 404 GLN I 459 ASN I 549 GLN ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106069 restraints weight = 47178.610| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.14 r_work: 0.3208 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 33486 Z= 0.232 Angle : 0.593 15.820 45804 Z= 0.295 Chirality : 0.045 0.210 4980 Planarity : 0.005 0.051 6021 Dihedral : 5.403 85.567 4443 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.11 % Allowed : 21.27 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.54 (0.13), residues: 3895 helix: -0.27 (0.42), residues: 117 sheet: -0.35 (0.16), residues: 978 loop : -0.33 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 58 HIS 0.010 0.001 HIS B 70 PHE 0.031 0.002 PHE I 266 TYR 0.028 0.002 TYR I 524 ARG 0.013 0.001 ARG G 408 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 386) hydrogen bonds : angle 5.85852 ( 702) SS BOND : bond 0.00522 ( 8) SS BOND : angle 1.17675 ( 16) covalent geometry : bond 0.00530 (33478) covalent geometry : angle 0.59240 (45788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1104 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8239 (t0) REVERT: A 77 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7566 (mm-30) REVERT: A 86 ASN cc_start: 0.7976 (p0) cc_final: 0.7405 (p0) REVERT: A 87 MET cc_start: 0.7918 (ttm) cc_final: 0.7663 (ttm) REVERT: A 144 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7571 (mt-10) REVERT: A 221 SER cc_start: 0.8883 (m) cc_final: 0.8556 (t) REVERT: A 239 ASP cc_start: 0.7932 (t0) cc_final: 0.7699 (t0) REVERT: A 245 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7814 (m) REVERT: A 268 PHE cc_start: 0.8651 (m-80) cc_final: 0.8171 (m-80) REVERT: A 296 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7681 (mm-40) REVERT: A 302 ASN cc_start: 0.7525 (m110) cc_final: 0.6996 (m110) REVERT: A 339 SER cc_start: 0.8759 (m) cc_final: 0.8295 (p) REVERT: A 460 VAL cc_start: 0.8821 (m) cc_final: 0.8500 (p) REVERT: A 471 ASP cc_start: 0.7899 (t0) cc_final: 0.7590 (t0) REVERT: A 530 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8442 (ttmt) REVERT: B 51 PHE cc_start: 0.8468 (m-80) cc_final: 0.8220 (m-80) REVERT: B 77 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7102 (tm-30) REVERT: B 87 MET cc_start: 0.8083 (ptm) cc_final: 0.7800 (ptm) REVERT: B 96 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8107 (ptp) REVERT: B 101 ILE cc_start: 0.8456 (mt) cc_final: 0.8104 (mt) REVERT: B 154 SER cc_start: 0.8747 (m) cc_final: 0.8307 (t) REVERT: B 172 SER cc_start: 0.8584 (p) cc_final: 0.8317 (p) REVERT: B 178 ASP cc_start: 0.7573 (t0) cc_final: 0.7363 (t0) REVERT: B 216 ARG cc_start: 0.8313 (ttt90) cc_final: 0.7903 (ttt90) REVERT: B 271 LYS cc_start: 0.8366 (ptmt) cc_final: 0.8050 (ptmt) REVERT: B 408 ARG cc_start: 0.5389 (mtm180) cc_final: 0.4170 (mtm180) REVERT: B 411 GLU cc_start: 0.8421 (tt0) cc_final: 0.7938 (tt0) REVERT: B 439 LYS cc_start: 0.8565 (mmtm) cc_final: 0.8232 (mmtt) REVERT: B 479 LYS cc_start: 0.8655 (mmtm) cc_final: 0.8109 (mmtm) REVERT: B 485 ASN cc_start: 0.8434 (p0) cc_final: 0.8146 (p0) REVERT: B 553 ILE cc_start: 0.6478 (mp) cc_final: 0.5945 (tt) REVERT: B 556 ASP cc_start: 0.7933 (m-30) cc_final: 0.7722 (m-30) REVERT: B 576 SER cc_start: 0.8409 (t) cc_final: 0.7942 (p) REVERT: C 52 LYS cc_start: 0.8341 (ttpt) cc_final: 0.7934 (ttpt) REVERT: C 71 LEU cc_start: 0.8498 (tp) cc_final: 0.8226 (tm) REVERT: C 77 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7275 (tm-30) REVERT: C 133 MET cc_start: 0.8159 (mmt) cc_final: 0.7899 (mmm) REVERT: C 155 GLU cc_start: 0.7594 (pp20) cc_final: 0.7201 (pp20) REVERT: C 193 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7251 (mt-10) REVERT: C 204 ILE cc_start: 0.9013 (pt) cc_final: 0.8780 (pp) REVERT: C 209 ARG cc_start: 0.8473 (pmt170) cc_final: 0.8034 (pmt170) REVERT: C 216 ARG cc_start: 0.8389 (ptm160) cc_final: 0.8087 (ttt90) REVERT: C 260 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7540 (mt-10) REVERT: C 397 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7441 (mtm-85) REVERT: C 404 GLN cc_start: 0.7869 (pp30) cc_final: 0.7519 (pp30) REVERT: C 470 TRP cc_start: 0.8669 (p90) cc_final: 0.8395 (p90) REVERT: C 509 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7163 (mm-30) REVERT: C 511 ASP cc_start: 0.7810 (t0) cc_final: 0.7485 (t0) REVERT: C 569 MET cc_start: 0.8259 (tpp) cc_final: 0.8049 (ttp) REVERT: C 574 