Starting phenix.real_space_refine on Fri Mar 6 17:17:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7utu_26789/03_2026/7utu_26789.cif Found real_map, /net/cci-nas-00/data/ceres_data/7utu_26789/03_2026/7utu_26789.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 { model { file = "/net/cci-nas-00/data/ceres_data/7utu_26789/03_2026/7utu_26789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7utu_26789/03_2026/7utu_26789.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7utu_26789/03_2026/7utu_26789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7utu_26789/03_2026/7utu_26789.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.008 sd= 0.057 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 124 5.16 5 C 20993 2.51 5 N 5652 2.21 5 O 6235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33004 Number of models: 1 Model: "" Number of chains: 10 Chain: "L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 480 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'TRANS': 95} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'UNK:plan-1': 96} Unresolved non-hydrogen planarities: 96 Chain: "H" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 570 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'TRANS': 113} Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'UNK:plan-1': 114} Unresolved non-hydrogen planarities: 114 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: "D" Number of atoms: 3444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3444 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 397} Chain breaks: 4 Chain: "B" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4150 Classifications: {'peptide': 519} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 480} Chain breaks: 4 Chain: "I" Number of atoms: 4178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4178 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 485} Chain breaks: 3 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: "C" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3243 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 376} Chain breaks: 5 Chain: "G" Number of atoms: 4225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4225 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 490} Chain breaks: 3 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 Time building chain proxies: 6.90, per 1000 atoms: 0.21 Number of scatterers: 33004 At special positions: 0 Unit cell: (192.5, 198, 144.1, 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 124 16.00 O 6235 8.00 N 5652 7.00 C 20993 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 D 490 " - pdb=" SG CYS D 494 " distance=2.04 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 494 " distance=2.04 Simple disulfide: pdb=" SG CYS I 490 " - pdb=" SG CYS I 494 " distance=2.03 Simple disulfide: pdb=" SG CYS E 490 " - pdb=" SG CYS E 494 " distance=2.04 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 494 " distance=2.03 Simple disulfide: pdb=" SG CYS G 490 " - pdb=" SG CYS G 494 " distance=2.03 Simple disulfide: pdb=" SG CYS F 490 " - pdb=" SG CYS F 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: 2.36 Conformation dependent library (CDL) restraints added in 1.3 seconds 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7888 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 59 sheets defined 12.0% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'H' and resid 25 through 29 removed outlier: 3.859A pdb=" N UNK H 29 " --> pdb=" O UNK H 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 116 through 121 removed outlier: 4.182A pdb=" N TRP A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.719A pdb=" N THR A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.004A pdb=" N MET A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.504A pdb=" N ASP A 240 " --> pdb=" O ASP A 237 " (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 309 through 313 removed outlier: 3.851A pdb=" N ARG A 313 " --> pdb=" O GLN A 310 " (cutoff:3.500A) 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 447 Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.638A pdb=" N ASN A 560 " --> pdb=" O ASN A 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 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 245 through 250 Processing helix chain 'D' and resid 381 through 385 removed outlier: 4.133A pdb=" N GLY D 385 " --> pdb=" O ARG D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 562 removed outlier: 3.720A pdb=" N VAL D 562 " --> pdb=" O PHE D 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 removed outlier: 4.350A pdb=" N VAL B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 4.105A 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 237 through 241 removed outlier: 3.600A pdb=" N ASP B 240 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 241 " --> pdb=" O PRO B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 237 through 241' Processing helix chain 'B' and resid 245 through 250 Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.666A pdb=" N ASP B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'I' and resid 86 through 92 removed outlier: 4.431A pdb=" N VAL I 92 " --> pdb=" O ASP I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 121 removed outlier: 4.190A pdb=" N TRP I 120 " --> pdb=" O ALA I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 132 removed outlier: 3.745A pdb=" N THR I 132 " --> pdb=" O LEU I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 192 removed outlier: 3.537A pdb=" N MET I 190 " --> pdb=" O PRO I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 241 removed outlier: 3.574A pdb=" N VAL I 241 " --> pdb=" O PRO I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 285 removed outlier: 3.791A pdb=" N LEU I 285 " --> pdb=" O ASN I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 313 removed outlier: 3.618A pdb=" N ARG I 313 " --> pdb=" O GLN I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 385 removed outlier: 3.623A pdb=" N GLY I 385 " --> pdb=" O ARG I 382 " (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 448 removed outlier: 3.565A pdb=" N ILE I 447 " --> pdb=" O TYR I 444 " (cutoff:3.500A) Processing helix chain 'I' and resid 558 through 562 removed outlier: 3.610A pdb=" N TYR I 561 " --> pdb=" O GLN I 558 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL I 562 " --> pdb=" O PHE I 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 558 through 562' Processing helix chain 'E' and resid 86 through 92 removed outlier: 3.825A pdb=" N VAL E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 237 through 241 removed outlier: 3.721A pdb=" N ASP E 240 " --> pdb=" O ASP E 237 " (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: 3.575A pdb=" N ARG E 313 " --> pdb=" O GLN E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 427 No H-bonds generated for 'chain 'E' and resid 425 through 427' Processing helix chain 'E' and resid 443 through 447 Processing helix chain 'E' and resid 557 through 562 removed outlier: 3.818A pdb=" N VAL E 562 " --> pdb=" O PHE E 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.962A pdb=" N GLY C 385 " --> pdb=" O ARG C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 562 removed outlier: 4.029A pdb=" N VAL C 562 " --> pdb=" O PHE C 559 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 91 Processing helix chain 'G' and resid 95 through 99 removed outlier: 3.537A pdb=" N ASP G 99 " --> pdb=" O MET G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 120 Processing helix chain 'G' and resid 122 through 132 Processing helix chain 'G' and resid 237 through 241 removed outlier: 3.550A pdb=" N ASP G 240 " --> pdb=" O ASP G 237 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL G 241 " --> pdb=" O PRO G 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 237 through 241' 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: 3.860A pdb=" N ARG G 313 " --> pdb=" O GLN G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 413 removed outlier: 3.516A pdb=" N ASP G 413 " --> pdb=" O PRO G 410 " (cutoff:3.500A) 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 435 through 439 removed outlier: 3.869A pdb=" N GLY G 438 " --> pdb=" O PRO G 435 " (cutoff:3.500A) Processing helix chain 'G' and resid 443 through 448 removed outlier: 3.599A pdb=" N PHE G 448 " --> pdb=" O THR G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 562 removed outlier: 4.269A pdb=" N TYR G 561 " --> pdb=" O ASN G 557 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL G 562 " --> pdb=" O GLN G 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 557 through 562' Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 245 through 250 Processing helix chain 'F' and resid 281 through 285 removed outlier: 3.663A pdb=" N LEU F 285 " --> pdb=" O ASN F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 313 removed outlier: 3.596A pdb=" N ARG F 313 " --> pdb=" O GLN F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 385 removed outlier: 3.860A pdb=" N GLY F 385 " --> pdb=" O ARG F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 413 removed outlier: 3.715A pdb=" N ASP F 413 " --> pdb=" O PRO F 410 " (cutoff:3.500A) 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 447 Processing helix chain 'F' and resid 557 through 561 removed outlier: 3.602A pdb=" N ASN F 560 " --> pdb=" O ASN F 557 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR F 561 " --> pdb=" O GLN F 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 557 through 561' Processing sheet with id=AA1, first strand: chain 'L' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'L' and resid 41 through 42 removed outlier: 3.673A pdb=" N UNK L 74 " --> pdb=" O UNK L 35 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N UNK L 77 " --> pdb=" O UNK L 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 55 through 57 removed outlier: 3.507A pdb=" N UNK L 55 " --> pdb=" O UNK L 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.585A pdb=" N UNK H 4 " --> pdb=" O UNK H 20 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N UNK H 18 " --> pdb=" O UNK H 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 42 through 47 removed outlier: 6.882A pdb=" N UNK H 33 " --> pdb=" O UNK H 44 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N UNK H 46 " --> pdb=" O UNK H 31 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N UNK H 31 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N UNK H 88 " --> pdb=" O UNK H 105 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N UNK H 105 " --> pdb=" O UNK H 88 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N UNK H 90 " --> pdb=" O UNK H 103 " (cutoff:3.500A) Processing sheet with id=AA6, 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=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 49 through 54 removed outlier: 4.046A pdb=" N TRP A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) 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=AA8, first strand: chain 'A' and resid 80 through 84 Processing sheet with id=AA9, first strand: chain 'A' and resid 215 through 218 removed outlier: 3.823A pdb=" N GLY A 235 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N THR A 217 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N TYR A 233 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 276 through 277 Processing sheet with id=AB2, first strand: chain 'A' and resid 315 through 317 removed outlier: 3.604A pdb=" N PHE G 398 " --> pdb=" O TYR G 378 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.792A pdb=" N GLU A 335 " --> pdb=" O ALA A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 351 through 354 removed outlier: 3.616A pdb=" N SER A 348 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 396 through 399 removed outlier: 6.813A pdb=" N ASN A 375 " --> pdb=" O MET F 319 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET F 319 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.653A pdb=" N SER G 348 " --> pdb=" O GLY G 351 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 470 through 472 removed outlier: 7.036A pdb=" N ASP A 471 " --> pdb=" O CYS A 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 44 through 45 current: chain 'E' and resid 102 through 111 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 49 through 53 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=AC1, first strand: chain 'D' and resid 80 through 84 Processing sheet with id=AC2, first strand: chain 'D' and resid 215 through 218 removed outlier: 7.255A pdb=" N THR D 217 " --> pdb=" O TYR D 233 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TYR D 233 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 276 through 278 Processing sheet with id=AC4, first strand: chain 'D' and resid 345 through 348 Processing sheet with id=AC5, first strand: chain 'D' and resid 377 through 380 Processing sheet with id=AC6, 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=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 49 through 53 removed outlier: 3.608A pdb=" N LYS B 52 " --> pdb=" O GLU B 60 " (cutoff:3.500A) 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=AC8, first strand: chain 'B' and resid 215 through 218 removed outlier: 6.246A pdb=" N ASP B 215 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 217 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=AD1, first strand: chain 'B' and resid 335 through 336 removed outlier: 6.728A pdb=" N GLU B 335 " --> pdb=" O ALA B 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 351 through 354 removed outlier: 3.636A pdb=" N SER B 348 " --> pdb=" O GLY B 351 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 396 through 399 removed outlier: 3.506A pdb=" N GLU B 396 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN B 375 " --> pdb=" O MET I 319 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET I 319 " --> pdb=" O ASN B 375 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 415 through 416 Processing sheet with id=AD5, first strand: chain 'I' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 44 through 45 current: chain 'G' and resid 102 through 112 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, 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=AD7, first strand: chain 'I' and resid 80 through 84 Processing sheet with id=AD8, first strand: chain 'I' and resid 276 through 278 Processing sheet with id=AD9, first strand: chain 'I' and resid 379 through 380 Processing sheet with id=AE1, 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=AE2, first strand: chain 'E' and resid 215 through 218 removed outlier: 6.574A pdb=" N ASP E 215 " --> pdb=" O HIS E 234 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR E 217 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE E 232 " --> pdb=" O THR E 217 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 276 through 278 Processing sheet with id=AE4, first strand: chain 'E' and resid 335 through 336 removed outlier: 6.800A pdb=" N GLU E 335 " --> pdb=" O ALA E 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 345 through 348 removed outlier: 3.652A pdb=" N SER E 348 " --> pdb=" O GLY E 351 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 377 through 380 Processing sheet with id=AE7, first strand: chain 'E' and resid 415 through 416 Processing sheet with id=AE8, 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 164 through 167 Processing sheet with id=AE9, first strand: chain 'C' and resid 215 through 218 removed outlier: 3.552A pdb=" N GLY C 235 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N THR C 217 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TYR C 233 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 345 through 348 Processing sheet with id=AF2, first strand: chain 'C' and resid 377 through 380 Processing sheet with id=AF3, first strand: chain 'C' and resid 463 through 464 removed outlier: 4.028A pdb=" N TYR C 464 " --> pdb=" O GLU C 574 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU C 574 " --> pdb=" O TYR C 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, 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=AF5, first strand: chain 'G' and resid 215 through 218 removed outlier: 3.625A pdb=" N GLY G 235 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR G 217 " --> pdb=" O TYR G 233 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TYR G 233 " --> pdb=" O THR G 217 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 276 through 278 Processing sheet with id=AF7, first strand: chain 'G' and resid 315 through 319 removed outlier: 3.977A pdb=" N MET G 319 " --> pdb=" O ASN F 375 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN F 375 " --> pdb=" O MET G 319 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 335 through 336 removed outlier: 6.713A pdb=" N GLU G 335 " --> pdb=" O ALA G 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'G' and resid 429 through 430 Processing sheet with id=AG1, 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=AG2, first strand: chain 'F' and resid 80 through 84 Processing sheet with id=AG3, first strand: chain 'F' and resid 216 through 218 removed outlier: 3.544A pdb=" N THR F 217 " --> pdb=" O ILE F 232 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 276 through 278 removed outlier: 5.990A pdb=" N HIS F 277 " --> pdb=" O ARG F 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'F' and resid 335 through 336 removed outlier: 6.818A pdb=" N GLU F 335 " --> pdb=" O ALA F 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 355 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.36 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10784 1.34 - 1.47: 9069 1.47 - 1.60: 13875 1.60 - 1.73: 0 1.73 - 1.86: 216 Bond restraints: 33944 Sorted by residual: bond pdb=" CA GLN E 404 " pdb=" C GLN E 404 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.72e-02 3.38e+03 1.17e+01 bond pdb=" C CYS I 494 " pdb=" N PRO I 495 " ideal model delta sigma weight residual 1.330 1.368 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" CA ASP B 168 " pdb=" CB ASP B 168 " ideal model delta sigma weight residual 1.526 1.579 -0.053 1.70e-02 3.46e+03 9.77e+00 bond pdb=" C THR G 107 " pdb=" N PRO G 108 " ideal model delta sigma weight residual 1.331 1.356 -0.025 7.90e-03 1.60e+04 9.77e+00 bond pdb=" N GLY I 37 " pdb=" CA GLY I 37 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.41e+00 ... (remaining 33939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 44821 2.36 - 4.73: 1261 4.73 - 7.09: 310 7.09 - 9.46: 28 9.46 - 11.82: 3 Bond angle restraints: 46423 Sorted by residual: angle pdb=" C ASN E 493 " pdb=" CA ASN E 493 " pdb=" CB ASN E 493 " ideal model delta sigma weight residual 109.99 118.44 -8.45 1.61e+00 3.86e-01 2.76e+01 angle pdb=" CA GLU B 411 " pdb=" CB GLU B 411 " pdb=" CG GLU B 411 " ideal model delta sigma weight residual 114.10 123.11 -9.01 2.00e+00 2.50e-01 2.03e+01 angle pdb=" CA GLU B 60 " pdb=" CB GLU B 60 " pdb=" CG GLU B 60 " ideal model delta sigma weight residual 114.10 123.10 -9.00 2.00e+00 2.50e-01 2.03e+01 angle pdb=" CA VAL E 250 " pdb=" C VAL E 250 " pdb=" N PRO E 251 " ideal model delta sigma weight residual 116.57 120.97 -4.40 9.80e-01 1.04e+00 2.02e+01 angle pdb=" CA VAL D 250 " pdb=" C VAL D 250 " pdb=" N PRO D 251 " ideal model delta sigma weight residual 116.57 120.87 -4.30 9.80e-01 1.04e+00 1.93e+01 ... (remaining 46418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 17815 17.88 - 35.77: 1560 35.77 - 53.65: 392 53.65 - 71.54: 72 71.54 - 89.42: 46 Dihedral angle restraints: 19885 sinusoidal: 7654 harmonic: 12231 Sorted by residual: dihedral pdb=" CA CYS I 494 " pdb=" C CYS I 494 " pdb=" N PRO I 495 " pdb=" CA PRO I 495 " ideal model delta harmonic sigma weight residual 180.00 -147.37 -32.63 0 5.00e+00 4.00e-02 4.26e+01 dihedral pdb=" CA THR B 425 " pdb=" C THR B 425 " pdb=" N ASN B 426 " pdb=" CA ASN B 426 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA CYS F 494 " pdb=" C CYS F 494 " pdb=" N PRO F 495 " pdb=" CA PRO F 495 " ideal model delta harmonic sigma weight residual -180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 19882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3987 0.058 - 0.117: 849 0.117 - 0.175: 203 0.175 - 0.233: 13 0.233 - 0.291: 1 Chirality restraints: 5053 Sorted by residual: chirality pdb=" CB VAL A 130 " pdb=" CA VAL A 130 " pdb=" CG1 VAL A 130 " pdb=" CG2 VAL A 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ILE B 219 " pdb=" N ILE B 219 " pdb=" C ILE B 219 " pdb=" CB ILE B 219 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE D 219 " pdb=" N ILE D 219 " pdb=" C ILE D 219 " pdb=" CB ILE D 219 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 5050 not shown) Planarity restraints: 6105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 141 " 0.023 2.00e-02 2.50e+03 3.16e-02 1.75e+01 pdb=" CG PHE I 141 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE I 141 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE I 141 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE I 141 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE I 141 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE I 141 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 45 " 0.016 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE C 45 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE C 45 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE C 45 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE C 45 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 45 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 45 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 237 " 0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO D 238 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO D 238 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 238 " 0.045 5.00e-02 4.00e+02 ... (remaining 6102 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 441 2.63 - 3.20: 29446 3.20 - 3.77: 49383 3.77 - 4.33: 70875 4.33 - 4.90: 117163 Nonbonded interactions: 267308 Sorted by model distance: nonbonded pdb=" OG1 THR A 326 " pdb=" OD1 ASP G 100 " model vdw 2.067 3.040 nonbonded pdb=" OE1 GLN I 558 " pdb=" OG1 THR G 236 " model vdw 2.081 3.040 nonbonded pdb=" OG SER I 339 " pdb=" OG1 THR I 450 " model vdw 2.114 3.040 nonbonded pdb=" OD1 ASN B 443 " pdb=" OG1 THR B 445 " model vdw 2.116 3.040 nonbonded pdb=" OD1 ASN E 443 " pdb=" OG1 THR E 445 " model vdw 2.116 3.040 ... (remaining 267303 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 290 or resid 302 through 306 or resid 309 throu \ gh 391 or resid 394 through 508 or resid 517 through 584)) selection = (chain 'B' and (resid 37 through 391 or resid 394 through 508 or resid 517 throu \ gh 584)) selection = (chain 'E' and (resid 37 through 290 or resid 302 through 306 or resid 309 throu \ gh 391 or resid 394 through 508 or resid 517 through 584)) selection = (chain 'F' and (resid 37 through 290 or resid 302 through 306 or resid 309 throu \ gh 391 or resid 394 through 508 or resid 517 through 584)) selection = (chain 'G' and (resid 37 through 290 or resid 302 through 306 or resid 309 throu \ gh 508 or resid 517 through 584)) selection = (chain 'I' and (resid 37 through 290 or resid 302 through 306 or resid 309 throu \ gh 391 or resid 394 through 584)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 37 through 277 or resid 340 through 404 or resid 457 throu \ gh 540 or resid 549 through 579)) } 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 26.130 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 33952 Z= 0.269 Angle : 0.992 11.821 46439 Z= 0.527 Chirality : 0.052 0.291 5053 Planarity : 0.007 0.121 6105 Dihedral : 15.291 89.423 11973 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.26 % Allowed : 16.90 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.12), residues: 3937 helix: -0.22 (0.44), residues: 93 sheet: -0.87 (0.15), residues: 1000 loop : -0.80 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 520 TYR 0.048 0.002 TYR C 464 PHE 0.072 0.003 PHE I 141 TRP 0.044 0.002 TRP I 214 HIS 0.018 0.002 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00649 (33944) covalent geometry : angle 0.98980 (46423) SS BOND : bond 0.00666 ( 8) SS BOND : angle 3.61638 ( 16) hydrogen bonds : bond 0.27183 ( 355) hydrogen bonds : angle 8.37573 ( 714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1181 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 PHE cc_start: 0.8652 (p90) cc_final: 0.8387 (p90) REVERT: A 444 TYR cc_start: 0.8305 (p90) cc_final: 0.7797 (p90) REVERT: A 558 GLN cc_start: 0.7893 (tt0) cc_final: 0.7677 (tt0) REVERT: A 576 SER cc_start: 0.8603 (t) cc_final: 0.8172 (m) REVERT: D 60 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6902 (tm-30) REVERT: D 145 ILE cc_start: 0.8680 (mt) cc_final: 0.8462 (mp) REVERT: D 185 PHE cc_start: 0.8786 (t80) cc_final: 0.8518 (t80) REVERT: D 209 ARG cc_start: 0.8031 (pmt170) cc_final: 0.5507 (pmt-80) REVERT: D 214 TRP cc_start: 0.7890 (p90) cc_final: 0.7549 (p90) REVERT: D 246 ILE cc_start: 0.8087 (mm) cc_final: 0.7866 (mp) REVERT: D 274 ARG cc_start: 0.8338 (mmm-85) cc_final: 0.7479 (mmm-85) REVERT: D 377 ARG cc_start: 0.8428 (ttt-90) cc_final: 0.8212 (ttm-80) REVERT: D 383 GLN cc_start: 0.8076 (mt0) cc_final: 0.7865 (mt0) REVERT: D 488 PHE cc_start: 0.8217 (m-80) cc_final: 0.7787 (m-80) REVERT: D 566 ILE cc_start: 0.8010 (pt) cc_final: 0.7711 (pp) REVERT: D 581 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7373 (ttp80) REVERT: B 167 ASN cc_start: 0.7978 (m-40) cc_final: 0.7767 (m-40) REVERT: B 277 HIS cc_start: 0.8296 (p-80) cc_final: 0.8064 (p90) REVERT: B 329 THR cc_start: 0.8304 (p) cc_final: 0.8034 (t) REVERT: B 378 TYR cc_start: 0.8354 (m-80) cc_final: 0.7948 (m-80) REVERT: B 396 GLU cc_start: 0.7767 (tt0) cc_final: 0.7356 (tt0) REVERT: B 397 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7844 (mtt180) REVERT: I 67 ARG cc_start: 0.7591 (mmt-90) cc_final: 0.6996 (mmt180) REVERT: I 73 MET cc_start: 0.7127 (ptt) cc_final: 0.6567 (ptt) REVERT: I 104 GLN cc_start: 0.7745 (pt0) cc_final: 0.7267 (pp30) REVERT: I 107 THR cc_start: 0.8506 (m) cc_final: 0.8264 (t) REVERT: I 151 LYS cc_start: 0.7795 (mmmt) cc_final: 0.7312 (mmmt) REVERT: I 198 TYR cc_start: 0.8345 (m-80) cc_final: 0.7977 (m-80) REVERT: I 213 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7576 (tm-30) REVERT: I 283 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7888 (mmm160) REVERT: I 311 ASP cc_start: 0.7876 (p0) cc_final: 0.7580 (p0) REVERT: I 380 PHE cc_start: 0.8260 (p90) cc_final: 0.7811 (p90) REVERT: I 382 ARG cc_start: 0.8073 (mtt90) cc_final: 0.7844 (mtt90) REVERT: I 443 ASN cc_start: 0.7997 (p0) cc_final: 0.7776 (p0) REVERT: I 472 LYS cc_start: 0.8244 (tptm) cc_final: 0.7991 (mmtp) REVERT: I 528 TRP cc_start: 0.8247 (m100) cc_final: 0.7682 (m100) REVERT: E 216 ARG cc_start: 0.7654 (ttt90) cc_final: 0.7284 (ttt180) REVERT: E 309 GLN cc_start: 0.7557 (mt0) cc_final: 0.6876 (mt0) REVERT: E 312 LYS cc_start: 0.8538 (mttt) cc_final: 0.7436 (mttt) REVERT: E 417 ASN cc_start: 0.8475 (t0) cc_final: 0.7710 (t0) REVERT: E 419 ASN cc_start: 0.8573 (m-40) cc_final: 0.8067 (p0) REVERT: E 428 ASN cc_start: 0.8359 (m-40) cc_final: 0.7909 (t0) REVERT: E 479 LYS cc_start: 0.8699 (mttp) cc_final: 0.8370 (mttp) REVERT: E 582 LYS cc_start: 0.8072 (ttmt) cc_final: 0.7843 (tttt) REVERT: C 54 LEU cc_start: 0.8466 (mt) cc_final: 0.8230 (mm) REVERT: C 77 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7045 (mm-30) REVERT: C 128 LEU cc_start: 0.7961 (tp) cc_final: 0.7730 (tm) REVERT: C 143 GLN cc_start: 0.8085 (mt0) cc_final: 0.7783 (mt0) REVERT: C 183 MET cc_start: 0.7115 (mmm) cc_final: 0.6880 (mmm) REVERT: C 209 ARG cc_start: 0.6973 (pmt170) cc_final: 0.6729 (pmt-80) REVERT: C 387 LYS cc_start: 0.8313 (tttt) cc_final: 0.8082 (tttm) REVERT: C 464 TYR cc_start: 0.7574 (t80) cc_final: 0.7171 (t80) REVERT: C 522 VAL cc_start: 0.8636 (t) cc_final: 0.8309 (m) REVERT: C 538 LYS cc_start: 0.8213 (tptp) cc_final: 0.7659 (tptp) REVERT: G 128 LEU cc_start: 0.8477 (tp) cc_final: 0.8238 (tm) REVERT: G 135 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7106 (mp0) REVERT: G 144 GLU cc_start: 0.7566 (pt0) cc_final: 0.7223 (pt0) REVERT: G 177 LEU cc_start: 0.7989 (tp) cc_final: 0.7696 (tm) REVERT: G 190 MET cc_start: 0.7562 (mmm) cc_final: 0.6831 (mmm) REVERT: G 204 ILE cc_start: 0.8594 (pt) cc_final: 0.8255 (pp) REVERT: G 213 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7939 (tm-30) REVERT: G 266 PHE cc_start: 0.8271 (t80) cc_final: 0.8054 (t80) REVERT: G 276 THR cc_start: 0.8344 (p) cc_final: 0.8119 (t) REVERT: G 469 ILE cc_start: 0.8600 (mt) cc_final: 0.8382 (mm) REVERT: G 527 PHE cc_start: 0.7921 (p90) cc_final: 0.7698 (p90) REVERT: G 536 LYS cc_start: 0.8320 (ttpp) cc_final: 0.8093 (ttpp) REVERT: G 577 GLN cc_start: 0.8486 (mt0) cc_final: 0.8245 (mt0) REVERT: F 73 MET cc_start: 0.7766 (ptt) cc_final: 0.7542 (ptt) REVERT: F 81 ARG cc_start: 0.7448 (ttp-170) cc_final: 0.7147 (pmt170) REVERT: F 115 ASN cc_start: 0.8444 (t0) cc_final: 0.8217 (t0) REVERT: F 177 LEU cc_start: 0.8128 (tp) cc_final: 0.7886 (tt) REVERT: F 186 THR cc_start: 0.8460 (p) cc_final: 0.8180 (p) REVERT: F 254 LEU cc_start: 0.8366 (mt) cc_final: 0.8137 (mt) REVERT: F 380 PHE cc_start: 0.8391 (p90) cc_final: 0.8095 (p90) REVERT: F 532 LYS cc_start: 0.8709 (ptmm) cc_final: 0.8313 (ptmm) outliers start: 9 outliers final: 5 residues processed: 1182 average time/residue: 0.6357 time to fit residues: 899.3484 Evaluate side-chains 1130 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1125 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 558 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 321 ASN A 428 ASN A 565 ASN D 48 GLN D 104 GLN D 213 GLN D 485 ASN D 543 HIS B 242 GLN B 560 ASN I 48 GLN E 48 GLN E 147 ASN E 222 HIS E 234 HIS E 280 GLN C 104 GLN C 143 GLN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 GLN C 549 GLN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN F 85 ASN F 222 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.156107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126180 restraints weight = 49006.034| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.34 r_work: 0.3410 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33952 Z= 0.137 Angle : 0.565 8.577 46439 Z= 0.288 Chirality : 0.043 0.158 5053 Planarity : 0.005 0.059 6105 Dihedral : 5.572 57.815 4518 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.02 % Allowed : 16.19 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.12), residues: 3937 helix: 0.54 (0.46), residues: 89 sheet: -0.54 (0.16), residues: 982 loop : -0.56 (0.11), residues: 2866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 382 TYR 0.030 0.001 TYR B 409 PHE 0.023 0.001 PHE F 448 TRP 0.019 0.001 TRP I 214 HIS 0.007 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00316 (33944) covalent geometry : angle 0.56408 (46423) SS BOND : bond 0.00275 ( 8) SS BOND : angle 1.63078 ( 16) hydrogen bonds : bond 0.03909 ( 355) hydrogen bonds : angle 6.06806 ( 714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1279 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 1173 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 THR cc_start: 0.8567 (t) cc_final: 0.8290 (m) REVERT: A 457 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8045 (mp) REVERT: A 473 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7406 (tm-30) REVERT: A 576 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.8047 (m) REVERT: D 79 TYR cc_start: 0.8745 (m-80) cc_final: 0.8429 (m-80) REVERT: D 209 ARG cc_start: 0.8251 (pmt170) cc_final: 0.5979 (ptm160) REVERT: D 213 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7367 (tm-30) REVERT: D 214 TRP cc_start: 0.8068 (p90) cc_final: 0.7694 (p90) REVERT: D 246 ILE cc_start: 0.7990 (mm) cc_final: 0.7771 (mp) REVERT: D 269 ASP cc_start: 0.7186 (p0) cc_final: 0.6914 (p0) REVERT: D 544 THR cc_start: 0.7980 (m) cc_final: 0.7495 (t) REVERT: B 89 LYS cc_start: 0.8522 (tptt) cc_final: 0.8168 (tptm) REVERT: B 99 ASP cc_start: 0.7516 (t0) cc_final: 0.7271 (t0) REVERT: B 133 MET cc_start: 0.7727 (mmt) cc_final: 0.7437 (mmt) REVERT: B 213 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8112 (tm-30) REVERT: B 230 THR cc_start: 0.8676 (m) cc_final: 0.8446 (t) REVERT: B 269 ASP cc_start: 0.7307 (p0) cc_final: 0.7022 (p0) REVERT: B 329 THR cc_start: 0.8357 (p) cc_final: 0.8142 (t) REVERT: B 378 TYR cc_start: 0.8379 (m-80) cc_final: 0.7539 (m-80) REVERT: B 394 THR cc_start: 0.8716 (t) cc_final: 0.8442 (p) REVERT: B 396 GLU cc_start: 0.8096 (tt0) cc_final: 0.7737 (tt0) REVERT: B 408 ARG cc_start: 0.7860 (mmt-90) cc_final: 0.7220 (mpt180) REVERT: B 464 TYR cc_start: 0.8426 (t80) cc_final: 0.7932 (t80) REVERT: B 473 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7282 (mm-30) REVERT: I 49 THR cc_start: 0.8276 (m) cc_final: 0.7963 (t) REVERT: I 71 LEU cc_start: 0.8375 (tp) cc_final: 0.8105 (tm) REVERT: I 73 MET cc_start: 0.7356 (ptt) cc_final: 0.6873 (ptt) REVERT: I 107 THR cc_start: 0.8700 (m) cc_final: 0.8360 (t) REVERT: I 149 VAL cc_start: 0.7610 (t) cc_final: 0.7251 (p) REVERT: I 151 LYS cc_start: 0.7860 (mmmt) cc_final: 0.7395 (mmmt) REVERT: I 231 ASN cc_start: 0.7735 (t0) cc_final: 0.7527 (t0) REVERT: I 332 ARG cc_start: 0.8514 (mmt180) cc_final: 0.8129 (mmm160) REVERT: I 408 ARG cc_start: 0.8584 (tpp80) cc_final: 0.8229 (tpp80) REVERT: I 472 LYS cc_start: 0.8405 (tptm) cc_final: 0.8105 (mmtp) REVERT: I 500 VAL cc_start: 0.8108 (p) cc_final: 0.7862 (t) REVERT: I 572 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8552 (m) REVERT: E 81 ARG cc_start: 0.8637 (tmm-80) cc_final: 0.8398 (tmm-80) REVERT: E 164 VAL cc_start: 0.8712 (m) cc_final: 0.8400 (p) REVERT: E 168 ASP cc_start: 0.7287 (t0) cc_final: 0.6987 (t0) REVERT: E 216 ARG cc_start: 0.7813 (ttt90) cc_final: 0.7436 (ttt180) REVERT: E 242 GLN cc_start: 0.8535 (mt0) cc_final: 0.8165 (mt0) REVERT: E 244 TYR cc_start: 0.8559 (m-80) cc_final: 0.7890 (m-80) REVERT: E 309 GLN cc_start: 0.7791 (mt0) cc_final: 0.7155 (mt0) REVERT: E 312 LYS cc_start: 0.8650 (mttt) cc_final: 0.7743 (mttt) REVERT: E 411 GLU cc_start: 0.7742 (mp0) cc_final: 0.7210 (mp0) REVERT: E 417 ASN cc_start: 0.8524 (t0) cc_final: 0.8048 (t0) REVERT: E 471 ASP cc_start: 0.8051 (t0) cc_final: 0.7834 (t70) REVERT: E 479 LYS cc_start: 0.8702 (mttp) cc_final: 0.8421 (mtpp) REVERT: C 54 LEU cc_start: 0.8556 (mt) cc_final: 0.8318 (mm) REVERT: C 128 LEU cc_start: 0.8148 (tp) cc_final: 0.7905 (tm) REVERT: C 143 GLN cc_start: 0.8273 (mt0) cc_final: 0.8040 (mt0) REVERT: C 183 MET cc_start: 0.7294 (mmm) cc_final: 0.7056 (mmm) REVERT: C 237 ASP cc_start: 0.7418 (t0) cc_final: 0.7154 (t0) REVERT: C 387 LYS cc_start: 0.8330 (tttt) cc_final: 0.7985 (ttpp) REVERT: C 397 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7525 (pmm-80) REVERT: C 464 TYR cc_start: 0.7613 (t80) cc_final: 0.7384 (t80) REVERT: C 522 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8290 (m) REVERT: C 538 LYS cc_start: 0.8422 (tptp) cc_final: 0.7870 (tptp) REVERT: C 540 ARG cc_start: 0.7617 (ptt90) cc_final: 0.7379 (ptt90) REVERT: C 549 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7321 (pm20) REVERT: G 52 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7693 (ttmm) REVERT: G 79 TYR cc_start: 0.8516 (m-80) cc_final: 0.8124 (m-80) REVERT: G 89 LYS cc_start: 0.8466 (tptt) cc_final: 0.8243 (tptt) REVERT: G 190 MET cc_start: 0.7647 (mmm) cc_final: 0.6940 (mmm) REVERT: G 213 GLN cc_start: 0.8255 (tm-30) cc_final: 0.8046 (tm-30) REVERT: G 240 ASP cc_start: 0.6927 (m-30) cc_final: 0.6639 (m-30) REVERT: G 247 GLU cc_start: 0.8048 (mp0) cc_final: 0.7568 (mp0) REVERT: G 276 THR cc_start: 0.8464 (p) cc_final: 0.8203 (t) REVERT: G 327 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7481 (mm-30) REVERT: G 425 THR cc_start: 0.8383 (t) cc_final: 0.8007 (p) REVERT: G 577 GLN cc_start: 0.8501 (mt0) cc_final: 0.8281 (mt0) REVERT: G 578 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8166 (mm) REVERT: F 73 MET cc_start: 0.8121 (ptt) cc_final: 0.7901 (ptt) REVERT: F 177 LEU cc_start: 0.8155 (tp) cc_final: 0.7831 (tt) REVERT: F 186 THR cc_start: 0.8578 (p) cc_final: 0.8273 (p) REVERT: F 212 PHE cc_start: 0.8456 (t80) cc_final: 0.8225 (t80) REVERT: F 214 TRP cc_start: 0.8546 (p90) cc_final: 0.8112 (p90) REVERT: F 216 ARG cc_start: 0.8089 (ttt90) cc_final: 0.7763 (ttt90) REVERT: F 243 PHE cc_start: 0.8564 (t80) cc_final: 0.8328 (t80) REVERT: F 247 GLU cc_start: 0.7941 (mp0) cc_final: 0.7671 (mp0) REVERT: F 309 GLN cc_start: 0.8055 (tt0) cc_final: 0.7849 (tt0) REVERT: F 336 VAL cc_start: 0.8725 (t) cc_final: 0.8519 (p) REVERT: F 387 LYS cc_start: 0.8390 (tttt) cc_final: 0.8150 (tttt) REVERT: F 475 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7151 (t0) outliers start: 106 outliers final: 56 residues processed: 1203 average time/residue: 0.6079 time to fit residues: 884.0924 Evaluate side-chains 1207 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 1144 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain I residue 46 ASN Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 556 ASP Chi-restraints excluded: chain I residue 564 SER Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 538 LYS Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain C residue 558 GLN Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 511 ASP Chi-restraints excluded: chain G residue 578 LEU Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 475 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 243 optimal weight: 5.9990 chunk 315 optimal weight: 0.9990 chunk 264 optimal weight: 8.9990 chunk 249 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 321 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 GLN D 166 ASN D 167 ASN ** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 GLN B 242 GLN E 48 GLN E 222 HIS E 234 HIS E 280 GLN E 404 GLN E 558 GLN C 549 GLN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN F 102 HIS F 147 ASN F 497 GLN F 549 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.154893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124581 restraints weight = 48611.959| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.36 r_work: 0.3380 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33952 Z= 0.233 Angle : 0.590 8.071 46439 Z= 0.301 Chirality : 0.045 0.159 5053 Planarity : 0.005 0.053 6105 Dihedral : 5.391 54.905 4512 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.79 % Allowed : 17.82 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.12), residues: 3937 helix: 0.22 (0.44), residues: 101 sheet: -0.55 (0.16), residues: 1010 loop : -0.55 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 314 TYR 0.024 0.002 TYR C 464 PHE 0.034 0.002 PHE C 353 TRP 0.022 0.002 TRP I 109 HIS 0.019 0.001 HIS E 222 Details of bonding type rmsd covalent geometry : bond 0.00529 (33944) covalent geometry : angle 0.58921 (46423) SS BOND : bond 0.00326 ( 8) SS BOND : angle 1.83509 ( 16) hydrogen bonds : bond 0.04130 ( 355) hydrogen bonds : angle 5.81409 ( 714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1304 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 1171 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.8245 (m-30) cc_final: 0.8030 (m-30) REVERT: A 396 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7490 (tm-30) REVERT: A 457 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8190 (mp) REVERT: A 510 TYR cc_start: 0.8642 (t80) cc_final: 0.7938 (t80) REVERT: A 576 SER cc_start: 0.8516 (t) cc_final: 0.8117 (m) REVERT: D 79 TYR cc_start: 0.8825 (m-80) cc_final: 0.8533 (m-80) REVERT: D 142 GLU cc_start: 0.8296 (pm20) cc_final: 0.8051 (pm20) REVERT: D 209 ARG cc_start: 0.8347 (pmt170) cc_final: 0.5998 (ptm160) REVERT: D 237 ASP cc_start: 0.7533 (t0) cc_final: 0.7204 (t0) REVERT: D 246 ILE cc_start: 0.7938 (mm) cc_final: 0.7729 (mp) REVERT: D 269 ASP cc_start: 0.7201 (p0) cc_final: 0.6926 (p0) REVERT: D 488 PHE cc_start: 0.8236 (m-80) cc_final: 0.7818 (m-80) REVERT: D 544 THR cc_start: 0.8051 (m) cc_final: 0.7579 (t) REVERT: B 75 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7207 (mm-30) REVERT: B 89 LYS cc_start: 0.8568 (tptt) cc_final: 0.8303 (tptm) REVERT: B 133 MET cc_start: 0.7770 (mmt) cc_final: 0.7383 (mmt) REVERT: B 144 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: B 178 ASP cc_start: 0.7352 (t0) cc_final: 0.6923 (t0) REVERT: B 210 TYR cc_start: 0.8877 (p90) cc_final: 0.8408 (p90) REVERT: B 213 GLN cc_start: 0.8469 (tm-30) cc_final: 0.7972 (tm-30) REVERT: B 230 THR cc_start: 0.8715 (m) cc_final: 0.8482 (t) REVERT: B 247 GLU cc_start: 0.7939 (mp0) cc_final: 0.7455 (mp0) REVERT: B 269 ASP cc_start: 0.7215 (p0) cc_final: 0.6956 (p0) REVERT: B 378 TYR cc_start: 0.8342 (m-80) cc_final: 0.7584 (m-80) REVERT: B 394 THR cc_start: 0.8744 (t) cc_final: 0.8466 (p) REVERT: B 396 GLU cc_start: 0.8080 (tt0) cc_final: 0.7712 (tt0) REVERT: B 408 ARG cc_start: 0.7942 (mmt-90) cc_final: 0.7243 (mpt180) REVERT: B 464 TYR cc_start: 0.8490 (t80) cc_final: 0.7999 (t80) REVERT: B 473 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7317 (mm-30) REVERT: I 49 THR cc_start: 0.8375 (m) cc_final: 0.7998 (t) REVERT: I 71 LEU cc_start: 0.8425 (tp) cc_final: 0.8153 (tm) REVERT: I 73 MET cc_start: 0.7377 (ptt) cc_final: 0.6863 (ptt) REVERT: I 87 MET cc_start: 0.8662 (tpt) cc_final: 0.7730 (tpt) REVERT: I 107 THR cc_start: 0.8490 (m) cc_final: 0.8250 (t) REVERT: I 149 VAL cc_start: 0.7623 (t) cc_final: 0.7275 (p) REVERT: I 151 LYS cc_start: 0.7747 (mmmt) cc_final: 0.7307 (mmmt) REVERT: I 209 ARG cc_start: 0.5754 (OUTLIER) cc_final: 0.5115 (ppt170) REVERT: I 231 ASN cc_start: 0.7849 (t0) cc_final: 0.7539 (t0) REVERT: I 242 GLN cc_start: 0.7660 (mt0) cc_final: 0.7458 (mm110) REVERT: I 332 ARG cc_start: 0.8497 (mmt180) cc_final: 0.8084 (mmm160) REVERT: I 335 GLU cc_start: 0.7738 (tp30) cc_final: 0.7528 (tp30) REVERT: I 338 TYR cc_start: 0.8375 (p90) cc_final: 0.7545 (p90) REVERT: I 408 ARG cc_start: 0.8564 (tpp80) cc_final: 0.8197 (tpp80) REVERT: I 411 GLU cc_start: 0.8217 (mp0) cc_final: 0.7802 (mp0) REVERT: I 464 TYR cc_start: 0.8783 (t80) cc_final: 0.8549 (t80) REVERT: I 466 ASN cc_start: 0.8226 (m-40) cc_final: 0.8003 (m-40) REVERT: I 500 VAL cc_start: 0.8149 (p) cc_final: 0.7806 (t) REVERT: I 572 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8554 (m) REVERT: E 164 VAL cc_start: 0.8743 (m) cc_final: 0.8413 (p) REVERT: E 168 ASP cc_start: 0.7261 (t0) cc_final: 0.6851 (t0) REVERT: E 190 MET cc_start: 0.8470 (tpp) cc_final: 0.7935 (ttp) REVERT: E 216 ARG cc_start: 0.7952 (ttt90) cc_final: 0.7568 (ttt180) REVERT: E 242 GLN cc_start: 0.8573 (mt0) cc_final: 0.8177 (mt0) REVERT: E 244 TYR cc_start: 0.8569 (m-80) cc_final: 0.7872 (m-80) REVERT: E 309 GLN cc_start: 0.7813 (mt0) cc_final: 0.7144 (mt0) REVERT: E 312 LYS cc_start: 0.8633 (mttt) cc_final: 0.7708 (mttt) REVERT: E 404 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: E 411 GLU cc_start: 0.7754 (mp0) cc_final: 0.7197 (mp0) REVERT: E 417 ASN cc_start: 0.8622 (t0) cc_final: 0.8152 (t0) REVERT: C 54 LEU cc_start: 0.8626 (mt) cc_final: 0.8394 (mm) REVERT: C 128 LEU cc_start: 0.8163 (tp) cc_final: 0.7952 (tm) REVERT: C 143 GLN cc_start: 0.8324 (mt0) cc_final: 0.8090 (mt0) REVERT: C 183 MET cc_start: 0.7476 (mmm) cc_final: 0.7220 (mmm) REVERT: C 237 ASP cc_start: 0.7475 (t0) cc_final: 0.7092 (t0) REVERT: C 397 ARG cc_start: 0.7871 (mtt180) cc_final: 0.7542 (pmm-80) REVERT: C 464 TYR cc_start: 0.7624 (t80) cc_final: 0.7248 (t80) REVERT: C 522 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8321 (m) REVERT: C 538 LYS cc_start: 0.8419 (tptp) cc_final: 0.7794 (tptp) REVERT: C 540 ARG cc_start: 0.7579 (ptt90) cc_final: 0.7197 (ptt90) REVERT: C 575 LYS cc_start: 0.7620 (mmtm) cc_final: 0.7288 (mmtm) REVERT: G 52 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7728 (ttmm) REVERT: G 77 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7758 (mm-30) REVERT: G 79 TYR cc_start: 0.8454 (m-80) cc_final: 0.7973 (m-80) REVERT: G 89 LYS cc_start: 0.8482 (tptt) cc_final: 0.8256 (tptt) REVERT: G 135 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: G 190 MET cc_start: 0.7681 (mmm) cc_final: 0.6985 (mmm) REVERT: G 204 ILE cc_start: 0.8644 (pt) cc_final: 0.8288 (pp) REVERT: G 213 GLN cc_start: 0.8294 (tm-30) cc_final: 0.8033 (tm-30) REVERT: G 247 GLU cc_start: 0.8107 (mp0) cc_final: 0.7562 (mp0) REVERT: G 276 THR cc_start: 0.8501 (p) cc_final: 0.8230 (t) REVERT: G 327 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7568 (mm-30) REVERT: G 344 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8407 (p) REVERT: G 439 LYS cc_start: 0.8001 (mmtp) cc_final: 0.7735 (mmtm) REVERT: G 530 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8176 (ttmt) REVERT: G 577 GLN cc_start: 0.8489 (mt0) cc_final: 0.8243 (mt0) REVERT: F 50 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7580 (mp0) REVERT: F 148 VAL cc_start: 0.8739 (t) cc_final: 0.8334 (p) REVERT: F 177 LEU cc_start: 0.8151 (tp) cc_final: 0.7851 (tt) REVERT: F 214 TRP cc_start: 0.8607 (p90) cc_final: 0.8048 (p90) REVERT: F 216 ARG cc_start: 0.8141 (ttt90) cc_final: 0.7926 (ttt-90) REVERT: F 243 PHE cc_start: 0.8639 (t80) cc_final: 0.8316 (t80) REVERT: F 247 GLU cc_start: 0.8007 (mp0) cc_final: 0.7705 (mp0) REVERT: F 309 GLN cc_start: 0.8183 (tt0) cc_final: 0.7952 (tt0) REVERT: F 387 LYS cc_start: 0.8402 (tttt) cc_final: 0.8163 (tttt) REVERT: F 475 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7043 (t0) REVERT: F 525 SER cc_start: 0.8542 (t) cc_final: 0.7989 (p) outliers start: 133 outliers final: 78 residues processed: 1206 average time/residue: 0.6090 time to fit residues: 885.7000 Evaluate side-chains 1233 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1145 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 209 ARG Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 445 THR Chi-restraints excluded: chain I residue 481 ARG Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 564 SER Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 538 LYS Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 511 ASP Chi-restraints excluded: chain G residue 530 LYS Chi-restraints excluded: chain G residue 574 GLU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 475 ASP Chi-restraints excluded: chain F residue 497 GLN Chi-restraints excluded: chain F residue 536 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 80 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 chunk 274 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN D 104 GLN D 231 ASN B 137 HIS E 48 GLN E 64 ASN E 222 HIS E 234 HIS E 280 GLN E 404 GLN E 558 GLN C 386 GLN C 549 GLN C 558 GLN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN F 85 ASN F 147 ASN F 302 ASN F 549 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.125893 restraints weight = 48140.690| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.32 r_work: 0.3401 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33952 Z= 0.139 Angle : 0.543 8.590 46439 Z= 0.275 Chirality : 0.043 0.147 5053 Planarity : 0.004 0.048 6105 Dihedral : 5.000 53.449 4509 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.51 % Allowed : 19.90 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 3937 helix: 0.54 (0.46), residues: 95 sheet: -0.44 (0.16), residues: 947 loop : -0.46 (0.11), residues: 2895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 314 TYR 0.024 0.001 TYR E 233 PHE 0.032 0.001 PHE C 53 TRP 0.023 0.001 TRP I 214 HIS 0.005 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00321 (33944) covalent geometry : angle 0.54196 (46423) SS BOND : bond 0.00200 ( 8) SS BOND : angle 1.54742 ( 16) hydrogen bonds : bond 0.03537 ( 355) hydrogen bonds : angle 5.65338 ( 714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1279 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1156 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.7704 (t70) cc_final: 0.7330 (t70) REVERT: A 265 THR cc_start: 0.8545 (m) cc_final: 0.8241 (t) REVERT: A 380 PHE cc_start: 0.8517 (p90) cc_final: 0.8301 (p90) REVERT: A 396 