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7193 (mm-30) REVERT: D 51 PHE cc_start: 0.8380 (m-80) cc_final: 0.7935 (m-80) REVERT: D 82 VAL cc_start: 0.8404 (t) cc_final: 0.8110 (m) REVERT: D 101 ILE cc_start: 0.8645 (mt) cc_final: 0.8374 (mp) REVERT: D 167 ASN cc_start: 0.8167 (m110) cc_final: 0.7859 (m-40) REVERT: D 178 ASP cc_start: 0.7911 (t0) cc_final: 0.7342 (t0) REVERT: D 232 ILE cc_start: 0.8570 (pt) cc_final: 0.8351 (pp) REVERT: D 257 THR cc_start: 0.7684 (t) cc_final: 0.7256 (m) REVERT: D 345 PHE cc_start: 0.8582 (m-80) cc_final: 0.8075 (m-80) REVERT: D 400 TYR cc_start: 0.8664 (t80) cc_final: 0.8362 (t80) REVERT: D 511 ASP cc_start: 0.7864 (t0) cc_final: 0.7462 (t0) REVERT: D 513 ASP cc_start: 0.7949 (t0) cc_final: 0.7657 (t0) REVERT: D 581 ARG cc_start: 0.8497 (ttp80) cc_final: 0.8238 (ttp80) REVERT: D 583 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7907 (mt) REVERT: E 77 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7564 (mm-30) REVERT: E 96 MET cc_start: 0.8141 (pmm) cc_final: 0.6532 (ptt) REVERT: E 101 ILE cc_start: 0.8489 (mt) cc_final: 0.8219 (mt) REVERT: E 135 GLU cc_start: 0.8099 (pt0) cc_final: 0.7854 (pt0) REVERT: E 149 VAL cc_start: 0.8913 (t) cc_final: 0.8481 (p) REVERT: E 179 SER cc_start: 0.8487 (p) cc_final: 0.8276 (p) REVERT: E 193 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7465 (mt-10) REVERT: E 255 LEU cc_start: 0.8258 (mp) cc_final: 0.7957 (mm) REVERT: E 260 GLU cc_start: 0.7707 (tt0) cc_final: 0.7244 (tt0) REVERT: E 296 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8194 (mm-40) REVERT: E 305 ASP cc_start: 0.8469 (m-30) cc_final: 0.6130 (m-30) REVERT: E 312 LYS cc_start: 0.5421 (tptp) cc_final: 0.4390 (tptp) REVERT: E 314 ARG cc_start: 0.8488 (mtt90) cc_final: 0.7284 (mtt-85) REVERT: E 325 ILE cc_start: 0.8574 (mt) cc_final: 0.8299 (mp) REVERT: E 342 TYR cc_start: 0.7956 (p90) cc_final: 0.7708 (p90) REVERT: E 411 GLU cc_start: 0.7969 (mp0) cc_final: 0.7508 (mp0) REVERT: E 473 GLU cc_start: 0.7973 (tp30) cc_final: 0.7703 (tp30) REVERT: E 549 GLN cc_start: 0.8287 (tp40) cc_final: 0.8042 (tt0) REVERT: F 77 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7639 (mm-30) REVERT: F 89 LYS cc_start: 0.8433 (tppt) cc_final: 0.8073 (tppt) REVERT: F 163 LYS cc_start: 0.8260 (mttt) cc_final: 0.8000 (mttt) REVERT: F 173 LEU cc_start: 0.8579 (tp) cc_final: 0.8279 (tt) REVERT: F 222 HIS cc_start: 0.8971 (p90) cc_final: 0.8322 (p-80) REVERT: F 244 TYR cc_start: 0.8569 (m-80) cc_final: 0.8318 (m-80) REVERT: F 265 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8167 (p) REVERT: F 293 SER cc_start: 0.8397 (t) cc_final: 0.8061 (p) REVERT: F 319 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7416 (mtm) REVERT: F 346 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7466 (mt-10) REVERT: F 411 GLU cc_start: 0.7873 (mp0) cc_final: 0.7600 (mp0) REVERT: F 425 THR cc_start: 0.8576 (m) cc_final: 0.8227 (t) REVERT: F 472 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8377 (ttpp) REVERT: F 475 ASP cc_start: 0.7845 (t70) cc_final: 0.7326 (t70) REVERT: F 566 ILE cc_start: 0.9182 (pt) cc_final: 0.8932 (pp) REVERT: G 49 THR cc_start: 0.8542 (m) cc_final: 0.8158 (t) REVERT: G 77 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7431 (mm-30) REVERT: G 87 MET cc_start: 0.7385 (ptm) cc_final: 0.7178 (ptm) REVERT: G 89 LYS cc_start: 0.8700 (tttt) cc_final: 0.8367 (ttmm) REVERT: G 115 ASN cc_start: 0.8397 (t0) cc_final: 0.8183 (t160) REVERT: G 130 VAL cc_start: 0.8466 (m) cc_final: 0.8200 (p) REVERT: G 177 LEU cc_start: 0.8535 (tm) cc_final: 0.8261 (tm) REVERT: G 187 PRO cc_start: 0.8843 (Cg_endo) cc_final: 0.8557 (Cg_exo) REVERT: G 204 ILE cc_start: 0.8938 (pt) cc_final: 0.8708 (pp) REVERT: G 335 GLU cc_start: 0.7766 (tt0) cc_final: 0.7369 (tt0) REVERT: G 375 ASN cc_start: 0.7926 (m110) cc_final: 0.7647 (m110) REVERT: G 393 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7715 (mt-10) REVERT: G 396 GLU cc_start: 0.8019 (tp30) cc_final: 0.7804 (tp30) REVERT: G 426 ASN cc_start: 0.8598 (t0) cc_final: 0.8337 (t0) REVERT: G 439 LYS cc_start: 0.8840 (mmmm) cc_final: 0.8592 (mmtm) REVERT: G 473 GLU cc_start: 0.7852 (tp30) cc_final: 0.7606 (tp30) REVERT: G 475 ASP cc_start: 0.7721 (t70) cc_final: 0.7338 (t70) REVERT: G 511 ASP cc_start: 0.7952 (t0) cc_final: 0.7718 (t0) REVERT: G 552 SER cc_start: 0.8571 (p) cc_final: 0.8256 (t) REVERT: I 40 ILE cc_start: 0.8612 (mt) cc_final: 0.8393 (mp) REVERT: I 41 SER cc_start: 0.8450 (t) cc_final: 0.8119 (p) REVERT: I 89 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8286 (ttmt) REVERT: I 96 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.6621 (ptt) REVERT: I 163 LYS cc_start: 0.8109 (mttp) cc_final: 0.7908 (mttp) REVERT: I 193 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7624 (mt-10) REVERT: I 233 TYR cc_start: 0.8204 (t80) cc_final: 0.7588 (t80) REVERT: I 249 SER cc_start: 0.8559 (t) cc_final: 0.8210 (p) REVERT: I 303 PHE cc_start: 0.8386 (m-80) cc_final: 0.8064 (m-10) REVERT: I 312 LYS cc_start: 0.8714 (mttt) cc_final: 0.8468 (mttt) REVERT: I 387 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8526 (mtpp) REVERT: I 436 ILE cc_start: 0.8681 (mm) cc_final: 0.8449 (mp) REVERT: I 439 LYS cc_start: 0.4826 (mmtt) cc_final: 0.3163 (mmmt) REVERT: I 501 LYS cc_start: 0.8822 (tttt) cc_final: 0.8564 (tttm) REVERT: I 518 MET cc_start: 0.7130 (ptp) cc_final: 0.6683 (ptp) outliers start: 108 outliers final: 69 residues processed: 1140 average time/residue: 1.4113 time to fit residues: 1932.0530 Evaluate side-chains 1160 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 1081 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 403 HIS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 403 HIS Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 411 GLU Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 265 THR Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 387 LYS Chi-restraints excluded: chain I residue 429 VAL Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 569 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 167 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 305 optimal weight: 1.9990 chunk 358 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 247 optimal weight: 2.9990 chunk 341 optimal weight: 7.9990 chunk 375 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 242 GLN A 309 GLN ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 HIS A 468 GLN B 95 ASN B 166 ASN B 383 GLN B 403 HIS B 404 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 248 ASN C 383 GLN C 550 GLN D 383 GLN E 47 ASN E 102 HIS E 137 HIS E 180 ASN E 483 HIS E 497 GLN F 180 ASN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 ASN F 554 ASN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN G 577 GLN I 72 ASN ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN I 404 GLN I 459 ASN I 549 GLN ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107966 restraints weight = 47122.697| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.14 r_work: 0.3237 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33486 Z= 0.134 Angle : 0.558 15.749 45804 Z= 0.276 Chirality : 0.043 0.208 4980 Planarity : 0.005 0.077 6021 Dihedral : 5.186 84.382 4443 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.74 % Allowed : 22.05 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.39 (0.13), residues: 3895 helix: -0.26 (0.42), residues: 117 sheet: -0.20 (0.17), residues: 908 loop : -0.24 (0.11), residues: 2870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 58 HIS 0.009 0.001 HIS A 384 PHE 0.026 0.001 PHE I 266 TYR 0.026 0.001 TYR A 444 ARG 0.019 0.001 ARG C 520 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 386) hydrogen bonds : angle 5.76581 ( 702) SS BOND : bond 0.00454 ( 8) SS BOND : angle 0.94005 ( 16) covalent geometry : bond 0.00307 (33478) covalent geometry : angle 0.55781 (45788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1122 time to evaluate : 3.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8235 (t0) REVERT: A 77 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 86 ASN cc_start: 0.7934 (p0) cc_final: 0.7387 (p0) REVERT: A 87 MET cc_start: 0.7909 (ttm) cc_final: 0.7647 (ttm) REVERT: A 96 MET cc_start: 0.8341 (mpp) cc_final: 0.8123 (pmm) REVERT: A 144 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7487 (mt-10) REVERT: A 221 SER cc_start: 0.8906 (m) cc_final: 0.8487 (t) REVERT: A 239 ASP cc_start: 0.7874 (t0) cc_final: 0.7592 (t0) REVERT: A 245 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7563 (m) REVERT: A 249 SER cc_start: 0.8113 (p) cc_final: 0.7855 (p) REVERT: A 268 PHE cc_start: 0.8623 (m-80) cc_final: 0.8167 (m-80) REVERT: A 296 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7684 (mm-40) REVERT: A 302 ASN cc_start: 0.7556 (m110) cc_final: 0.7024 (m110) REVERT: A 327 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7511 (mm-30) REVERT: A 339 SER cc_start: 0.8634 (m) cc_final: 0.8269 (p) REVERT: A 460 VAL cc_start: 0.8828 (m) cc_final: 0.8523 (p) REVERT: A 511 ASP cc_start: 0.7427 (t0) cc_final: 0.7198 (t0) REVERT: A 530 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8425 (ttmt) REVERT: B 51 PHE cc_start: 0.8449 (m-80) cc_final: 0.8134 (m-80) REVERT: B 53 PHE cc_start: 0.8582 (m-80) cc_final: 0.8186 (m-80) REVERT: B 77 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7045 (tm-30) REVERT: B 78 ASN cc_start: 0.8500 (p0) cc_final: 0.8253 (p0) REVERT: B 87 MET cc_start: 0.8061 (ptm) cc_final: 0.7771 (ptm) REVERT: B 96 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8077 (ptp) REVERT: B 101 ILE cc_start: 0.8340 (mt) cc_final: 0.7953 (mt) REVERT: B 135 GLU cc_start: 0.8236 (pt0) cc_final: 0.7996 (pt0) REVERT: B 154 SER cc_start: 0.8736 (m) cc_final: 0.8286 (t) REVERT: B 172 SER cc_start: 0.8625 (p) cc_final: 0.8325 (p) REVERT: B 178 ASP cc_start: 0.7572 (t0) cc_final: 0.7351 (t0) REVERT: B 216 ARG cc_start: 0.8308 (ttt90) cc_final: 0.7880 (ttt90) REVERT: B 234 HIS cc_start: 0.8031 (m-70) cc_final: 0.7585 (m-70) REVERT: B 271 LYS cc_start: 0.8308 (ptmt) cc_final: 0.8009 (ptmt) REVERT: B 408 ARG cc_start: 0.5343 (mtm180) cc_final: 0.4316 (mtm180) REVERT: B 411 GLU cc_start: 0.8393 (tt0) cc_final: 0.7911 (tt0) REVERT: B 436 ILE cc_start: 0.8344 (tt) cc_final: 0.7915 (pt) REVERT: B 439 LYS cc_start: 0.8536 (mmtm) cc_final: 0.8279 (mmtt) REVERT: B 468 GLN cc_start: 0.8509 (mt0) cc_final: 0.7962 (mt0) REVERT: B 479 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8127 (mmtm) REVERT: B 556 ASP cc_start: 0.7840 (m-30) cc_final: 0.7625 (m-30) REVERT: C 52 LYS cc_start: 0.8326 (ttpt) cc_final: 0.7913 (ttpt) REVERT: C 71 LEU cc_start: 0.8531 (tp) cc_final: 0.8255 (tm) REVERT: C 77 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7225 (tm-30) REVERT: C 130 VAL cc_start: 0.8164 (t) cc_final: 0.7933 (m) REVERT: C 133 MET cc_start: 0.8163 (mmt) cc_final: 0.7892 (mmm) REVERT: C 155 GLU cc_start: 0.7566 (pp20) cc_final: 0.7163 (pp20) REVERT: C 193 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7242 (mt-10) REVERT: C 204 ILE cc_start: 0.8997 (pt) cc_final: 0.8781 (pp) REVERT: C 209 ARG cc_start: 0.8408 (pmt170) cc_final: 0.7995 (pmt170) REVERT: C 260 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7568 (mt-10) REVERT: C 397 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7384 (mtm-85) REVERT: C 404 GLN cc_start: 0.7821 (pp30) cc_final: 0.7478 (pp30) REVERT: C 470 TRP cc_start: 0.8651 (p90) cc_final: 0.8369 (p90) REVERT: C 509 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7125 (mm-30) REVERT: C 511 ASP cc_start: 0.7790 (t0) cc_final: 0.7451 (t0) REVERT: C 574 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7049 (mm-30) REVERT: D 51 PHE cc_start: 0.8362 (m-80) cc_final: 0.7897 (m-80) REVERT: D 77 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7264 (mm-30) REVERT: D 82 VAL cc_start: 0.8349 (t) cc_final: 0.8083 (m) REVERT: D 98 LEU cc_start: 0.8354 (mm) cc_final: 0.8139 (mp) REVERT: D 101 ILE cc_start: 0.8617 (mt) cc_final: 0.8340 (mp) REVERT: D 167 ASN cc_start: 0.8150 (m110) cc_final: 0.7854 (m-40) REVERT: D 232 ILE cc_start: 0.8587 (pt) cc_final: 0.8364 (pp) REVERT: D 257 THR cc_start: 0.7531 (t) cc_final: 0.7076 (m) REVERT: D 260 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7657 (mp0) REVERT: D 345 PHE cc_start: 0.8577 (m-80) cc_final: 0.7998 (m-80) REVERT: D 511 ASP cc_start: 0.7839 (t0) cc_final: 0.7412 (t0) REVERT: D 513 ASP cc_start: 0.7983 (t0) cc_final: 0.7651 (t0) REVERT: D 581 ARG cc_start: 0.8509 (ttp80) cc_final: 0.8280 (ttp80) REVERT: D 583 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7894 (mt) REVERT: E 77 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7533 (mm-30) REVERT: E 80 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7997 (mtp-110) REVERT: E 96 MET cc_start: 0.8073 (pmm) cc_final: 0.6518 (ptt) REVERT: E 101 ILE cc_start: 0.8526 (mt) cc_final: 0.8235 (mt) REVERT: E 135 GLU cc_start: 0.8090 (pt0) cc_final: 0.7854 (pt0) REVERT: E 149 VAL cc_start: 0.8957 (t) cc_final: 0.8502 (p) REVERT: E 179 SER cc_start: 0.8483 (p) cc_final: 0.8259 (p) REVERT: E 193 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7451 (mt-10) REVERT: E 255 LEU cc_start: 0.8270 (mp) cc_final: 0.7968 (mm) REVERT: E 260 GLU cc_start: 0.7654 (tt0) cc_final: 0.7221 (tt0) REVERT: E 285 LEU cc_start: 0.8307 (mp) cc_final: 0.8085 (mm) REVERT: E 296 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8173 (mm-40) REVERT: E 305 ASP cc_start: 0.8470 (m-30) cc_final: 0.6158 (m-30) REVERT: E 314 ARG cc_start: 0.8488 (mtt90) cc_final: 0.7313 (mtt-85) REVERT: E 325 ILE cc_start: 0.8513 (mt) cc_final: 0.8245 (mp) REVERT: E 332 ARG cc_start: 0.8642 (mmt180) cc_final: 0.8357 (mpt180) REVERT: E 411 GLU cc_start: 0.7942 (mp0) cc_final: 0.7498 (mp0) REVERT: E 473 GLU cc_start: 0.7973 (tp30) cc_final: 0.7695 (tp30) REVERT: F 77 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7623 (mm-30) REVERT: F 89 LYS cc_start: 0.8449 (tppt) cc_final: 0.8093 (tppt) REVERT: F 163 LYS cc_start: 0.8243 (mttt) cc_final: 0.7980 (mttt) REVERT: F 173 LEU cc_start: 0.8547 (tp) cc_final: 0.8241 (tt) REVERT: F 192 SER cc_start: 0.8388 (t) cc_final: 0.7939 (p) REVERT: F 222 HIS cc_start: 0.8953 (p90) cc_final: 0.8245 (p-80) REVERT: F 244 TYR cc_start: 0.8544 (m-80) cc_final: 0.8318 (m-80) REVERT: F 265 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8134 (p) REVERT: F 319 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7619 (mmm) REVERT: F 346 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7474 (mt-10) REVERT: F 411 GLU cc_start: 0.7860 (mp0) cc_final: 0.7590 (mp0) REVERT: F 425 THR cc_start: 0.8560 (m) cc_final: 0.8193 (t) REVERT: F 472 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8358 (ttpp) REVERT: F 475 ASP cc_start: 0.7791 (t70) cc_final: 0.7281 (t70) REVERT: G 49 THR cc_start: 0.8507 (m) cc_final: 0.8136 (t) REVERT: G 51 PHE cc_start: 0.8590 (m-80) cc_final: 0.8386 (m-80) REVERT: G 77 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7406 (mm-30) REVERT: G 89 LYS cc_start: 0.8682 (tttt) cc_final: 0.8406 (ttmm) REVERT: G 115 ASN cc_start: 0.8375 (t0) cc_final: 0.8121 (t0) REVERT: G 130 VAL cc_start: 0.8458 (m) cc_final: 0.8189 (p) REVERT: G 177 LEU cc_start: 0.8543 (tm) cc_final: 0.8265 (tm) REVERT: G 187 PRO cc_start: 0.8761 (Cg_endo) cc_final: 0.8503 (Cg_exo) REVERT: G 204 ILE cc_start: 0.8928 (pt) cc_final: 0.8692 (pp) REVERT: G 260 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7264 (mt-10) REVERT: G 274 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8177 (ttm110) REVERT: G 335 GLU cc_start: 0.7752 (tt0) cc_final: 0.7384 (tt0) REVERT: G 375 ASN cc_start: 0.7973 (m110) cc_final: 0.7671 (m110) REVERT: G 393 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7733 (mt-10) REVERT: G 396 GLU cc_start: 0.7997 (tp30) cc_final: 0.7791 (tp30) REVERT: G 426 ASN cc_start: 0.8536 (t0) cc_final: 0.8287 (t0) REVERT: G 439 LYS cc_start: 0.8755 (mmmm) cc_final: 0.8536 (mmtp) REVERT: G 473 GLU cc_start: 0.7868 (tp30) cc_final: 0.7630 (tp30) REVERT: G 475 ASP cc_start: 0.7712 (t70) cc_final: 0.7317 (t70) REVERT: G 501 LYS cc_start: 0.8723 (tttp) cc_final: 0.8488 (pttp) REVERT: G 511 ASP cc_start: 0.7909 (t0) cc_final: 0.7679 (t0) REVERT: G 549 GLN cc_start: 0.8181 (tp-100) cc_final: 0.7800 (tt0) REVERT: I 40 ILE cc_start: 0.8597 (mt) cc_final: 0.8364 (mp) REVERT: I 41 SER cc_start: 0.8435 (t) cc_final: 0.8143 (p) REVERT: I 89 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8289 (ttmt) REVERT: I 96 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.6643 (ptt) REVERT: I 193 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7627 (mt-10) REVERT: I 233 TYR cc_start: 0.8073 (t80) cc_final: 0.7598 (t80) REVERT: I 249 SER cc_start: 0.8515 (t) cc_final: 0.8158 (p) REVERT: I 303 PHE cc_start: 0.8351 (m-80) cc_final: 0.8025 (m-10) REVERT: I 312 LYS cc_start: 0.8711 (mttt) cc_final: 0.8462 (mttt) REVERT: I 387 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8432 (mtpp) REVERT: I 436 ILE cc_start: 0.8670 (mm) cc_final: 0.8422 (mp) REVERT: I 439 LYS cc_start: 0.4769 (mmtt) cc_final: 0.3103 (mmmt) REVERT: I 501 LYS cc_start: 0.8815 (tttt) cc_final: 0.8603 (tttp) REVERT: I 518 MET cc_start: 0.7170 (ptp) cc_final: 0.6717 (ptp) outliers start: 95 outliers final: 60 residues processed: 1154 average time/residue: 1.3423 time to fit residues: 1858.6555 Evaluate side-chains 1150 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 1079 time to evaluate : 3.