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7411 (tm-30) REVERT: A 457 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8144 (mp) REVERT: A 576 SER cc_start: 0.8485 (t) cc_final: 0.8083 (m) REVERT: D 77 GLU cc_start: 0.7227 (mm-30) cc_final: 0.7000 (mm-30) REVERT: D 79 TYR cc_start: 0.8840 (m-80) cc_final: 0.8473 (m-80) REVERT: D 142 GLU cc_start: 0.8276 (pm20) cc_final: 0.8006 (pm20) REVERT: D 209 ARG cc_start: 0.8279 (pmt170) cc_final: 0.5855 (ptm160) REVERT: D 237 ASP cc_start: 0.7524 (t0) cc_final: 0.7260 (t0) REVERT: D 246 ILE cc_start: 0.7851 (mm) cc_final: 0.7620 (mp) REVERT: D 269 ASP cc_start: 0.7117 (p0) cc_final: 0.6804 (p0) REVERT: D 355 THR cc_start: 0.7824 (m) cc_final: 0.7300 (p) REVERT: D 488 PHE cc_start: 0.8249 (m-80) cc_final: 0.7859 (m-80) REVERT: D 544 THR cc_start: 0.8021 (m) cc_final: 0.7555 (t) REVERT: D 574 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6970 (mm-30) REVERT: D 581 ARG cc_start: 0.8088 (ttm110) cc_final: 0.7879 (ttp80) REVERT: B 42 THR cc_start: 0.8446 (t) cc_final: 0.8046 (t) REVERT: B 89 LYS cc_start: 0.8579 (tptt) cc_final: 0.8338 (tptm) REVERT: B 96 MET cc_start: 0.8263 (ptp) cc_final: 0.8037 (ptp) REVERT: B 133 MET cc_start: 0.7703 (mmt) cc_final: 0.7296 (mmt) REVERT: B 230 THR cc_start: 0.8634 (m) cc_final: 0.8390 (t) REVERT: B 269 ASP cc_start: 0.7253 (p0) cc_final: 0.6970 (p0) REVERT: B 378 TYR cc_start: 0.8337 (m-80) cc_final: 0.7566 (m-80) REVERT: B 387 LYS cc_start: 0.8593 (tttt) cc_final: 0.8320 (tttt) REVERT: B 394 THR cc_start: 0.8757 (t) cc_final: 0.8533 (p) REVERT: B 396 GLU cc_start: 0.8094 (tt0) cc_final: 0.7681 (tt0) REVERT: B 408 ARG cc_start: 0.7972 (mmt-90) cc_final: 0.7312 (mpt180) REVERT: B 464 TYR cc_start: 0.8489 (t80) cc_final: 0.8097 (t80) REVERT: B 473 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7279 (mm-30) REVERT: I 49 THR cc_start: 0.8340 (m) cc_final: 0.8026 (t) REVERT: I 71 LEU cc_start: 0.8436 (tp) cc_final: 0.8173 (tm) REVERT: I 73 MET cc_start: 0.7454 (ptt) cc_final: 0.6951 (ptt) REVERT: I 87 MET cc_start: 0.8640 (tpt) cc_final: 0.7808 (tpt) REVERT: I 107 THR cc_start: 0.8489 (m) cc_final: 0.8246 (t) REVERT: I 138 LEU cc_start: 0.8153 (mt) cc_final: 0.7810 (mm) REVERT: I 149 VAL cc_start: 0.7631 (t) cc_final: 0.7281 (p) REVERT: I 151 LYS cc_start: 0.7679 (mmmt) cc_final: 0.7249 (mmmt) REVERT: I 209 ARG cc_start: 0.5626 (OUTLIER) cc_final: 0.4596 (ppt170) REVERT: I 213 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7771 (tp40) REVERT: I 231 ASN cc_start: 0.7793 (t0) cc_final: 0.7530 (t0) REVERT: I 280 GLN cc_start: 0.8406 (mt0) cc_final: 0.8188 (mt0) REVERT: I 314 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.8015 (ttm110) REVERT: I 330 ILE cc_start: 0.8629 (tt) cc_final: 0.8342 (tp) REVERT: I 408 ARG cc_start: 0.8531 (tpp-160) cc_final: 0.8312 (tpp80) REVERT: I 418 ILE cc_start: 0.8752 (tt) cc_final: 0.8548 (mm) REVERT: I 466 ASN cc_start: 0.8196 (m-40) cc_final: 0.7976 (m-40) REVERT: I 548 ILE cc_start: 0.7965 (pt) cc_final: 0.7629 (pp) REVERT: I 572 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8538 (m) REVERT: E 164 VAL cc_start: 0.8747 (m) cc_final: 0.8417 (p) REVERT: E 168 ASP cc_start: 0.7234 (t0) cc_final: 0.6759 (t0) REVERT: E 216 ARG cc_start: 0.7865 (ttt90) cc_final: 0.7460 (ttt180) REVERT: E 244 TYR cc_start: 0.8602 (m-80) cc_final: 0.8275 (m-80) REVERT: E 309 GLN cc_start: 0.7769 (mt0) cc_final: 0.7276 (mt0) REVERT: E 312 LYS cc_start: 0.8630 (mttt) cc_final: 0.7851 (mttt) REVERT: E 404 GLN cc_start: 0.8150 (pt0) cc_final: 0.7659 (tm-30) REVERT: E 411 GLU cc_start: 0.7731 (mp0) cc_final: 0.7216 (mp0) REVERT: E 417 ASN cc_start: 0.8628 (t0) cc_final: 0.7831 (t0) REVERT: E 419 ASN cc_start: 0.8711 (m-40) cc_final: 0.8083 (p0) REVERT: E 434 ASP cc_start: 0.7674 (m-30) cc_final: 0.7338 (m-30) REVERT: C 128 LEU cc_start: 0.8152 (tp) cc_final: 0.7902 (tm) REVERT: C 143 GLN cc_start: 0.8299 (mt0) cc_final: 0.8065 (mt0) REVERT: C 183 MET cc_start: 0.7390 (mmm) cc_final: 0.7162 (mmm) REVERT: C 237 ASP cc_start: 0.7354 (t0) cc_final: 0.6964 (t0) REVERT: C 387 LYS cc_start: 0.8377 (tttt) cc_final: 0.7980 (tmtt) REVERT: C 397 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7555 (pmm-80) REVERT: C 463 VAL cc_start: 0.8662 (t) cc_final: 0.8384 (t) REVERT: C 464 TYR cc_start: 0.7617 (t80) cc_final: 0.7298 (t80) REVERT: C 522 VAL cc_start: 0.8671 (t) cc_final: 0.8308 (m) REVERT: C 526 ASP cc_start: 0.7662 (m-30) cc_final: 0.7404 (m-30) REVERT: C 538 LYS cc_start: 0.8444 (tptp) cc_final: 0.7809 (tptp) REVERT: C 540 ARG cc_start: 0.7566 (ptt90) cc_final: 0.7147 (ptt90) REVERT: C 575 LYS cc_start: 0.7518 (mmtm) cc_final: 0.7260 (mmtm) REVERT: G 52 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7740 (ttmm) REVERT: G 72 ASN cc_start: 0.8271 (m-40) cc_final: 0.7953 (m-40) REVERT: G 77 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7223 (mm-30) REVERT: G 79 TYR cc_start: 0.8441 (m-80) cc_final: 0.8222 (m-80) REVERT: G 89 LYS cc_start: 0.8475 (tptt) cc_final: 0.8245 (tptt) REVERT: G 135 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7739 (mp0) REVERT: G 190 MET cc_start: 0.7656 (mmm) cc_final: 0.6930 (mmm) REVERT: G 204 ILE cc_start: 0.8635 (pt) cc_final: 0.8280 (pp) REVERT: G 276 THR cc_start: 0.8468 (p) cc_final: 0.8204 (p) REVERT: G 285 LEU cc_start: 0.8503 (mm) cc_final: 0.8266 (mm) REVERT: G 327 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7669 (mm-30) REVERT: G 527 PHE cc_start: 0.8228 (p90) cc_final: 0.7931 (p90) REVERT: G 530 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8081 (ttmt) REVERT: G 536 LYS cc_start: 0.8532 (ttpp) cc_final: 0.8281 (mtpp) REVERT: G 577 GLN cc_start: 0.8473 (mt0) cc_final: 0.8233 (mt0) REVERT: G 578 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8204 (mm) REVERT: G 582 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7859 (mtmt) REVERT: F 50 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7582 (mp0) REVERT: F 81 ARG cc_start: 0.7977 (ttp-170) cc_final: 0.7316 (pmt170) REVERT: F 109 TRP cc_start: 0.8459 (m100) cc_final: 0.8182 (m100) REVERT: F 148 VAL cc_start: 0.8750 (t) cc_final: 0.8373 (m) REVERT: F 177 LEU cc_start: 0.8089 (tp) cc_final: 0.7848 (tp) REVERT: F 214 TRP cc_start: 0.8582 (p90) cc_final: 0.8058 (p90) REVERT: F 216 ARG cc_start: 0.8148 (ttt90) cc_final: 0.7640 (ttt-90) REVERT: F 247 GLU cc_start: 0.7972 (mp0) cc_final: 0.7666 (mp0) REVERT: F 473 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6811 (tm-30) REVERT: F 475 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7068 (t0) REVERT: F 525 SER cc_start: 0.8568 (t) cc_final: 0.7976 (p) outliers start: 123 outliers final: 74 residues processed: 1195 average time/residue: 0.6034 time to fit residues: 871.5519 Evaluate side-chains 1234 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 1154 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 209 ARG Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 448 PHE Chi-restraints excluded: chain I residue 481 ARG Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 564 SER Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 530 LYS Chi-restraints excluded: chain G residue 578 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 475 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 10 optimal weight: 10.0000 chunk 367 optimal weight: 8.9990 chunk 291 optimal weight: 6.9990 chunk 358 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 280 optimal weight: 10.0000 chunk 286 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 397 optimal weight: 0.4980 chunk 284 optimal weight: 9.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN D 104 GLN D 231 ASN B 70 HIS B 72 ASN B 137 HIS B 242 GLN I 127 GLN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 550 GLN E 48 GLN E 222 HIS E 234 HIS E 280 GLN E 350 GLN E 558 GLN C 72 ASN C 167 ASN C 491 GLN C 549 GLN G 104 GLN G 242 GLN G 416 GLN F 85 ASN F 147 ASN F 302 ASN F 309 GLN F 468 GLN F 497 GLN F 549 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.151915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.121959 restraints weight = 48744.839| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.32 r_work: 0.3360 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 33952 Z= 0.341 Angle : 0.639 8.587 46439 Z= 0.328 Chirality : 0.048 0.180 5053 Planarity : 0.005 0.057 6105 Dihedral : 5.341 52.880 4509 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.16 % Allowed : 20.30 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.12), residues: 3937 helix: 0.58 (0.49), residues: 94 sheet: -0.70 (0.16), residues: 972 loop : -0.52 (0.11), residues: 2871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 80 TYR 0.027 0.002 TYR F 342 PHE 0.034 0.002 PHE C 53 TRP 0.025 0.002 TRP G 58 HIS 0.005 0.001 HIS F 403 Details of bonding type rmsd covalent geometry : bond 0.00769 (33944) covalent geometry : angle 0.63793 (46423) SS BOND : bond 0.00367 ( 8) SS BOND : angle 2.18596 ( 16) hydrogen bonds : bond 0.04191 ( 355) hydrogen bonds : angle 5.73959 ( 714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 1190 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.8103 (m-30) cc_final: 0.7815 (m-30) REVERT: A 396 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: A 457 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8415 (mp) REVERT: A 510 TYR cc_start: 0.8653 (t80) cc_final: 0.7992 (t80) REVERT: A 551 MET cc_start: 0.8083 (ttt) cc_final: 0.7858 (ttt) REVERT: A 576 SER cc_start: 0.8518 (t) cc_final: 0.8156 (m) REVERT: D 60 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7478 (tm-30) REVERT: D 77 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7052 (mm-30) REVERT: D 79 TYR cc_start: 0.8872 (m-80) cc_final: 0.8523 (m-80) REVERT: D 106 VAL cc_start: 0.8389 (t) cc_final: 0.7864 (m) REVERT: D 120 TRP cc_start: 0.8572 (m100) cc_final: 0.8189 (m100) REVERT: D 142 GLU cc_start: 0.8252 (pm20) cc_final: 0.8010 (pm20) REVERT: D 209 ARG cc_start: 0.8397 (pmt170) cc_final: 0.6017 (ptm160) REVERT: D 246 ILE cc_start: 0.7933 (mm) cc_final: 0.7701 (mp) REVERT: D 269 ASP cc_start: 0.7228 (p0) cc_final: 0.6943 (p0) REVERT: D 355 THR cc_start: 0.7846 (m) cc_final: 0.7329 (p) REVERT: D 518 MET cc_start: 0.7800 (ptp) cc_final: 0.7489 (ptp) REVERT: D 532 LYS cc_start: 0.8642 (tttt) cc_final: 0.8206 (tttt) REVERT: D 544 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7618 (t) REVERT: D 574 GLU cc_start: 0.7259 (mm-30) cc_final: 0.7008 (mm-30) REVERT: B 42 THR cc_start: 0.8443 (t) cc_final: 0.8064 (t) REVERT: B 51 PHE cc_start: 0.8434 (m-80) cc_final: 0.8070 (m-80) REVERT: B 89 LYS cc_start: 0.8552 (tptt) cc_final: 0.8332 (tptm) REVERT: B 92 VAL cc_start: 0.8590 (p) cc_final: 0.8296 (m) REVERT: B 96 MET cc_start: 0.8343 (ptp) cc_final: 0.8085 (ptp) REVERT: B 133 MET cc_start: 0.7677 (mmt) cc_final: 0.7292 (mmt) REVERT: B 144 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8005 (pt0) REVERT: B 201 LYS cc_start: 0.8496 (mtpt) cc_final: 0.8200 (mtpt) REVERT: B 210 TYR cc_start: 0.8963 (p90) cc_final: 0.8533 (p90) REVERT: B 230 THR cc_start: 0.8749 (m) cc_final: 0.8485 (t) REVERT: B 236 THR cc_start: 0.8030 (m) cc_final: 0.7697 (p) REVERT: B 247 GLU cc_start: 0.7913 (mp0) cc_final: 0.7450 (mp0) REVERT: B 269 ASP cc_start: 0.7284 (p0) cc_final: 0.7032 (p0) REVERT: B 378 TYR cc_start: 0.8370 (m-80) cc_final: 0.7662 (m-80) REVERT: B 394 THR cc_start: 0.8744 (t) cc_final: 0.8502 (p) REVERT: B 396 GLU cc_start: 0.8099 (tt0) cc_final: 0.7586 (tt0) REVERT: B 408 ARG cc_start: 0.7958 (mmt-90) cc_final: 0.7184 (mpt180) REVERT: B 435 PRO cc_start: 0.8675 (Cg_endo) cc_final: 0.8366 (Cg_exo) REVERT: B 464 TYR cc_start: 0.8536 (t80) cc_final: 0.8119 (t80) REVERT: B 473 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7148 (mm-30) REVERT: B 509 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7334 (mm-30) REVERT: B 535 PHE cc_start: 0.8425 (m-80) cc_final: 0.7884 (m-10) REVERT: B 575 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7666 (mmtm) REVERT: I 49 THR cc_start: 0.8280 (m) cc_final: 0.7856 (p) REVERT: I 67 ARG cc_start: 0.7614 (mmt-90) cc_final: 0.6923 (mtt-85) REVERT: I 71 LEU cc_start: 0.8492 (tp) cc_final: 0.8204 (tm) REVERT: I 73 MET cc_start: 0.7385 (ptt) cc_final: 0.6892 (ptt) REVERT: I 87 MET cc_start: 0.8515 (tpt) cc_final: 0.7716 (tpt) REVERT: I 107 THR cc_start: 0.8518 (m) cc_final: 0.8263 (t) REVERT: I 138 LEU cc_start: 0.8170 (mt) cc_final: 0.7797 (mm) REVERT: I 149 VAL cc_start: 0.7654 (t) cc_final: 0.7312 (p) REVERT: I 151 LYS cc_start: 0.7724 (mmmt) cc_final: 0.7282 (mmmt) REVERT: I 209 ARG cc_start: 0.5739 (OUTLIER) cc_final: 0.5349 (ppt170) REVERT: I 314 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.8027 (ttm110) REVERT: I 330 ILE cc_start: 0.8644 (tt) cc_final: 0.8386 (tp) REVERT: I 408 ARG cc_start: 0.8547 (tpp-160) cc_final: 0.8346 (tpp80) REVERT: I 411 GLU cc_start: 0.8307 (mp0) cc_final: 0.7909 (mp0) REVERT: I 415 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8302 (mm) REVERT: I 466 ASN cc_start: 0.8262 (m-40) cc_final: 0.8012 (m-40) REVERT: I 472 LYS cc_start: 0.8325 (tptm) cc_final: 0.7919 (tppt) REVERT: I 548 ILE cc_start: 0.8065 (pt) cc_final: 0.7806 (pp) REVERT: I 566 ILE cc_start: 0.8413 (pp) cc_final: 0.8208 (pt) REVERT: I 572 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8350 (m) REVERT: I 574 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7180 (mm-30) REVERT: E 99 ASP cc_start: 0.8241 (t0) cc_final: 0.7351 (t0) REVERT: E 133 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8024 (mmm) REVERT: E 168 ASP cc_start: 0.7278 (t0) cc_final: 0.6707 (t0) REVERT: E 216 ARG cc_start: 0.7962 (ttt90) cc_final: 0.7413 (ttt90) REVERT: E 269 ASP cc_start: 0.7697 (p0) cc_final: 0.7427 (p0) REVERT: E 309 GLN cc_start: 0.7831 (mt0) cc_final: 0.7166 (mt0) REVERT: E 312 LYS cc_start: 0.8672 (mttt) cc_final: 0.7714 (mttt) REVERT: E 405 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6613 (m-30) REVERT: E 411 GLU cc_start: 0.7744 (mp0) cc_final: 0.7242 (mp0) REVERT: E 416 GLN cc_start: 0.8584 (pt0) cc_final: 0.8248 (pt0) REVERT: E 417 ASN cc_start: 0.8615 (t0) cc_final: 0.8184 (t0) REVERT: E 447 ILE cc_start: 0.8100 (pt) cc_final: 0.7683 (mm) REVERT: E 475 ASP cc_start: 0.7935 (t0) cc_final: 0.7728 (t0) REVERT: E 479 LYS cc_start: 0.8658 (mttp) cc_final: 0.8428 (mttp) REVERT: C 54 LEU cc_start: 0.8678 (mt) cc_final: 0.8427 (mm) REVERT: C 128 LEU cc_start: 0.8224 (tp) cc_final: 0.7990 (tm) REVERT: C 183 MET cc_start: 0.7561 (mmm) cc_final: 0.7297 (mmm) REVERT: C 190 MET cc_start: 0.7962 (mmm) cc_final: 0.7371 (mmm) REVERT: C 209 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6335 (pmt-80) REVERT: C 222 HIS cc_start: 0.3264 (OUTLIER) cc_final: 0.2480 (t-170) REVERT: C 247 GLU cc_start: 0.7694 (mp0) cc_final: 0.7330 (mp0) REVERT: C 382 ARG cc_start: 0.8720 (mpp80) cc_final: 0.8314 (tpp80) REVERT: C 397 ARG cc_start: 0.7902 (mtt180) cc_final: 0.7553 (pmm-80) REVERT: C 463 VAL cc_start: 0.8598 (t) cc_final: 0.8310 (t) REVERT: C 464 TYR cc_start: 0.7793 (t80) cc_final: 0.7273 (t80) REVERT: C 511 ASP cc_start: 0.7776 (p0) cc_final: 0.7527 (p0) REVERT: C 522 VAL cc_start: 0.8738 (t) cc_final: 0.8362 (m) REVERT: C 526 ASP cc_start: 0.7701 (m-30) cc_final: 0.7469 (m-30) REVERT: C 538 LYS cc_start: 0.8422 (tptp) cc_final: 0.7798 (tptp) REVERT: C 540 ARG cc_start: 0.7605 (ptt90) cc_final: 0.7358 (ptt90) REVERT: C 559 PHE cc_start: 0.8593 (m-80) cc_final: 0.8367 (m-80) REVERT: C 560 ASN cc_start: 0.8437 (m-40) cc_final: 0.8007 (m110) REVERT: G 52 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7780 (ttmm) REVERT: G 77 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7255 (tm-30) REVERT: G 79 TYR cc_start: 0.8475 (m-80) cc_final: 0.8241 (m-80) REVERT: G 89 LYS cc_start: 0.8496 (tptt) cc_final: 0.8278 (tptt) REVERT: G 106 VAL cc_start: 0.8209 (t) cc_final: 0.7761 (m) REVERT: G 135 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: G 190 MET cc_start: 0.7640 (mmm) cc_final: 0.6976 (mmm) REVERT: G 204 ILE cc_start: 0.8737 (pt) cc_final: 0.8381 (pp) REVERT: G 239 ASP cc_start: 0.7576 (p0) cc_final: 0.7301 (p0) REVERT: G 276 THR cc_start: 0.8479 (p) cc_final: 0.8230 (p) REVERT: G 327 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7683 (mm-30) REVERT: G 344 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8417 (p) REVERT: G 440 THR cc_start: 0.8458 (p) cc_final: 0.8211 (t) REVERT: G 530 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8188 (ttmt) REVERT: G 536 LYS cc_start: 0.8593 (ttpp) cc_final: 0.8338 (mtpp) REVERT: G 577 GLN cc_start: 0.8527 (mt0) cc_final: 0.8256 (mt0) REVERT: F 50 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7544 (mp0) REVERT: F 81 ARG cc_start: 0.8073 (ttp-170) cc_final: 0.7448 (pmt170) REVERT: F 102 HIS cc_start: 0.8623 (p-80) cc_final: 0.8156 (p-80) REVERT: F 148 VAL cc_start: 0.8707 (t) cc_final: 0.8365 (m) REVERT: F 177 LEU cc_start: 0.8112 (tp) cc_final: 0.7859 (tt) REVERT: F 214 TRP cc_start: 0.8644 (p90) cc_final: 0.8123 (p90) REVERT: F 216 ARG cc_start: 0.8224 (ttt90) cc_final: 0.7845 (ttt-90) REVERT: F 243 PHE cc_start: 0.8652 (t80) cc_final: 0.8414 (t80) REVERT: F 247 GLU cc_start: 0.8072 (mp0) cc_final: 0.7696 (mp0) REVERT: F 326 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8235 (t) REVERT: F 448 PHE cc_start: 0.8446 (t80) cc_final: 0.8240 (t80) REVERT: F 473 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6390 (tm-30) REVERT: F 475 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7155 (t0) REVERT: F 491 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7836 (mm-40) REVERT: F 525 SER cc_start: 0.8562 (t) cc_final: 0.8025 (p) REVERT: F 544 THR cc_start: 0.8582 (p) cc_final: 0.8377 (p) outliers start: 146 outliers final: 92 residues processed: 1238 average time/residue: 0.5993 time to fit residues: 897.0919 Evaluate side-chains 1271 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1163 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 209 ARG Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 448 PHE Chi-restraints excluded: chain I residue 481 ARG Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 530 LYS Chi-restraints excluded: chain I residue 564 SER Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain G residue 280 GLN Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 511 ASP Chi-restraints excluded: chain G residue 530 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 475 ASP Chi-restraints excluded: chain F residue 497 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 404 optimal weight: 0.5980 chunk 323 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 254 optimal weight: 0.9990 chunk 321 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 335 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 274 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN D 104 GLN D 231 ASN D 577 GLN B 137 HIS ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 222 HIS E 280 GLN E 404 GLN E 558 GLN C 167 ASN C 549 GLN G 85 ASN G 95 ASN G 104 GLN G 416 GLN G 419 ASN F 72 ASN F 85 ASN F 147 ASN F 222 HIS ** F 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 ASN F 309 GLN F 549 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.154465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124874 restraints weight = 48405.838| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.29 r_work: 0.3381 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 33952 Z= 0.197 Angle : 0.581 9.210 46439 Z= 0.296 Chirality : 0.044 0.156 5053 Planarity : 0.005 0.083 6105 Dihedral : 5.089 55.014 4509 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.36 % Allowed : 21.44 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.13), residues: 3937 helix: 0.62 (0.48), residues: 94 sheet: -0.65 (0.16), residues: 963 loop : -0.49 (0.11), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 216 TYR 0.025 0.002 TYR E 233 PHE 0.036 0.002 PHE C 53 TRP 0.026 0.001 TRP G 58 HIS 0.014 0.001 HIS E 222 Details of bonding type rmsd covalent geometry : bond 0.00450 (33944) covalent geometry : angle 0.57983 (46423) SS BOND : bond 0.00340 ( 8) SS BOND : angle 1.75939 ( 16) hydrogen bonds : bond 0.03666 ( 355) hydrogen bonds : angle 5.66213 ( 714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 1183 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 99 ASP cc_start: 0.7730 (t70) cc_final: 0.7360 (t70) REVERT: A 380 PHE cc_start: 0.8525 (p90) cc_final: 0.8299 (p90) REVERT: A 396 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 457 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8263 (mp) REVERT: A 576 SER cc_start: 0.8514 (t) cc_final: 0.8154 (m) REVERT: D 52 LYS cc_start: 0.8285 (ttmm) cc_final: 0.7967 (ttmm) REVERT: D 60 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7590 (tm-30) REVERT: D 77 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7110 (mm-30) REVERT: D 79 TYR cc_start: 0.8871 (m-80) cc_final: 0.8602 (m-80) REVERT: D 142 GLU cc_start: 0.8189 (pm20) cc_final: 0.7959 (pm20) REVERT: D 209 ARG cc_start: 0.8354 (pmt170) cc_final: 0.6099 (ptm160) REVERT: D 214 TRP cc_start: 0.8182 (p90) cc_final: 0.7933 (p90) REVERT: D 237 ASP cc_start: 0.7700 (t0) cc_final: 0.7428 (t0) REVERT: D 246 ILE cc_start: 0.7924 (mm) cc_final: 0.7687 (mp) REVERT: D 269 ASP cc_start: 0.7149 (p0) cc_final: 0.6848 (p0) REVERT: D 355 THR cc_start: 0.7867 (m) cc_final: 0.7359 (p) REVERT: D 488 PHE cc_start: 0.8282 (m-80) cc_final: 0.7925 (m-80) REVERT: D 518 MET cc_start: 0.7766 (ptp) cc_final: 0.7401 (ptp) REVERT: D 532 LYS cc_start: 0.8638 (tttt) cc_final: 0.8226 (tttt) REVERT: D 544 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7604 (t) REVERT: D 558 GLN cc_start: 0.8457 (pt0) cc_final: 0.8226 (pt0) REVERT: D 574 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6990 (mm-30) REVERT: B 51 PHE cc_start: 0.8375 (m-80) cc_final: 0.8112 (m-80) REVERT: B 89 LYS cc_start: 0.8573 (tptt) cc_final: 0.8360 (tptm) REVERT: B 92 VAL cc_start: 0.8572 (p) cc_final: 0.8270 (m) REVERT: B 96 MET cc_start: 0.8315 (ptp) cc_final: 0.8002 (ptp) REVERT: B 133 MET cc_start: 0.7658 (mmt) cc_final: 0.7296 (mmt) REVERT: B 144 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7967 (pt0) REVERT: B 168 ASP cc_start: 0.7195 (t0) cc_final: 0.6855 (t0) REVERT: B 230 THR cc_start: 0.8693 (m) cc_final: 0.8448 (t) REVERT: B 247 GLU cc_start: 0.7903 (mp0) cc_final: 0.7435 (mp0) REVERT: B 269 ASP cc_start: 0.7302 (p0) cc_final: 0.7030 (p0) REVERT: B 346 GLU cc_start: 0.6894 (tt0) cc_final: 0.6545 (tt0) REVERT: B 378 TYR cc_start: 0.8356 (m-80) cc_final: 0.7552 (m-80) REVERT: B 394 THR cc_start: 0.8758 (t) cc_final: 0.8533 (p) REVERT: B 396 GLU cc_start: 0.8048 (tt0) cc_final: 0.7529 (tt0) REVERT: B 408 ARG cc_start: 0.7961 (mmt-90) cc_final: 0.7251 (mpt180) REVERT: B 435 PRO cc_start: 0.8645 (Cg_endo) cc_final: 0.8332 (Cg_exo) REVERT: B 464 TYR cc_start: 0.8499 (t80) cc_final: 0.8106 (t80) REVERT: B 473 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7245 (mm-30) REVERT: B 497 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: B 509 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7269 (mm-30) REVERT: B 535 PHE cc_start: 0.8362 (m-80) cc_final: 0.7822 (m-10) REVERT: B 551 MET cc_start: 0.7154 (ttt) cc_final: 0.6817 (ttt) REVERT: B 575 LYS cc_start: 0.8098 (mmtm) cc_final: 0.7815 (mmtm) REVERT: I 49 THR cc_start: 0.8192 (m) cc_final: 0.7887 (p) REVERT: I 55 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7188 (tp30) REVERT: I 71 LEU cc_start: 0.8453 (tp) cc_final: 0.8159 (tm) REVERT: I 73 MET cc_start: 0.7384 (ptt) cc_final: 0.6893 (ptt) REVERT: I 86 ASN cc_start: 0.7903 (p0) cc_final: 0.7657 (p0) REVERT: I 87 MET cc_start: 0.8487 (tpt) cc_final: 0.8233 (tpt) REVERT: I 96 MET cc_start: 0.5458 (OUTLIER) cc_final: 0.4672 (tmm) REVERT: I 107 THR cc_start: 0.8541 (m) cc_final: 0.8333 (t) REVERT: I 138 LEU cc_start: 0.8158 (mt) cc_final: 0.7834 (mt) REVERT: I 149 VAL cc_start: 0.7676 (t) cc_final: 0.7331 (p) REVERT: I 151 LYS cc_start: 0.7729 (mmmt) cc_final: 0.7253 (mmmt) REVERT: I 209 ARG cc_start: 0.5268 (OUTLIER) cc_final: 0.4535 (ppt170) REVERT: I 314 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.8071 (ttm110) REVERT: I 323 ASN cc_start: 0.8032 (m-40) cc_final: 0.7692 (m110) REVERT: I 330 ILE cc_start: 0.8649 (tt) cc_final: 0.8395 (tp) REVERT: I 397 ARG cc_start: 0.8136 (tmt-80) cc_final: 0.7920 (tmt-80) REVERT: I 408 ARG cc_start: 0.8487 (tpp-160) cc_final: 0.7273 (tpp-160) REVERT: I 411 GLU cc_start: 0.8263 (mp0) cc_final: 0.7880 (mp0) REVERT: I 415 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8314 (mm) REVERT: I 420 PHE cc_start: 0.8201 (t80) cc_final: 0.7965 (t80) REVERT: I 466 ASN cc_start: 0.8276 (m-40) cc_final: 0.7978 (m-40) REVERT: I 472 LYS cc_start: 0.8281 (tptm) cc_final: 0.7866 (tppt) REVERT: I 548 ILE cc_start: 0.8036 (pt) cc_final: 0.7774 (pp) REVERT: I 550 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: I 566 ILE cc_start: 0.8381 (pp) cc_final: 0.8166 (pt) REVERT: I 572 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8323 (m) REVERT: I 574 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7178 (mm-30) REVERT: E 164 VAL cc_start: 0.8720 (m) cc_final: 0.8383 (p) REVERT: E 168 ASP cc_start: 0.7276 (t0) cc_final: 0.6706 (t0) REVERT: E 216 ARG cc_start: 0.7935 (ttt90) cc_final: 0.7432 (ttt180) REVERT: E 269 ASP cc_start: 0.7522 (p0) cc_final: 0.7267 (p0) REVERT: E 302 ASN cc_start: 0.7590 (t0) cc_final: 0.7311 (t0) REVERT: E 309 GLN cc_start: 0.7820 (mt0) cc_final: 0.7156 (mt0) REVERT: E 312 LYS cc_start: 0.8637 (mttt) cc_final: 0.7706 (mttt) REVERT: E 332 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7598 (mpt180) REVERT: E 411 GLU cc_start: 0.7719 (mp0) cc_final: 0.7233 (mp0) REVERT: E 416 GLN cc_start: 0.8474 (pt0) cc_final: 0.8145 (pt0) REVERT: E 417 ASN cc_start: 0.8626 (t0) cc_final: 0.8192 (t0) REVERT: E 434 ASP cc_start: 0.7694 (m-30) cc_final: 0.7307 (m-30) REVERT: E 447 ILE cc_start: 0.8069 (pt) cc_final: 0.7706 (mm) REVERT: E 479 LYS cc_start: 0.8731 (mttp) cc_final: 0.8502 (mttp) REVERT: C 54 LEU cc_start: 0.8636 (mt) cc_final: 0.8392 (mm) REVERT: C 128 LEU cc_start: 0.8230 (tp) cc_final: 0.7999 (tm) REVERT: C 153 VAL cc_start: 0.8701 (t) cc_final: 0.8451 (m) REVERT: C 190 MET cc_start: 0.7951 (mmm) cc_final: 0.7337 (mmm) REVERT: C 222 HIS cc_start: 0.3123 (OUTLIER) cc_final: 0.2435 (t-170) REVERT: C 247 GLU cc_start: 0.7677 (mp0) cc_final: 0.7280 (mp0) REVERT: C 382 ARG cc_start: 0.8746 (mpp80) cc_final: 0.8305 (tpp80) REVERT: C 387 LYS cc_start: 0.8375 (tttt) cc_final: 0.7949 (tmtt) REVERT: C 397 ARG cc_start: 0.7885 (mtt180) cc_final: 0.7592 (pmm-80) REVERT: C 463 VAL cc_start: 0.8638 (t) cc_final: 0.8360 (t) REVERT: C 464 TYR cc_start: 0.7794 (t80) cc_final: 0.7180 (t80) REVERT: C 538 LYS cc_start: 0.8410 (tptp) cc_final: 0.7766 (tptp) REVERT: G 52 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7761 (ttmm) REVERT: G 68 LEU cc_start: 0.8145 (tp) cc_final: 0.7819 (tm) REVERT: G 77 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7268 (tm-30) REVERT: G 79 TYR cc_start: 0.8417 (m-80) cc_final: 0.8152 (m-80) REVERT: G 83 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8253 (m) REVERT: G 89 LYS cc_start: 0.8476 (tptt) cc_final: 0.8259 (tptt) REVERT: G 106 VAL cc_start: 0.8245 (t) cc_final: 0.7814 (m) REVERT: G 135 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: G 190 MET cc_start: 0.7660 (mmm) cc_final: 0.6950 (mmm) REVERT: G 204 ILE cc_start: 0.8691 (pt) cc_final: 0.8330 (pp) REVERT: G 213 GLN cc_start: 0.8144 (tp40) cc_final: 0.7754 (tm-30) REVERT: G 239 ASP cc_start: 0.7626 (p0) cc_final: 0.7330 (p0) REVERT: G 276 THR cc_start: 0.8409 (p) cc_final: 0.8153 (p) REVERT: G 318 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8083 (mt0) REVERT: G 327 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7712 (mm-30) REVERT: G 439 LYS cc_start: 0.7893 (mmtm) cc_final: 0.7666 (mmtm) REVERT: G 440 THR cc_start: 0.8260 (p) cc_final: 0.8011 (t) REVERT: G 530 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8144 (ttmt) REVERT: G 536 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8320 (mtpp) REVERT: G 577 GLN cc_start: 0.8471 (mt0) cc_final: 0.8264 (mt0) REVERT: F 50 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7593 (mp0) REVERT: F 73 MET cc_start: 0.8075 (ptt) cc_final: 0.7870 (ptt) REVERT: F 81 ARG cc_start: 0.8060 (ttp-170) cc_final: 0.7248 (pmt170) REVERT: F 109 TRP cc_start: 0.8524 (m100) cc_final: 0.8217 (m100) REVERT: F 148 VAL cc_start: 0.8698 (t) cc_final: 0.8355 (m) REVERT: F 177 LEU cc_start: 0.8087 (tp) cc_final: 0.7819 (tt) REVERT: F 214 TRP cc_start: 0.8644 (p90) cc_final: 0.8104 (p90) REVERT: F 216 ARG cc_start: 0.8227 (ttt90) cc_final: 0.7967 (ttt90) REVERT: F 243 PHE cc_start: 0.8722 (t80) cc_final: 0.8439 (t80) REVERT: F 247 GLU cc_start: 0.8009 (mp0) cc_final: 0.7661 (mp0) REVERT: F 326 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8235 (t) REVERT: F 473 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6808 (tm-30) REVERT: F 475 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7192 (t0) REVERT: F 491 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7583 (mm-40) REVERT: F 522 VAL cc_start: 0.8245 (p) cc_final: 0.7937 (m) REVERT: F 525 SER cc_start: 0.8658 (t) cc_final: 0.8066 (p) outliers start: 153 outliers final: 88 residues processed: 1230 average time/residue: 0.6038 time to fit residues: 897.8955 Evaluate side-chains 1273 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 1167 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 209 ARG Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 448 PHE Chi-restraints excluded: chain I residue 481 ARG Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 530 LYS Chi-restraints excluded: chain I residue 550 GLN Chi-restraints excluded: chain I residue 556 ASP Chi-restraints excluded: chain I residue 564 SER Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 280 GLN Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 444 TYR Chi-restraints excluded: chain G residue 530 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 475 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 6 optimal weight: 20.0000 chunk 217 optimal weight: 0.9980 chunk 166 optimal weight: 30.0000 chunk 135 optimal weight: 0.9990 chunk 332 optimal weight: 4.9990 chunk 329 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 307 optimal weight: 5.9990 chunk 287 optimal weight: 0.9980 chunk 246 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 321 ASN D 104 GLN D 231 ASN B 137 HIS I 48 GLN ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 GLN ** I 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 222 HIS E 280 GLN E 558 GLN C 72 ASN C 167 ASN C 549 GLN G 85 ASN G 104 GLN G 416 GLN F 85 ASN F 147 ASN ** F 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 ASN F 549 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.155734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125786 restraints weight = 48148.453| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.35 r_work: 0.3403 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33952 Z= 0.126 Angle : 0.546 9.160 46439 Z= 0.278 Chirality : 0.042 0.169 5053 Planarity : 0.005 0.100 6105 Dihedral : 4.789 54.201 4509 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.68 % Allowed : 22.63 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 3937 helix: 0.89 (0.49), residues: 89 sheet: -0.55 (0.16), residues: 950 loop : -0.40 (0.11), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 520 TYR 0.026 0.001 TYR E 233 PHE 0.037 0.001 PHE C 53 TRP 0.030 0.001 TRP I 214 HIS 0.005 0.001 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00292 (33944) covalent geometry : angle 0.54576 (46423) SS BOND : bond 0.00245 ( 8) SS BOND : angle 1.40135 ( 16) hydrogen bonds : bond 0.03344 ( 355) hydrogen bonds : angle 5.53192 ( 714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1183 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.8225 (p) cc_final: 0.7982 (t) REVERT: A 47 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7840 (t0) REVERT: A 75 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7655 (mm-30) REVERT: A 149 VAL cc_start: 0.8646 (t) cc_final: 0.8330 (p) REVERT: A 265 THR cc_start: 0.8582 (m) cc_final: 0.8319 (t) REVERT: A 357 ILE cc_start: 0.8423 (mt) cc_final: 0.8194 (mp) REVERT: A 380 PHE cc_start: 0.8514 (p90) cc_final: 0.8153 (p90) REVERT: A 396 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: A 398 PHE cc_start: 0.8628 (p90) cc_final: 0.8385 (p90) REVERT: A 457 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8155 (mp) REVERT: A 576 SER cc_start: 0.8507 (t) cc_final: 0.8263 (m) REVERT: D 52 LYS cc_start: 0.8395 (ttmm) cc_final: 0.8061 (ttmm) REVERT: D 60 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7537 (tm-30) REVERT: D 77 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6994 (mm-30) REVERT: D 79 TYR cc_start: 0.8852 (m-80) cc_final: 0.8591 (m-80) REVERT: D 104 GLN cc_start: 0.8487 (pt0) cc_final: 0.8285 (pt0) REVERT: D 142 GLU cc_start: 0.8196 (pm20) cc_final: 0.7989 (pm20) REVERT: D 209 ARG cc_start: 0.8287 (pmt170) cc_final: 0.6030 (ptm160) REVERT: D 214 TRP cc_start: 0.8129 (p90) cc_final: 0.7874 (p90) REVERT: D 237 ASP cc_start: 0.7609 (t0) cc_final: 0.7300 (t0) REVERT: D 246 ILE cc_start: 0.7886 (mm) cc_final: 0.7654 (mp) REVERT: D 269 ASP cc_start: 0.7043 (p0) cc_final: 0.6742 (p0) REVERT: D 355 THR cc_start: 0.7849 (m) cc_final: 0.7352 (p) REVERT: D 488 PHE cc_start: 0.8272 (m-80) cc_final: 0.7904 (m-80) REVERT: D 532 LYS cc_start: 0.8659 (tttt) cc_final: 0.8244 (tttt) REVERT: D 544 THR cc_start: 0.8083 (m) cc_final: 0.7591 (t) REVERT: D 574 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6981 (mm-30) REVERT: B 75 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7411 (mm-30) REVERT: B 89 LYS cc_start: 0.8526 (tptt) cc_final: 0.8304 (tptm) REVERT: B 92 VAL cc_start: 0.8564 (p) cc_final: 0.8260 (m) REVERT: B 96 MET cc_start: 0.8313 (ptp) cc_final: 0.8024 (ptp) REVERT: B 133 MET cc_start: 0.7645 (mmt) cc_final: 0.7273 (mmt) REVERT: B 144 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7979 (pt0) REVERT: B 168 ASP cc_start: 0.7206 (t0) cc_final: 0.6908 (t0) REVERT: B 210 TYR cc_start: 0.8840 (p90) cc_final: 0.8589 (p90) REVERT: B 216 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7188 (ttt180) REVERT: B 230 THR cc_start: 0.8610 (m) cc_final: 0.8344 (t) REVERT: B 236 THR cc_start: 0.7869 (m) cc_final: 0.7566 (p) REVERT: B 247 GLU cc_start: 0.7861 (mp0) cc_final: 0.7331 (mp0) REVERT: B 260 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: B 269 ASP cc_start: 0.7317 (p0) cc_final: 0.7043 (p0) REVERT: B 329 THR cc_start: 0.8467 (p) cc_final: 0.8210 (t) REVERT: B 346 GLU cc_start: 0.6927 (tt0) cc_final: 0.6499 (tt0) REVERT: B 378 TYR cc_start: 0.8301 (m-80) cc_final: 0.7497 (m-80) REVERT: B 396 GLU cc_start: 0.7997 (tt0) cc_final: 0.7498 (tt0) REVERT: B 408 ARG cc_start: 0.7948 (mmt-90) cc_final: 0.7225 (mpt180) REVERT: B 435 PRO cc_start: 0.8658 (Cg_endo) cc_final: 0.8379 (Cg_exo) REVERT: B 464 TYR cc_start: 0.8500 (t80) cc_final: 0.8053 (t80) REVERT: B 473 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7260 (mm-30) REVERT: B 509 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7388 (mm-30) REVERT: B 535 PHE cc_start: 0.8359 (m-80) cc_final: 0.7881 (m-10) REVERT: B 551 MET cc_start: 0.7119 (ttt) cc_final: 0.6791 (ttt) REVERT: B 575 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7879 (mmtm) REVERT: I 49 THR cc_start: 0.8189 (m) cc_final: 0.7831 (t) REVERT: I 55 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7189 (tp30) REVERT: I 67 ARG cc_start: 0.7598 (mmt-90) cc_final: 0.6726 (mmt180) REVERT: I 73 MET cc_start: 0.7361 (ptt) cc_final: 0.6934 (ptt) REVERT: I 86 ASN cc_start: 0.7924 (p0) cc_final: 0.7697 (p0) REVERT: I 87 MET cc_start: 0.8435 (tpt) cc_final: 0.8203 (tpt) REVERT: I 96 MET cc_start: 0.5132 (OUTLIER) cc_final: 0.4583 (tmm) REVERT: I 107 THR cc_start: 0.8498 (m) cc_final: 0.8267 (t) REVERT: I 138 LEU cc_start: 0.8081 (mt) cc_final: 0.7697 (mm) REVERT: I 149 VAL cc_start: 0.7665 (t) cc_final: 0.7320 (p) REVERT: I 151 LYS cc_start: 0.7709 (mmmt) cc_final: 0.7203 (mmmt) REVERT: I 209 ARG cc_start: 0.5285 (OUTLIER) cc_final: 0.4704 (ppt170) REVERT: I 213 GLN cc_start: 0.8005 (tp-100) cc_final: 0.7787 (tp40) REVERT: I 231 ASN cc_start: 0.7786 (t0) cc_final: 0.7555 (t0) REVERT: I 314 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.8128 (ttm110) REVERT: I 330 ILE cc_start: 0.8681 (tt) cc_final: 0.8415 (tp) REVERT: I 408 ARG cc_start: 0.8466 (tpp-160) cc_final: 0.7241 (tpp-160) REVERT: I 411 GLU cc_start: 0.8253 (mp0) cc_final: 0.7909 (mp0) REVERT: I 472 LYS cc_start: 0.8266 (tptm) cc_final: 0.7788 (tppt) REVERT: I 478 LEU cc_start: 0.8826 (mt) cc_final: 0.8170 (pp) REVERT: I 548 ILE cc_start: 0.8039 (pt) cc_final: 0.7779 (pp) REVERT: I 550 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: I 571 ILE cc_start: 0.9042 (mt) cc_final: 0.8798 (mm) REVERT: I 572 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8332 (m) REVERT: I 574 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7193 (mm-30) REVERT: E 51 PHE cc_start: 0.8382 (m-80) cc_final: 0.8125 (m-80) REVERT: E 164 VAL cc_start: 0.8727 (m) cc_final: 0.8393 (p) REVERT: E 168 ASP cc_start: 0.7258 (t0) cc_final: 0.6669 (t0) REVERT: E 216 ARG cc_start: 0.7863 (ttt90) cc_final: 0.7427 (ttt180) REVERT: E 269 ASP cc_start: 0.7487 (p0) cc_final: 0.7199 (p0) REVERT: E 302 ASN cc_start: 0.7545 (t0) cc_final: 0.7322 (t0) REVERT: E 309 GLN cc_start: 0.7717 (mt0) cc_final: 0.7240 (mt0) REVERT: E 312 LYS cc_start: 0.8602 (mttt) cc_final: 0.7795 (mttt) REVERT: E 411 GLU cc_start: 0.7712 (mp0) cc_final: 0.7223 (mp0) REVERT: E 416 GLN cc_start: 0.8368 (pt0) cc_final: 0.8024 (pt0) REVERT: E 417 ASN cc_start: 0.8585 (t0) cc_final: 0.7728 (t0) REVERT: E 419 ASN cc_start: 0.8700 (m-40) cc_final: 0.8023 (p0) REVERT: E 434 ASP cc_start: 0.7691 (m-30) cc_final: 0.7295 (m-30) REVERT: E 479 LYS cc_start: 0.8726 (mttp) cc_final: 0.8485 (mttp) REVERT: C 54 LEU cc_start: 0.8594 (mt) cc_final: 0.8345 (mm) REVERT: C 128 LEU cc_start: 0.8205 (tp) cc_final: 0.7974 (tm) REVERT: C 153 VAL cc_start: 0.8662 (t) cc_final: 0.8429 (m) REVERT: C 183 MET cc_start: 0.7695 (mmm) cc_final: 0.7490 (mmm) REVERT: C 190 MET cc_start: 0.7944 (mmm) cc_final: 0.7334 (mmm) REVERT: C 247 GLU cc_start: 0.7694 (mp0) cc_final: 0.7327 (mp0) REVERT: C 382 ARG cc_start: 0.8685 (mpp80) cc_final: 0.8253 (tpp80) REVERT: C 387 LYS cc_start: 0.8314 (tttt) cc_final: 0.7851 (tmtt) REVERT: C 397 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7594 (pmm-80) REVERT: C 463 VAL cc_start: 0.8630 (t) cc_final: 0.8357 (t) REVERT: C 464 TYR cc_start: 0.7765 (t80) cc_final: 0.7111 (t80) REVERT: C 511 ASP cc_start: 0.7668 (p0) cc_final: 0.7461 (p0) REVERT: C 538 LYS cc_start: 0.8396 (tptp) cc_final: 0.7730 (tptp) REVERT: G 52 LYS cc_start: 0.8127 (ttmm) cc_final: 0.7735 (ttmm) REVERT: G 68 LEU cc_start: 0.8080 (tp) cc_final: 0.7638 (tm) REVERT: G 77 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7252 (tm-30) REVERT: G 79 TYR cc_start: 0.8411 (m-80) cc_final: 0.8155 (m-80) REVERT: G 83 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8230 (m) REVERT: G 87 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8173 (ttp) REVERT: G 89 LYS cc_start: 0.8477 (tptt) cc_final: 0.8236 (tptt) REVERT: G 95 ASN cc_start: 0.8329 (m-40) cc_final: 0.8044 (m110) REVERT: G 106 VAL cc_start: 0.8258 (t) cc_final: 0.7804 (m) REVERT: G 135 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: G 190 MET cc_start: 0.7665 (mmm) cc_final: 0.6921 (mmm) REVERT: G 204 ILE cc_start: 0.8663 (pt) cc_final: 0.8305 (pp) REVERT: G 213 GLN cc_start: 0.8151 (tp40) cc_final: 0.7805 (tm-30) REVERT: G 239 ASP cc_start: 0.7627 (p0) cc_final: 0.7339 (p0) REVERT: G 316 VAL cc_start: 0.8714 (t) cc_final: 0.8285 (m) REVERT: G 318 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7973 (mt0) REVERT: G 327 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7676 (mm-30) REVERT: G 526 ASP cc_start: 0.7481 (t0) cc_final: 0.7184 (t0) REVERT: G 527 PHE cc_start: 0.8252 (p90) cc_final: 0.7869 (p90) REVERT: G 530 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8160 (ttmt) REVERT: G 536 LYS cc_start: 0.8564 (ttpp) cc_final: 0.8310 (mtpp) REVERT: G 577 GLN cc_start: 0.8472 (mt0) cc_final: 0.8207 (mt0) REVERT: F 50 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7596 (mp0) REVERT: F 81 ARG cc_start: 0.8040 (ttp-170) cc_final: 0.7307 (pmt170) REVERT: F 148 VAL cc_start: 0.8678 (t) cc_final: 0.8345 (m) REVERT: F 177 LEU cc_start: 0.8057 (tp) cc_final: 0.7784 (tp) REVERT: F 214 TRP cc_start: 0.8662 (p90) cc_final: 0.8027 (p90) REVERT: F 216 ARG cc_start: 0.8182 (ttt90) cc_final: 0.7401 (ttt-90) REVERT: F 247 GLU cc_start: 0.7968 (mp0) cc_final: 0.7572 (mp0) REVERT: F 457 LEU cc_start: 0.8377 (mt) cc_final: 0.8160 (mt) REVERT: F 473 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6922 (tm-30) REVERT: F 475 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7164 (t0) REVERT: F 498 LEU cc_start: 0.8086 (tt) cc_final: 0.7818 (tp) REVERT: F 522 VAL cc_start: 0.8216 (p) cc_final: 0.7903 (m) REVERT: F 525 SER cc_start: 0.8619 (t) cc_final: 0.8003 (p) outliers start: 129 outliers final: 71 residues processed: 1226 average time/residue: 0.6009 time to fit residues: 890.2432 Evaluate side-chains 1246 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1158 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 209 ARG Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 448 PHE Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 500 VAL Chi-restraints excluded: chain I residue 530 LYS Chi-restraints excluded: chain I residue 550 GLN Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 530 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 475 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 405 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 366 optimal weight: 0.8980 chunk 187 optimal weight: 20.0000 chunk 296 optimal weight: 3.9990 chunk 297 optimal weight: 6.9990 chunk 290 optimal weight: 0.7980 chunk 411 optimal weight: 9.9990 chunk 305 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 321 ASN B 137 HIS I 48 GLN I 280 GLN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 222 HIS E 280 GLN E 404 GLN E 558 GLN C 72 ASN C 549 GLN G 104 GLN G 416 GLN F 85 ASN F 147 ASN ** F 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 ASN F 309 GLN F 491 GLN F 549 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.155884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125979 restraints weight = 48287.488| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.33 r_work: 0.3399 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 33952 Z= 0.143 Angle : 0.557 9.963 46439 Z= 0.282 Chirality : 0.043 0.176 5053 Planarity : 0.004 0.087 6105 Dihedral : 4.703 52.449 4509 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.53 % Allowed : 23.43 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 3937 helix: 0.92 (0.50), residues: 89 sheet: -0.51 (0.17), residues: 941 loop : -0.38 (0.11), residues: 2907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 520 TYR 0.026 0.001 TYR E 233 PHE 0.037 0.001 PHE C 53 TRP 0.027 0.001 TRP G 58 HIS 0.006 0.001 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00331 (33944) covalent geometry : angle 0.55689 (46423) SS BOND : bond 0.00200 ( 8) SS BOND : angle 1.44011 ( 16) hydrogen bonds : bond 0.03405 ( 355) hydrogen bonds : angle 5.45399 ( 714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1287 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1163 time to evaluate : 0.784 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: 0.8244 (OUTLIER) cc_final: 0.7851 (t0) REVERT: A 75 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 99 ASP cc_start: 0.7767 (t70) cc_final: 0.7407 (t70) REVERT: A 149 VAL cc_start: 0.8652 (t) cc_final: 0.8345 (p) REVERT: A 190 MET cc_start: 0.7684 (mtm) cc_final: 0.7476 (ptp) REVERT: A 265 THR cc_start: 0.8614 (m) cc_final: 0.8321 (t) REVERT: A 344 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8384 (p) REVERT: A 357 ILE cc_start: 0.8401 (mt) cc_final: 0.8176 (mp) REVERT: A 380 PHE cc_start: 0.8549 (p90) cc_final: 0.8175 (p90) REVERT: A 396 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: A 398 PHE cc_start: 0.8671 (p90) cc_final: 0.8389 (p90) REVERT: A 457 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8183 (mp) REVERT: A 576 SER cc_start: 0.8538 (t) cc_final: 0.8265 (m) REVERT: D 52 LYS cc_start: 0.8373 (ttmm) cc_final: 0.8030 (ttmm) REVERT: D 60 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7442 (tm-30) REVERT: D 79 TYR cc_start: 0.8844 (m-80) cc_final: 0.8563 (m-80) REVERT: D 104 GLN cc_start: 0.8425 (pt0) cc_final: 0.8172 (pt0) REVERT: D 142 GLU cc_start: 0.8193 (pm20) cc_final: 0.7959 (pm20) REVERT: D 209 ARG cc_start: 0.8329 (pmt170) cc_final: 0.5928 (ptm160) REVERT: D 214 TRP cc_start: 0.8115 (p90) cc_final: 0.7854 (p90) REVERT: D 237 ASP cc_start: 0.7563 (t0) cc_final: 0.7207 (t0) REVERT: D 269 ASP cc_start: 0.6998 (p0) cc_final: 0.6704 (p0) REVERT: D 355 THR cc_start: 0.7915 (m) cc_final: 0.7416 (p) REVERT: D 398 PHE cc_start: 0.8691 (p90) cc_final: 0.8435 (p90) REVERT: D 488 PHE cc_start: 0.8252 (m-80) cc_final: 0.7852 (m-80) REVERT: D 532 LYS cc_start: 0.8648 (tttt) cc_final: 0.8219 (tttt) REVERT: D 544 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7540 (t) REVERT: D 574 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6996 (mm-30) REVERT: B 75 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7397 (mm-30) REVERT: B 89 LYS cc_start: 0.8503 (tptt) cc_final: 0.8269 (tptm) REVERT: B 96 MET cc_start: 0.8263 (ptp) cc_final: 0.7973 (ptp) REVERT: B 133 MET cc_start: 0.7538 (mmt) cc_final: 0.7187 (mmt) REVERT: B 144 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: B 168 ASP cc_start: 0.7200 (t0) cc_final: 0.6849 (t0) REVERT: B 210 TYR cc_start: 0.8850 (p90) cc_final: 0.8561 (p90) REVERT: B 216 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7464 (ttt180) REVERT: B 230 THR cc_start: 0.8605 (m) cc_final: 0.8336 (t) REVERT: B 236 THR cc_start: 0.7822 (m) cc_final: 0.7513 (p) REVERT: B 247 GLU cc_start: 0.7871 (mp0) cc_final: 0.7328 (mp0) REVERT: B 260 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: B 269 ASP cc_start: 0.7413 (p0) cc_final: 0.7018 (p0) REVERT: B 329 THR cc_start: 0.8410 (p) cc_final: 0.8146 (t) REVERT: B 346 GLU cc_start: 0.6862 (tt0) cc_final: 0.6501 (tt0) REVERT: B 378 TYR cc_start: 0.8290 (m-80) cc_final: 0.7475 (m-80) REVERT: B 396 GLU cc_start: 0.8065 (tt0) cc_final: 0.7587 (tt0) REVERT: B 408 ARG cc_start: 0.7938 (mmt-90) cc_final: 0.7240 (mpt180) REVERT: B 435 PRO cc_start: 0.8657 (Cg_endo) cc_final: 0.8369 (Cg_exo) REVERT: B 464 TYR cc_start: 0.8498 (t80) cc_final: 0.8079 (t80) REVERT: B 473 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7280 (mm-30) REVERT: B 509 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7375 (mm-30) REVERT: B 535 PHE cc_start: 0.8391 (m-80) cc_final: 0.7984 (m-10) REVERT: B 551 MET cc_start: 0.7058 (ttt) cc_final: 0.6785 (ttt) REVERT: I 49 THR cc_start: 0.8211 (m) cc_final: 0.7838 (t) REVERT: I 55 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7244 (tp30) REVERT: I 62 THR cc_start: 0.8603 (m) cc_final: 0.7967 (p) REVERT: I 67 ARG cc_start: 0.7553 (mmt-90) cc_final: 0.6677 (mmt180) REVERT: I 73 MET cc_start: 0.7311 (ptt) cc_final: 0.6862 (ptt) REVERT: I 87 MET cc_start: 0.8439 (tpt) cc_final: 0.8190 (tpt) REVERT: I 96 MET cc_start: 0.5095 (ttp) cc_final: 0.4518 (tmm) REVERT: I 107 THR cc_start: 0.8432 (m) cc_final: 0.8222 (t) REVERT: I 138 LEU cc_start: 0.8106 (mt) cc_final: 0.7818 (mm) REVERT: I 149 VAL cc_start: 0.7662 (t) cc_final: 0.7322 (p) REVERT: I 151 LYS cc_start: 0.7693 (mmmt) cc_final: 0.7190 (mmmt) REVERT: I 198 TYR cc_start: 0.8556 (m-80) cc_final: 0.7996 (m-80) REVERT: I 209 ARG cc_start: 0.5215 (OUTLIER) cc_final: 0.4663 (ppt170) REVERT: I 213 GLN cc_start: 0.7897 (tp-100) cc_final: 0.7522 (tp-100) REVERT: I 314 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.8088 (ttm110) REVERT: I 319 MET cc_start: 0.7564 (mtp) cc_final: 0.7267 (mtp) REVERT: I 324 TYR cc_start: 0.8311 (m-80) cc_final: 0.7856 (m-80) REVERT: I 330 ILE cc_start: 0.8660 (tt) cc_final: 0.8376 (tp) REVERT: I 408 ARG cc_start: 0.8462 (tpp-160) cc_final: 0.7243 (tpp-160) REVERT: I 411 GLU cc_start: 0.8302 (mp0) cc_final: 0.7918 (mp0) REVERT: I 415 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8347 (mm) REVERT: I 472 LYS cc_start: 0.8219 (tptm) cc_final: 0.7761 (tppt) REVERT: I 478 LEU cc_start: 0.8836 (mt) cc_final: 0.8177 (pp) REVERT: I 485 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.6973 (p0) REVERT: I 548 ILE cc_start: 0.8080 (pt) cc_final: 0.7821 (pp) REVERT: I 571 ILE cc_start: 0.9065 (mt) cc_final: 0.8751 (mm) REVERT: I 572 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8325 (m) REVERT: I 574 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7149 (mm-30) REVERT: E 51 PHE cc_start: 0.8405 (m-80) cc_final: 0.8134 (m-80) REVERT: E 164 VAL cc_start: 0.8737 (m) cc_final: 0.8392 (p) REVERT: E 168 ASP cc_start: 0.7294 (t0) cc_final: 0.6733 (t0) REVERT: E 269 ASP cc_start: 0.7548 (p0) cc_final: 0.7278 (p0) REVERT: E 302 ASN cc_start: 0.7467 (t0) cc_final: 0.7260 (t0) REVERT: E 309 GLN cc_start: 0.7689 (mt0) cc_final: 0.7002 (mt0) REVERT: E 312 LYS cc_start: 0.8635 (mttt) cc_final: 0.7680 (mttt) REVERT: E 396 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: E 411 GLU cc_start: 0.7711 (mp0) cc_final: 0.7190 (mp0) REVERT: E 416 GLN cc_start: 0.8334 (pt0) cc_final: 0.7994 (pt0) REVERT: E 417 ASN cc_start: 0.8571 (t0) cc_final: 0.7621 (t0) REVERT: E 419 ASN cc_start: 0.8689 (m-40) cc_final: 0.8017 (p0) REVERT: E 434 ASP cc_start: 0.7714 (m-30) cc_final: 0.7320 (m-30) REVERT: E 475 ASP cc_start: 0.7939 (t0) cc_final: 0.7710 (t0) REVERT: E 479 LYS cc_start: 0.8706 (mttp) cc_final: 0.8452 (mttp) REVERT: C 54 LEU cc_start: 0.8575 (mt) cc_final: 0.8320 (mm) REVERT: C 128 LEU cc_start: 0.8149 (tp) cc_final: 0.7920 (tm) REVERT: C 153 VAL cc_start: 0.8664 (t) cc_final: 0.8390 (m) REVERT: C 190 MET cc_start: 0.7933 (mmm) cc_final: 0.7314 (mmm) REVERT: C 209 ARG cc_start: 0.7166 (pmt-80) cc_final: 0.6933 (pmt-80) REVERT: C 247 GLU cc_start: 0.7667 (mp0) cc_final: 0.7285 (mp0) REVERT: C 382 ARG cc_start: 0.8639 (mpp80) cc_final: 0.8207 (tpp80) REVERT: C 397 ARG cc_start: 0.7893 (mtt180) cc_final: 0.7538 (pmm-80) REVERT: C 463 VAL cc_start: 0.8617 (t) cc_final: 0.8356 (t) REVERT: C 464 TYR cc_start: 0.7782 (t80) cc_final: 0.7115 (t80) REVERT: C 511 ASP cc_start: 0.7598 (p0) cc_final: 0.7380 (p0) REVERT: C 519 SER cc_start: 0.8624 (t) cc_final: 0.7983 (p) REVERT: C 538 LYS cc_start: 0.8410 (tptp) cc_final: 0.7732 (tptp) REVERT: C 540 ARG cc_start: 0.7530 (ptt90) cc_final: 0.7251 (ptt90) REVERT: G 52 LYS cc_start: 0.8132 (ttmm) cc_final: 0.7734 (ttmm) REVERT: G 68 LEU cc_start: 0.8000 (tp) cc_final: 0.7641 (tm) REVERT: G 77 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7218 (tm-30) REVERT: G 79 TYR cc_start: 0.8415 (m-80) cc_final: 0.8146 (m-80) REVERT: G 83 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8241 (m) REVERT: G 89 LYS cc_start: 0.8452 (tptt) cc_final: 0.8202 (tptt) REVERT: G 95 ASN cc_start: 0.8329 (m-40) cc_final: 0.8022 (m110) REVERT: G 106 VAL cc_start: 0.8231 (t) cc_final: 0.7769 (m) REVERT: G 135 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: G 190 MET cc_start: 0.7645 (mmm) cc_final: 0.6904 (mmm) REVERT: G 204 ILE cc_start: 0.8694 (pt) cc_final: 0.8309 (pp) REVERT: G 213 GLN cc_start: 0.8176 (tp40) cc_final: 0.7855 (tm-30) REVERT: G 239 ASP cc_start: 0.7606 (p0) cc_final: 0.7287 (p0) REVERT: G 254 LEU cc_start: 0.8190 (mp) cc_final: 0.7855 (mt) REVERT: G 318 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: G 327 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7639 (mm-30) REVERT: G 526 ASP cc_start: 0.7522 (t0) cc_final: 0.7235 (t0) REVERT: G 527 PHE cc_start: 0.8207 (p90) cc_final: 0.7816 (p90) REVERT: G 530 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8195 (ttmt) REVERT: G 536 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8274 (mtpp) REVERT: G 577 GLN cc_start: 0.8456 (mt0) cc_final: 0.8191 (mt0) REVERT: F 50 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7559 (mp0) REVERT: F 73 MET cc_start: 0.8054 (ptt) cc_final: 0.7848 (ptm) REVERT: F 81 ARG cc_start: 0.7991 (ttp-170) cc_final: 0.7318 (pmt170) REVERT: F 148 VAL cc_start: 0.8677 (t) cc_final: 0.8325 (m) REVERT: F 165 TYR cc_start: 0.8644 (m-80) cc_final: 0.8190 (m-80) REVERT: F 177 LEU cc_start: 0.8056 (tp) cc_final: 0.7829 (tp) REVERT: F 214 TRP cc_start: 0.8674 (p90) cc_final: 0.8028 (p90) REVERT: F 216 ARG cc_start: 0.8150 (ttt90) cc_final: 0.7812 (ttt180) REVERT: F 243 PHE cc_start: 0.8697 (t80) cc_final: 0.8441 (t80) REVERT: F 244 TYR cc_start: 0.8230 (m-80) cc_final: 0.7657 (m-80) REVERT: F 247 GLU cc_start: 0.7972 (mp0) cc_final: 0.7520 (mp0) REVERT: F 457 LEU cc_start: 0.8430 (mt) cc_final: 0.8194 (mt) REVERT: F 473 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6885 (tm-30) REVERT: F 475 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7122 (t0) REVERT: F 498 LEU cc_start: 0.8042 (tt) cc_final: 0.7841 (tp) REVERT: F 522 VAL cc_start: 0.8316 (p) cc_final: 0.8069 (m) REVERT: F 525 SER cc_start: 0.8600 (t) cc_final: 0.7920 (p) REVERT: F 528 TRP cc_start: 0.8301 (m100) cc_final: 0.7934 (m100) outliers start: 124 outliers final: 70 residues processed: 1208 average time/residue: 0.6051 time to fit residues: 883.9606 Evaluate side-chains 1250 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 1161 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 209 ARG Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 448 PHE Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 485 ASN Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 564 SER Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 501 LYS Chi-restraints excluded: chain G residue 530 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 475 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 320 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 296 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 231 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 177 optimal weight: 30.0000 chunk 72 optimal weight: 4.9990 chunk 196 optimal weight: 0.0970 overall best weight: 3.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN D 558 GLN B 137 HIS ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 383 GLN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 222 HIS E 280 GLN E 404 GLN E 558 GLN C 72 ASN C 549 GLN G 104 GLN G 253 HIS G 416 GLN F 147 ASN F 302 ASN F 309 GLN F 497 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.153131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123342 restraints weight = 48235.080| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.35 r_work: 0.3376 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 33952 Z= 0.253 Angle : 0.611 9.202 46439 Z= 0.312 Chirality : 0.046 0.189 5053 Planarity : 0.005 0.068 6105 Dihedral : 4.951 52.554 4509 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.34 % Allowed : 24.06 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.13), residues: 3937 helix: 0.63 (0.49), residues: 95 sheet: -0.62 (0.16), residues: 959 loop : -0.44 (0.11), residues: 2883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 520 TYR 0.026 0.002 TYR B 524 PHE 0.039 0.002 PHE C 53 TRP 0.033 0.002 TRP G 58 HIS 0.010 0.001 HIS E 222 Details of bonding type rmsd covalent geometry : bond 0.00577 (33944) covalent geometry : angle 0.61032 (46423) SS BOND : bond 0.00259 ( 8) SS BOND : angle 2.06179 ( 16) hydrogen bonds : bond 0.03787 ( 355) hydrogen bonds : angle 5.52046 ( 714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 1188 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7941 (tp30) cc_final: 0.7676 (tp30) REVERT: A 99 ASP cc_start: 0.7790 (t70) cc_final: 0.7400 (t70) REVERT: A 183 MET cc_start: 0.8264 (mmp) cc_final: 0.8003 (mmp) REVERT: A 190 MET cc_start: 0.7718 (mtm) cc_final: 0.7493 (ptp) REVERT: A 344 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8407 (p) REVERT: A 396 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: A 457 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8346 (mp) REVERT: A 576 SER cc_start: 0.8538 (t) cc_final: 0.8181 (m) REVERT: D 52 LYS cc_start: 0.8301 (ttmm) cc_final: 0.7937 (ttmm) REVERT: D 60 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7487 (tm-30) REVERT: D 79 TYR cc_start: 0.8834 (m-80) cc_final: 0.8563 (m-80) REVERT: D 142 GLU cc_start: 0.8213 (pm20) cc_final: 0.7976 (pm20) REVERT: D 209 ARG cc_start: 0.8374 (pmt170) cc_final: 0.5997 (ptm160) REVERT: D 214 TRP cc_start: 0.8167 (p90) cc_final: 0.7890 (p90) REVERT: D 237 ASP cc_start: 0.7605 (t0) cc_final: 0.7270 (t0) REVERT: D 249 SER cc_start: 0.8236 (m) cc_final: 0.7798 (p) REVERT: D 269 ASP cc_start: 0.7060 (p0) cc_final: 0.6779 (p0) REVERT: D 355 THR cc_start: 0.7916 (m) cc_final: 0.7381 (p) REVERT: D 398 PHE cc_start: 0.8665 (p90) cc_final: 0.8080 (p90) REVERT: D 488 PHE cc_start: 0.8275 (m-80) cc_final: 0.7895 (m-80) REVERT: D 532 LYS cc_start: 0.8664 (tttt) cc_final: 0.8219 (tttt) REVERT: D 544 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7600 (t) REVERT: D 574 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7005 (mm-30) REVERT: B 75 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7388 (mm-30) REVERT: B 89 LYS cc_start: 0.8512 (tptt) cc_final: 0.8302 (tptm) REVERT: B 96 MET cc_start: 0.8318 (ptp) cc_final: 0.7978 (ptp) REVERT: B 101 ILE cc_start: 0.8492 (mp) cc_final: 0.8198 (mp) REVERT: B 133 MET cc_start: 0.7608 (mmt) cc_final: 0.7258 (mmt) REVERT: B 144 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7997 (pt0) REVERT: B 168 ASP cc_start: 0.7246 (t0) cc_final: 0.6875 (t0) REVERT: B 230 THR cc_start: 0.8646 (m) cc_final: 0.8379 (t) REVERT: B 236 THR cc_start: 0.7940 (m) cc_final: 0.7631 (p) REVERT: B 247 GLU cc_start: 0.7868 (mp0) cc_final: 0.7395 (mp0) REVERT: B 269 ASP cc_start: 0.7398 (p0) cc_final: 0.7033 (p0) REVERT: B 329 THR cc_start: 0.8415 (p) cc_final: 0.8151 (t) REVERT: B 346 GLU cc_start: 0.6963 (tt0) cc_final: 0.6562 (tt0) REVERT: B 378 TYR cc_start: 0.8373 (m-80) cc_final: 0.7645 (m-80) REVERT: B 396 GLU cc_start: 0.8081 (tt0) cc_final: 0.7592 (tt0) REVERT: B 408 ARG cc_start: 0.7945 (mmt-90) cc_final: 0.7262 (mpt180) REVERT: B 435 PRO cc_start: 0.8721 (Cg_endo) cc_final: 0.8440 (Cg_exo) REVERT: B 464 TYR cc_start: 0.8505 (t80) cc_final: 0.8144 (t80) REVERT: B 473 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7318 (mm-30) REVERT: B 509 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7317 (mm-30) REVERT: B 535 PHE cc_start: 0.8400 (m-80) cc_final: 0.7936 (m-10) REVERT: B 551 MET cc_start: 0.7089 (ttt) cc_final: 0.6790 (ttt) REVERT: I 49 THR cc_start: 0.8269 (m) cc_final: 0.7850 (t) REVERT: I 55 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7265 (tp30) REVERT: I 62 THR cc_start: 0.8633 (m) cc_final: 0.8024 (p) REVERT: I 67 ARG cc_start: 0.7682 (mmt-90) cc_final: 0.6642 (mmt180) REVERT: I 73 MET cc_start: 0.7336 (ptt) cc_final: 0.6874 (ptt) REVERT: I 96 MET cc_start: 0.5402 (ttp) cc_final: 0.4697 (tmm) REVERT: I 107 THR cc_start: 0.8460 (m) cc_final: 0.8253 (t) REVERT: I 138 LEU cc_start: 0.8124 (mt) cc_final: 0.7791 (mm) REVERT: I 149 VAL cc_start: 0.7685 (t) cc_final: 0.7344 (p) REVERT: I 151 LYS cc_start: 0.7725 (mmmt) cc_final: 0.7212 (mmmt) REVERT: I 198 TYR cc_start: 0.8523 (m-80) cc_final: 0.7909 (m-80) REVERT: I 209 ARG cc_start: 0.5280 (OUTLIER) cc_final: 0.4387 (ppt170) REVERT: I 213 GLN cc_start: 0.7973 (tp-100) cc_final: 0.7448 (tp-100) REVERT: I 266 PHE cc_start: 0.7937 (t80) cc_final: 0.7524 (t80) REVERT: I 314 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.8139 (ttm110) REVERT: I 323 ASN cc_start: 0.8012 (m-40) cc_final: 0.7397 (m110) REVERT: I 324 TYR cc_start: 0.8418 (m-80) cc_final: 0.8074 (m-80) REVERT: I 408 ARG cc_start: 0.8505 (tpp-160) cc_final: 0.7291 (tpp-160) REVERT: I 411 GLU cc_start: 0.8340 (mp0) cc_final: 0.7960 (mp0) REVERT: I 415 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8379 (mm) REVERT: I 472 LYS cc_start: 0.8235 (tptm) cc_final: 0.7756 (tppt) REVERT: I 478 LEU cc_start: 0.8832 (mt) cc_final: 0.8161 (pp) REVERT: I 485 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7303 (p0) REVERT: I 548 ILE cc_start: 0.8099 (pt) cc_final: 0.7842 (pp) REVERT: I 571 ILE cc_start: 0.9071 (mt) cc_final: 0.8702 (mm) REVERT: I 572 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8385 (m) REVERT: I 573 TYR cc_start: 0.8069 (p90) cc_final: 0.7703 (p90) REVERT: I 574 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7159 (mm-30) REVERT: E 164 VAL cc_start: 0.8715 (m) cc_final: 0.8364 (p) REVERT: E 168 ASP cc_start: 0.7312 (t0) cc_final: 0.6710 (t0) REVERT: E 213 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8158 (tm-30) REVERT: E 269 ASP cc_start: 0.7628 (p0) cc_final: 0.7356 (p0) REVERT: E 302 ASN cc_start: 0.7518 (t0) cc_final: 0.7263 (t0) REVERT: E 309 GLN cc_start: 0.7769 (mt0) cc_final: 0.7046 (mt0) REVERT: E 312 LYS cc_start: 0.8642 (mttt) cc_final: 0.7791 (mttt) REVERT: E 396 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: E 404 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: E 411 GLU cc_start: 0.7738 (mp0) cc_final: 0.7218 (mp0) REVERT: E 416 GLN cc_start: 0.8353 (pt0) cc_final: 0.8007 (pt0) REVERT: E 434 ASP cc_start: 0.7724 (m-30) cc_final: 0.7330 (m-30) REVERT: C 54 LEU cc_start: 0.8619 (mt) cc_final: 0.8365 (mm) REVERT: C 144 GLU cc_start: 0.7843 (pt0) cc_final: 0.7569 (pt0) REVERT: C 190 MET cc_start: 0.7987 (mmm) cc_final: 0.7383 (mmm) REVERT: C 222 HIS cc_start: 0.2976 (OUTLIER) cc_final: 0.2385 (t-170) REVERT: C 237 ASP cc_start: 0.7285 (t0) cc_final: 0.6924 (t0) REVERT: C 247 GLU cc_start: 0.7720 (mp0) cc_final: 0.7316 (mp0) REVERT: C 382 ARG cc_start: 0.8690 (mpp80) cc_final: 0.8285 (tpp80) REVERT: C 397 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7570 (pmm-80) REVERT: C 463 VAL cc_start: 0.8597 (t) cc_final: 0.8330 (t) REVERT: C 464 TYR cc_start: 0.7851 (t80) cc_final: 0.7170 (t80) REVERT: C 511 ASP cc_start: 0.7622 (p0) cc_final: 0.7396 (p0) REVERT: C 519 SER cc_start: 0.8641 (t) cc_final: 0.8026 (p) REVERT: C 522 VAL cc_start: 0.8632 (t) cc_final: 0.8328 (m) REVERT: C 538 LYS cc_start: 0.8424 (tptp) cc_final: 0.7743 (tptp) REVERT: C 540 ARG cc_start: 0.7594 (ptt90) cc_final: 0.7279 (ptt90) REVERT: G 44 THR cc_start: 0.8449 (t) cc_final: 0.7494 (p) REVERT: G 52 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7753 (ttmm) REVERT: G 68 LEU cc_start: 0.8290 (tp) cc_final: 0.7715 (tm) REVERT: G 77 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7290 (tm-30) REVERT: G 79 TYR cc_start: 0.8425 (m-80) cc_final: 0.8140 (m-80) REVERT: G 83 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8287 (m) REVERT: G 89 LYS cc_start: 0.8498 (tptt) cc_final: 0.8240 (tptt) REVERT: G 95 ASN cc_start: 0.8351 (m-40) cc_final: 0.7990 (m110) REVERT: G 106 VAL cc_start: 0.8276 (t) cc_final: 0.7848 (m) REVERT: G 135 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: G 177 LEU cc_start: 0.8131 (tm) cc_final: 0.7897 (tm) REVERT: G 190 MET cc_start: 0.7664 (mmm) cc_final: 0.6993 (mmm) REVERT: G 204 ILE cc_start: 0.8731 (pt) cc_final: 0.8369 (pp) REVERT: G 213 GLN cc_start: 0.8194 (tp40) cc_final: 0.7806 (tm-30) REVERT: G 239 ASP cc_start: 0.7541 (p0) cc_final: 0.7166 (p0) REVERT: G 254 LEU cc_start: 0.8100 (mp) cc_final: 0.7724 (mt) REVERT: G 275 LEU cc_start: 0.8572 (mp) cc_final: 0.8346 (mm) REVERT: G 318 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: G 327 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7712 (mm-30) REVERT: G 439 LYS cc_start: 0.7939 (mmtm) cc_final: 0.7480 (mmtm) REVERT: G 526 ASP cc_start: 0.7557 (t0) cc_final: 0.7253 (t0) REVERT: G 527 PHE cc_start: 0.8218 (p90) cc_final: 0.7809 (p90) REVERT: G 530 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8231 (ttmt) REVERT: G 536 LYS cc_start: 0.8620 (ttpp) cc_final: 0.8346 (mtpp) REVERT: G 538 LYS cc_start: 0.8505 (tptp) cc_final: 0.8285 (tppt) REVERT: G 577 GLN cc_start: 0.8466 (mt0) cc_final: 0.8195 (mt0) REVERT: F 50 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7601 (mp0) REVERT: F 73 MET cc_start: 0.7926 (ptt) cc_final: 0.7701 (ptm) REVERT: F 81 ARG cc_start: 0.8047 (ttp-170) cc_final: 0.7248 (pmt170) REVERT: F 148 VAL cc_start: 0.8684 (t) cc_final: 0.8342 (m) REVERT: F 165 TYR cc_start: 0.8752 (m-80) cc_final: 0.8168 (m-80) REVERT: F 177 LEU cc_start: 0.8055 (tp) cc_final: 0.7813 (tp) REVERT: F 214 TRP cc_start: 0.8683 (p90) cc_final: 0.8100 (p90) REVERT: F 216 ARG cc_start: 0.8174 (ttt90) cc_final: 0.7435 (ttt-90) REVERT: F 247 GLU cc_start: 0.8089 (mp0) cc_final: 0.7673 (mp0) REVERT: F 457 LEU cc_start: 0.8501 (mt) cc_final: 0.8256 (mt) REVERT: F 473 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6924 (tm-30) REVERT: F 475 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7176 (t0) REVERT: F 498 LEU cc_start: 0.8070 (tt) cc_final: 0.7852 (tp) REVERT: F 522 VAL cc_start: 0.8333 (p) cc_final: 0.8119 (m) REVERT: F 525 SER cc_start: 0.8563 (t) cc_final: 0.7943 (p) REVERT: F 527 PHE cc_start: 0.8460 (p90) cc_final: 0.8236 (p90) REVERT: F 528 TRP cc_start: 0.8371 (m100) cc_final: 0.7947 (m100) outliers start: 117 outliers final: 75 residues processed: 1228 average time/residue: 0.6145 time to fit residues: 909.2389 Evaluate side-chains 1251 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 1158 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 459 ASN Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 209 ARG Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 383 GLN Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 448 PHE Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 485 ASN Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 556 ASP Chi-restraints excluded: chain I residue 564 SER Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 280 GLN Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 530 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 475 ASP Chi-restraints excluded: chain F residue 497 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 134 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 416 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 393 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 385 optimal weight: 6.9990 chunk 275 optimal weight: 9.9990 chunk 340 optimal weight: 2.