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 403 HIS Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 274 ARG Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 265 THR Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 429 VAL Chi-restraints excluded: chain I residue 442 ILE Chi-restraints excluded: chain I residue 569 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 212 optimal weight: 10.0000 chunk 1 optimal weight: 50.0000 chunk 58 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 188 optimal weight: 0.0870 chunk 269 optimal weight: 0.6980 chunk 261 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 243 optimal weight: 0.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 309 GLN A 383 GLN A 384 HIS ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN B 48 GLN B 166 ASN B 383 GLN B 404 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN C 383 GLN D 350 GLN D 383 GLN E 47 ASN E 102 HIS E 137 HIS E 180 ASN E 483 HIS E 497 GLN F 180 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 ASN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 550 GLN G 560 ASN G 577 GLN I 72 ASN I 147 ASN I 234 HIS I 404 GLN I 459 ASN I 549 GLN ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 560 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108343 restraints weight = 46835.953| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.13 r_work: 0.3238 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33486 Z= 0.132 Angle : 0.562 16.022 45804 Z= 0.277 Chirality : 0.043 0.227 4980 Planarity : 0.005 0.074 6021 Dihedral : 5.102 84.323 4443 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.42 % Allowed : 22.89 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 (0.13), residues: 3895 helix: -0.17 (0.43), residues: 111 sheet: -0.20 (0.17), residues: 908 loop : -0.21 (0.11), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 58 HIS 0.008 0.001 HIS B 70 PHE 0.025 0.001 PHE I 266 TYR 0.029 0.001 TYR A 444 ARG 0.014 0.001 ARG G 408 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 386) hydrogen bonds : angle 5.74284 ( 702) SS BOND : bond 0.00414 ( 8) SS BOND : angle 0.89187 ( 16) covalent geometry : bond 0.00306 (33478) covalent geometry : angle 0.56222 (45788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 1096 time to evaluate : 4.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8241 (t0) REVERT: A 77 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7523 (mm-30) REVERT: A 86 ASN cc_start: 0.7894 (p0) cc_final: 0.7376 (p0) REVERT: A 87 MET cc_start: 0.7922 (ttm) cc_final: 0.7636 (ttm) REVERT: A 98 LEU cc_start: 0.8562 (mt) cc_final: 0.8333 (mm) REVERT: A 144 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7435 (mt-10) REVERT: A 221 SER cc_start: 0.8910 (m) cc_final: 0.8486 (t) REVERT: A 239 ASP cc_start: 0.7829 (t0) cc_final: 0.7578 (t0) REVERT: A 245 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7551 (m) REVERT: A 249 SER cc_start: 0.8125 (p) cc_final: 0.7853 (p) REVERT: A 263 THR cc_start: 0.8387 (m) cc_final: 0.8089 (t) REVERT: A 268 PHE cc_start: 0.8612 (m-80) cc_final: 0.8127 (m-80) REVERT: A 296 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7667 (mm-40) REVERT: A 302 ASN cc_start: 0.7568 (m110) cc_final: 0.7040 (m110) REVERT: A 339 SER cc_start: 0.8647 (m) cc_final: 0.8300 (p) REVERT: A 549 GLN cc_start: 0.8458 (tt0) cc_final: 0.7948 (tt0) REVERT: B 51 PHE cc_start: 0.8442 (m-80) cc_final: 0.8143 (m-80) REVERT: B 53 PHE cc_start: 0.8583 (m-80) cc_final: 0.8175 (m-80) REVERT: B 77 GLU cc_start: 0.7492 (tm-30) cc_final: 0.6999 (tm-30) REVERT: B 96 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8072 (ptp) REVERT: B 101 ILE cc_start: 0.8312 (mt) cc_final: 0.7918 (mt) REVERT: B 135 GLU cc_start: 0.8241 (pt0) cc_final: 0.8006 (pt0) REVERT: B 154 SER cc_start: 0.8719 (m) cc_final: 0.8280 (t) REVERT: B 172 SER cc_start: 0.8577 (p) cc_final: 0.8294 (p) REVERT: B 178 ASP cc_start: 0.7558 (t0) cc_final: 0.7332 (t0) REVERT: B 216 ARG cc_start: 0.8307 (ttt90) cc_final: 0.7892 (ttt90) REVERT: B 271 LYS cc_start: 0.8280 (ptmt) cc_final: 0.7980 (ptmt) REVERT: B 350 GLN cc_start: 0.8448 (mp10) cc_final: 0.8163 (mm-40) REVERT: B 408 ARG cc_start: 0.5292 (mtm180) cc_final: 0.4254 (mtm180) REVERT: B 411 GLU cc_start: 0.8365 (tt0) cc_final: 0.7868 (tt0) REVERT: B 436 ILE cc_start: 0.8324 (tt) cc_final: 0.7920 (pt) REVERT: B 468 GLN cc_start: 0.8508 (mt0) cc_final: 0.7964 (mt0) REVERT: B 479 LYS cc_start: 0.8652 (mmtm) cc_final: 0.8109 (mmtm) REVERT: B 556 ASP cc_start: 0.7827 (m-30) cc_final: 0.7579 (m-30) REVERT: B 576 SER cc_start: 0.8365 (t) cc_final: 0.7891 (p) REVERT: C 52 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7916 (ttpt) REVERT: C 71 LEU cc_start: 0.8489 (tp) cc_final: 0.8242 (tm) REVERT: C 77 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7268 (tm-30) REVERT: C 130 VAL cc_start: 0.8140 (t) cc_final: 0.7906 (m) REVERT: C 133 MET cc_start: 0.8123 (mmt) cc_final: 0.7543 (mmm) REVERT: C 155 GLU cc_start: 0.7593 (pp20) cc_final: 0.7188 (pp20) REVERT: C 193 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7233 (mt-10) REVERT: C 204 ILE cc_start: 0.8995 (pt) cc_final: 0.8780 (pp) REVERT: C 209 ARG cc_start: 0.8408 (pmt170) cc_final: 0.7992 (pmt170) REVERT: C 397 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7378 (mtm-85) REVERT: C 404 GLN cc_start: 0.7852 (pp30) cc_final: 0.7516 (pp30) REVERT: C 470 TRP cc_start: 0.8628 (p90) cc_final: 0.8340 (p90) REVERT: C 509 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7131 (mm-30) REVERT: C 511 ASP cc_start: 0.7786 (t0) cc_final: 0.7437 (t0) REVERT: C 520 ARG cc_start: 0.8543 (mtm-85) cc_final: 0.8331 (mtm110) REVERT: C 574 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7090 (mm-30) REVERT: D 51 PHE cc_start: 0.8345 (m-80) cc_final: 0.7884 (m-80) REVERT: D 82 VAL cc_start: 0.8354 (t) cc_final: 0.8087 (m) REVERT: D 101 ILE cc_start: 0.8630 (mt) cc_final: 0.8351 (mp) REVERT: D 167 ASN cc_start: 0.8150 (m110) cc_final: 0.7854 (m-40) REVERT: D 178 ASP cc_start: 0.8021 (t0) cc_final: 0.7432 (t0) REVERT: D 232 ILE cc_start: 0.8581 (pt) cc_final: 0.8359 (pp) REVERT: D 257 THR cc_start: 0.7479 (t) cc_final: 0.7035 (m) REVERT: D 260 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7656 (mp0) REVERT: D 345 PHE cc_start: 0.8590 (m-80) cc_final: 0.8013 (m-80) REVERT: D 511 ASP cc_start: 0.7830 (t0) cc_final: 0.7370 (t0) REVERT: D 513 ASP cc_start: 0.7982 (t0) cc_final: 0.7580 (t0) REVERT: D 583 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7897 (mt) REVERT: E 60 GLU cc_start: 0.7584 (tt0) cc_final: 0.7376 (tp30) REVERT: E 80 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7985 (mtp-110) REVERT: E 96 MET cc_start: 0.8067 (pmm) cc_final: 0.6525 (ptt) REVERT: E 101 ILE cc_start: 0.8494 (mt) cc_final: 0.8223 (mt) REVERT: E 135 GLU cc_start: 0.8100 (pt0) cc_final: 0.7856 (pt0) REVERT: E 149 VAL cc_start: 0.8936 (t) cc_final: 0.8508 (p) REVERT: E 179 SER cc_start: 0.8480 (p) cc_final: 0.8230 (p) REVERT: E 193 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7471 (mt-10) REVERT: E 255 LEU cc_start: 0.8267 (mp) cc_final: 0.7961 (mm) REVERT: E 260 GLU cc_start: 0.7651 (tt0) cc_final: 0.7231 (tt0) REVERT: E 285 LEU cc_start: 0.8287 (mp) cc_final: 0.8066 (mm) REVERT: E 296 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8148 (mm-40) REVERT: E 305 ASP cc_start: 0.8473 (m-30) cc_final: 0.6095 (m-30) REVERT: E 314 ARG cc_start: 0.8509 (mtt90) cc_final: 0.7333 (mtt-85) REVERT: E 325 ILE cc_start: 0.8507 (mt) cc_final: 0.8245 (mp) REVERT: E 332 ARG cc_start: 0.8660 (mmt180) cc_final: 0.8364 (mpt180) REVERT: E 411 GLU cc_start: 0.7923 (mp0) cc_final: 0.7511 (mp0) REVERT: E 473 GLU cc_start: 0.7976 (tp30) cc_final: 0.7711 (tp30) REVERT: E 524 TYR cc_start: 0.8722 (p90) cc_final: 0.8465 (p90) REVERT: F 77 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7612 (mm-30) REVERT: F 89 LYS cc_start: 0.8452 (tppt) cc_final: 0.8096 (tppt) REVERT: F 163 LYS cc_start: 0.8213 (mttt) cc_final: 0.7945 (mttt) REVERT: F 173 LEU cc_start: 0.8564 (tp) cc_final: 0.8250 (tt) REVERT: F 192 SER cc_start: 0.8386 (t) cc_final: 0.7943 (p) REVERT: F 244 TYR cc_start: 0.8540 (m-80) cc_final: 0.8280 (m-80) REVERT: F 276 THR cc_start: 0.8540 (m) cc_final: 0.8187 (t) REVERT: F 319 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7572 (mmm) REVERT: F 346 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7441 (mt-10) REVERT: F 411 GLU cc_start: 0.7836 (mp0) cc_final: 0.7562 (mp0) REVERT: F 425 THR cc_start: 0.8545 (m) cc_final: 0.8165 (t) REVERT: F 472 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8353 (ttpp) REVERT: F 475 ASP cc_start: 0.7804 (t70) cc_final: 0.7261 (t70) REVERT: G 49 THR cc_start: 0.8532 (m) cc_final: 0.8138 (t) REVERT: G 77 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7344 (mm-30) REVERT: G 89 LYS cc_start: 0.8674 (tttt) cc_final: 0.8404 (ttmm) REVERT: G 115 ASN cc_start: 0.8369 (t0) cc_final: 0.8159 (t160) REVERT: G 130 VAL cc_start: 0.8492 (m) cc_final: 0.8199 (p) REVERT: G 177 LEU cc_start: 0.8539 (tm) cc_final: 0.8251 (tm) REVERT: G 187 PRO cc_start: 0.8737 (Cg_endo) cc_final: 0.8491 (Cg_exo) REVERT: G 204 ILE cc_start: 0.8932 (pt) cc_final: 0.8699 (pp) REVERT: G 216 ARG cc_start: 0.8045 (ttt90) cc_final: 0.7767 (ttt180) REVERT: G 274 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8165 (ttm110) REVERT: G 335 GLU cc_start: 0.7762 (tt0) cc_final: 0.7385 (tt0) REVERT: G 375 ASN cc_start: 0.7975 (m110) cc_final: 0.7671 (m110) REVERT: G 393 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7679 (mt-10) REVERT: G 396 GLU cc_start: 0.7979 (tp30) cc_final: 0.7772 (tp30) REVERT: G 401 ILE cc_start: 0.8556 (mm) cc_final: 0.8272 (mp) REVERT: G 426 ASN cc_start: 0.8563 (t0) cc_final: 0.8358 (t0) REVERT: G 439 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8530 (mmtp) REVERT: G 473 GLU cc_start: 0.7872 (tp30) cc_final: 0.7629 (tp30) REVERT: G 475 ASP cc_start: 0.7682 (t70) cc_final: 0.7294 (t70) REVERT: G 501 LYS cc_start: 0.8714 (tttp) cc_final: 0.8469 (pttp) REVERT: G 511 ASP cc_start: 0.7862 (t0) cc_final: 0.7635 (t0) REVERT: G 549 GLN cc_start: 0.8184 (tp-100) cc_final: 0.7788 (tt0) REVERT: I 40 ILE cc_start: 0.8583 (mt) cc_final: 0.8353 (mp) REVERT: I 41 SER cc_start: 0.8425 (t) cc_final: 0.8149 (p) REVERT: I 89 LYS cc_start: 0.8581 (ttmt) cc_final: 0.8295 (ttmt) REVERT: I 96 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.6606 (ptt) REVERT: I 233 TYR cc_start: 0.8065 (t80) cc_final: 0.7591 (t80) REVERT: I 249 SER cc_start: 0.8518 (t) cc_final: 0.8153 (p) REVERT: I 303 PHE cc_start: 0.8334 (m-80) cc_final: 0.8019 (m-10) REVERT: I 312 LYS cc_start: 0.8723 (mttt) cc_final: 0.8476 (mttt) REVERT: I 387 LYS cc_start: 0.8760 (mmmm) cc_final: 0.8451 (mtpp) REVERT: I 436 ILE cc_start: 0.8677 (mm) cc_final: 0.8439 (mp) REVERT: I 439 LYS cc_start: 0.4745 (mmtt) cc_final: 0.3089 (mmmt) REVERT: I 501 LYS cc_start: 0.8810 (tttt) cc_final: 0.8541 (tttm) REVERT: I 518 MET cc_start: 0.7099 (ptp) cc_final: 0.6635 (ptp) outliers start: 84 outliers final: 54 residues processed: 1123 average time/residue: 1.5138 time to fit residues: 2076.7428 Evaluate side-chains 1139 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 1076 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 403 HIS Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 274 ARG Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 265 THR Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 442 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 406 optimal weight: 9.9990 chunk 331 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 240 optimal weight: 0.0050 chunk 184 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 368 optimal weight: 0.0870 chunk 109 optimal weight: 10.0000 chunk 266 optimal weight: 8.9990 chunk 9 optimal weight: 50.0000 overall best weight: 2.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 309 GLN A 383 GLN ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN B 48 GLN B 383 GLN B 404 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN C 47 ASN C 248 ASN C 550 GLN D 350 GLN D 383 GLN E 47 ASN E 102 HIS E 137 HIS E 180 ASN E 483 HIS E 497 GLN F 180 ASN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 ASN F 554 ASN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 577 GLN I 72 ASN I 147 ASN I 166 ASN I 404 GLN I 459 ASN I 549 GLN ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107395 restraints weight = 46867.252| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.12 r_work: 0.3224 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 33486 Z= 0.191 Angle : 0.589 15.921 45804 Z= 0.290 Chirality : 0.044 0.266 4980 Planarity : 0.005 0.076 6021 Dihedral : 5.170 84.167 4443 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.28 % Allowed : 23.32 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.43 (0.13), residues: 3895 helix: -0.25 (0.42), residues: 117 sheet: -0.24 (0.17), residues: 912 loop : -0.26 (0.11), residues: 2866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 58 HIS 0.009 0.001 HIS B 70 PHE 0.027 0.002 PHE I 266 TYR 0.029 0.002 TYR I 524 ARG 0.014 0.001 ARG B 382 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 386) hydrogen bonds : angle 5.79189 ( 702) SS BOND : bond 0.00512 ( 8) SS BOND : angle 0.92822 ( 16) covalent geometry : bond 0.00440 (33478) covalent geometry : angle 0.58922 (45788) =============================================================================== Job complete usr+sys time: 37054.52 seconds wall clock time: 643 minutes 10.37 seconds (38590.37 seconds total)