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 557 ASN D 104 GLN D 231 ASN B 137 HIS I 48 GLN ** I 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN I 383 GLN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 222 HIS E 280 GLN E 468 GLN E 558 GLN C 72 ASN C 549 GLN G 72 ASN G 85 ASN G 104 GLN G 416 GLN F 85 ASN F 147 ASN F 234 HIS F 302 ASN F 309 GLN F 497 GLN F 549 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.155359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125612 restraints weight = 48742.631| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.34 r_work: 0.3405 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 33952 Z= 0.135 Angle : 0.573 9.460 46439 Z= 0.291 Chirality : 0.043 0.183 5053 Planarity : 0.005 0.063 6105 Dihedral : 4.759 53.902 4509 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.79 % Allowed : 24.86 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.13), residues: 3937 helix: 0.92 (0.51), residues: 89 sheet: -0.54 (0.17), residues: 939 loop : -0.37 (0.11), residues: 2909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 382 TYR 0.036 0.001 TYR I 233 PHE 0.035 0.001 PHE C 53 TRP 0.038 0.001 TRP F 109 HIS 0.006 0.001 HIS I 384 Details of bonding type rmsd covalent geometry : bond 0.00314 (33944) covalent geometry : angle 0.57204 (46423) SS BOND : bond 0.00300 ( 8) SS BOND : angle 1.58325 ( 16) hydrogen bonds : bond 0.03369 ( 355) hydrogen bonds : angle 5.43239 ( 714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 1176 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.7681 (t70) cc_final: 0.7226 (t70) REVERT: A 101 ILE cc_start: 0.8522 (mm) cc_final: 0.8182 (tp) REVERT: A 149 VAL cc_start: 0.8634 (t) cc_final: 0.8342 (p) REVERT: A 265 THR cc_start: 0.8614 (m) cc_final: 0.8321 (t) REVERT: A 344 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8371 (p) REVERT: A 357 ILE cc_start: 0.8425 (mt) cc_final: 0.8200 (mp) REVERT: A 396 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: A 398 PHE cc_start: 0.8619 (p90) cc_final: 0.8397 (p90) REVERT: A 457 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8285 (mp) REVERT: A 576 SER cc_start: 0.8509 (t) cc_final: 0.8249 (m) REVERT: D 52 LYS cc_start: 0.8397 (ttmm) cc_final: 0.8063 (ttmm) REVERT: D 60 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7443 (tm-30) REVERT: D 79 TYR cc_start: 0.8821 (m-80) cc_final: 0.8540 (m-80) REVERT: D 104 GLN cc_start: 0.8378 (pt0) cc_final: 0.8014 (pt0) REVERT: D 142 GLU cc_start: 0.8167 (pm20) cc_final: 0.7941 (pm20) REVERT: D 209 ARG cc_start: 0.8350 (pmt170) cc_final: 0.6062 (ptm160) REVERT: D 214 TRP cc_start: 0.8178 (p90) cc_final: 0.7913 (p90) REVERT: D 237 ASP cc_start: 0.7598 (t0) cc_final: 0.7249 (t0) REVERT: D 246 ILE cc_start: 0.7749 (mm) cc_final: 0.7515 (mp) REVERT: D 249 SER cc_start: 0.8220 (m) cc_final: 0.7812 (p) REVERT: D 269 ASP cc_start: 0.7014 (p0) cc_final: 0.6723 (p0) REVERT: D 355 THR cc_start: 0.7897 (m) cc_final: 0.7414 (p) REVERT: D 398 PHE cc_start: 0.8678 (p90) cc_final: 0.8113 (p90) REVERT: D 488 PHE cc_start: 0.8265 (m-80) cc_final: 0.7888 (m-80) REVERT: D 532 LYS cc_start: 0.8677 (tttt) cc_final: 0.8230 (tttt) REVERT: D 544 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7597 (t) REVERT: B 42 THR cc_start: 0.8358 (t) cc_final: 0.7972 (t) REVERT: B 75 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7391 (mm-30) REVERT: B 81 ARG cc_start: 0.8403 (ttp80) cc_final: 0.8186 (ttp80) REVERT: B 89 LYS cc_start: 0.8514 (tptt) cc_final: 0.8282 (tptm) REVERT: B 96 MET cc_start: 0.8284 (ptp) cc_final: 0.7917 (ptp) REVERT: B 101 ILE cc_start: 0.8501 (mp) cc_final: 0.8184 (mp) REVERT: B 133 MET cc_start: 0.7529 (mmt) cc_final: 0.7190 (mmt) REVERT: B 144 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: B 168 ASP cc_start: 0.7206 (t0) cc_final: 0.6874 (t0) REVERT: B 230 THR cc_start: 0.8627 (m) cc_final: 0.8359 (t) REVERT: B 247 GLU cc_start: 0.7821 (mp0) cc_final: 0.7336 (mp0) REVERT: B 269 ASP cc_start: 0.7435 (p0) cc_final: 0.7025 (p0) REVERT: B 329 THR cc_start: 0.8397 (p) cc_final: 0.8127 (t) REVERT: B 346 GLU cc_start: 0.6901 (tt0) cc_final: 0.6417 (tt0) REVERT: B 349 THR cc_start: 0.8818 (p) cc_final: 0.8596 (p) REVERT: B 378 TYR cc_start: 0.8335 (m-80) cc_final: 0.7600 (m-80) REVERT: B 396 GLU cc_start: 0.8144 (tt0) cc_final: 0.7609 (tt0) REVERT: B 397 ARG cc_start: 0.8419 (mtt180) cc_final: 0.7879 (mtt180) REVERT: B 408 ARG cc_start: 0.7974 (mmt-90) cc_final: 0.7335 (mpt180) REVERT: B 435 PRO cc_start: 0.8835 (Cg_endo) cc_final: 0.8546 (Cg_exo) REVERT: B 464 TYR cc_start: 0.8478 (t80) cc_final: 0.8065 (t80) REVERT: B 509 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7371 (mm-30) REVERT: B 535 PHE cc_start: 0.8419 (m-80) cc_final: 0.8026 (m-10) REVERT: B 551 MET cc_start: 0.7040 (ttt) cc_final: 0.6743 (ttt) REVERT: I 49 THR cc_start: 0.8165 (m) cc_final: 0.7838 (t) REVERT: I 55 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7249 (tp30) REVERT: I 62 THR cc_start: 0.8630 (m) cc_final: 0.8017 (p) REVERT: I 65 SER cc_start: 0.8623 (t) cc_final: 0.8339 (p) REVERT: I 67 ARG cc_start: 0.7598 (mmt-90) cc_final: 0.6982 (mmt90) REVERT: I 71 LEU cc_start: 0.8388 (tp) cc_final: 0.8163 (tp) REVERT: I 73 MET cc_start: 0.7329 (ptt) cc_final: 0.6875 (ptt) REVERT: I 96 MET cc_start: 0.5080 (ttp) cc_final: 0.4478 (tmm) REVERT: I 105 ILE cc_start: 0.8797 (mp) cc_final: 0.8138 (OUTLIER) REVERT: I 138 LEU cc_start: 0.8080 (mt) cc_final: 0.7816 (mm) REVERT: I 149 VAL cc_start: 0.7696 (t) cc_final: 0.7338 (p) REVERT: I 151 LYS cc_start: 0.7697 (mmmt) cc_final: 0.7194 (mmmt) REVERT: I 213 GLN cc_start: 0.7956 (tp-100) cc_final: 0.7629 (tp-100) REVERT: I 312 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8449 (mmtt) REVERT: I 314 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.7982 (ttm-80) REVERT: I 323 ASN cc_start: 0.8026 (m-40) cc_final: 0.7545 (m-40) REVERT: I 408 ARG cc_start: 0.8420 (tpp-160) cc_final: 0.7139 (tpp-160) REVERT: I 411 GLU cc_start: 0.8318 (mp0) cc_final: 0.7949 (mp0) REVERT: I 415 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8327 (mm) REVERT: I 472 LYS cc_start: 0.8253 (tptm) cc_final: 0.7766 (tppt) REVERT: I 478 LEU cc_start: 0.8842 (mt) cc_final: 0.8179 (pp) REVERT: I 485 ASN cc_start: 0.7519 (OUTLIER) cc_final: 0.7003 (p0) REVERT: I 528 TRP cc_start: 0.8508 (m100) cc_final: 0.8285 (m100) REVERT: I 548 ILE cc_start: 0.8109 (pt) cc_final: 0.7847 (pp) REVERT: I 571 ILE cc_start: 0.9064 (mt) cc_final: 0.8824 (mm) REVERT: I 572 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8359 (m) REVERT: I 574 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7099 (mm-30) REVERT: E 51 PHE cc_start: 0.8406 (m-80) cc_final: 0.8172 (m-80) REVERT: E 164 VAL cc_start: 0.8745 (m) cc_final: 0.8405 (p) REVERT: E 168 ASP cc_start: 0.7277 (t0) cc_final: 0.6722 (t0) REVERT: E 269 ASP cc_start: 0.7529 (p0) cc_final: 0.7256 (p0) REVERT: E 302 ASN cc_start: 0.7497 (t0) cc_final: 0.7282 (t0) REVERT: E 309 GLN cc_start: 0.7729 (mt0) cc_final: 0.7026 (mt0) REVERT: E 312 LYS cc_start: 0.8649 (mttt) cc_final: 0.7781 (mttt) REVERT: E 396 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: E 405 ASP cc_start: 0.6339 (OUTLIER) cc_final: 0.5834 (m-30) REVERT: E 411 GLU cc_start: 0.7718 (mp0) cc_final: 0.7214 (mp0) REVERT: E 417 ASN cc_start: 0.8586 (t0) cc_final: 0.8161 (t0) REVERT: E 434 ASP cc_start: 0.7732 (m-30) cc_final: 0.7353 (m-30) REVERT: C 54 LEU cc_start: 0.8587 (mt) cc_final: 0.8331 (mm) REVERT: C 190 MET cc_start: 0.7963 (mmm) cc_final: 0.7345 (mmm) REVERT: C 209 ARG cc_start: 0.7129 (pmt-80) cc_final: 0.6909 (pmt-80) REVERT: C 247 GLU cc_start: 0.7706 (mp0) cc_final: 0.7262 (mp0) REVERT: C 382 ARG cc_start: 0.8680 (mpp80) cc_final: 0.8286 (tpp80) REVERT: C 387 LYS cc_start: 0.8306 (tttt) cc_final: 0.7800 (tmtt) REVERT: C 397 ARG cc_start: 0.7677 (mtt180) cc_final: 0.7368 (pmm-80) REVERT: C 463 VAL cc_start: 0.8625 (t) cc_final: 0.8369 (t) REVERT: C 464 TYR cc_start: 0.7782 (t80) cc_final: 0.7107 (t80) REVERT: C 511 ASP cc_start: 0.7607 (p0) cc_final: 0.7379 (p0) REVERT: C 519 SER cc_start: 0.8648 (t) cc_final: 0.8017 (p) REVERT: C 522 VAL cc_start: 0.8603 (t) cc_final: 0.8290 (m) REVERT: C 538 LYS cc_start: 0.8417 (tptp) cc_final: 0.7738 (tptp) REVERT: C 540 ARG cc_start: 0.7543 (ptt90) cc_final: 0.7256 (ptt90) REVERT: G 44 THR cc_start: 0.8404 (t) cc_final: 0.7445 (p) REVERT: G 52 LYS cc_start: 0.8163 (ttmm) cc_final: 0.7779 (ttmm) REVERT: G 68 LEU cc_start: 0.8257 (tp) cc_final: 0.7658 (tm) REVERT: G 77 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7252 (tm-30) REVERT: G 79 TYR cc_start: 0.8387 (m-80) cc_final: 0.8116 (m-80) REVERT: G 83 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8263 (m) REVERT: G 89 LYS cc_start: 0.8475 (tptt) cc_final: 0.8233 (tptt) REVERT: G 95 ASN cc_start: 0.8314 (m-40) cc_final: 0.8057 (m110) REVERT: G 106 VAL cc_start: 0.8264 (t) cc_final: 0.7851 (m) REVERT: G 135 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: G 177 LEU cc_start: 0.8109 (tm) cc_final: 0.7881 (tm) REVERT: G 190 MET cc_start: 0.7641 (mmm) cc_final: 0.6948 (mmm) REVERT: G 204 ILE cc_start: 0.8693 (pt) cc_final: 0.8338 (pp) REVERT: G 213 GLN cc_start: 0.8158 (tp40) cc_final: 0.7848 (tm-30) REVERT: G 254 LEU cc_start: 0.8081 (mp) cc_final: 0.7691 (mt) REVERT: G 274 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7416 (mtt180) REVERT: G 275 LEU cc_start: 0.8506 (mp) cc_final: 0.8305 (mm) REVERT: G 316 VAL cc_start: 0.8743 (t) cc_final: 0.8361 (m) REVERT: G 318 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7917 (mt0) REVERT: G 327 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7659 (mm-30) REVERT: G 526 ASP cc_start: 0.7590 (t0) cc_final: 0.7274 (t0) REVERT: G 527 PHE cc_start: 0.8266 (p90) cc_final: 0.7792 (p90) REVERT: G 530 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8204 (ttmt) REVERT: G 536 LYS cc_start: 0.8538 (ttpp) cc_final: 0.8295 (mtpp) REVERT: G 550 GLN cc_start: 0.8283 (mm110) cc_final: 0.7705 (mm110) REVERT: G 577 GLN cc_start: 0.8448 (mt0) cc_final: 0.8198 (mt0) REVERT: F 50 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7604 (mp0) REVERT: F 73 MET cc_start: 0.7857 (ptt) cc_final: 0.7625 (ptm) REVERT: F 81 ARG cc_start: 0.8030 (ttp-170) cc_final: 0.7314 (pmt170) REVERT: F 148 VAL cc_start: 0.8675 (t) cc_final: 0.8445 (m) REVERT: F 149 VAL cc_start: 0.8331 (p) cc_final: 0.7985 (m) REVERT: F 212 PHE cc_start: 0.8549 (t80) cc_final: 0.8064 (t80) REVERT: F 214 TRP cc_start: 0.8662 (p90) cc_final: 0.8015 (p90) REVERT: F 243 PHE cc_start: 0.8752 (t80) cc_final: 0.8547 (t80) REVERT: F 244 TYR cc_start: 0.8232 (m-80) cc_final: 0.7954 (m-80) REVERT: F 247 GLU cc_start: 0.8028 (mp0) cc_final: 0.7575 (mp0) REVERT: F 314 ARG cc_start: 0.8487 (mtt90) cc_final: 0.8269 (mtt90) REVERT: F 457 LEU cc_start: 0.8432 (mt) cc_final: 0.8208 (mt) REVERT: F 473 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6951 (tm-30) REVERT: F 475 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7034 (t0) REVERT: F 522 VAL cc_start: 0.8388 (p) cc_final: 0.8178 (m) REVERT: F 527 PHE cc_start: 0.8449 (p90) cc_final: 0.8249 (p90) REVERT: F 528 TRP cc_start: 0.8351 (m100) cc_final: 0.7945 (m100) outliers start: 98 outliers final: 65 residues processed: 1209 average time/residue: 0.6125 time to fit residues: 893.3211 Evaluate side-chains 1246 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 1166 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain I residue 46 ASN Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 448 PHE Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 485 ASN Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 564 SER Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 530 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 233 TYR Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 475 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 345 optimal weight: 6.9990 chunk 300 optimal weight: 0.9990 chunk 146 optimal weight: 0.0980 chunk 230 optimal weight: 0.5980 chunk 118 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 354 optimal weight: 6.9990 chunk 264 optimal weight: 5.9990 chunk 305 optimal weight: 5.9990 chunk 343 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN B 137 HIS B 421 ASN ** I 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 383 GLN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 222 HIS E 280 GLN E 468 GLN C 549 GLN G 85 ASN G 104 GLN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 ASN F 302 ASN F 309 GLN F 549 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.155334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124597 restraints weight = 48383.533| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.37 r_work: 0.3394 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 33952 Z= 0.178 Angle : 0.588 9.604 46439 Z= 0.299 Chirality : 0.044 0.189 5053 Planarity : 0.005 0.064 6105 Dihedral : 4.786 53.689 4509 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.71 % Allowed : 24.97 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 3937 helix: 0.93 (0.51), residues: 89 sheet: -0.55 (0.17), residues: 937 loop : -0.38 (0.11), residues: 2911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 382 TYR 0.032 0.002 TYR I 233 PHE 0.037 0.002 PHE I 380 TRP 0.051 0.002 TRP F 109 HIS 0.013 0.001 HIS F 234 Details of bonding type rmsd covalent geometry : bond 0.00411 (33944) covalent geometry : angle 0.58697 (46423) SS BOND : bond 0.00270 ( 8) SS BOND : angle 1.65965 ( 16) hydrogen bonds : bond 0.03493 ( 355) hydrogen bonds : angle 5.40909 ( 714) =============================================================================== Job complete usr+sys time: 17907.38 seconds wall clock time: 303 minutes 19.68 seconds (18199.68 seconds total)