Starting phenix.real_space_refine on Tue Aug 26 13:52:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8axl_15701/08_2025/8axl_15701.cif Found real_map, /net/cci-nas-00/data/ceres_data/8axl_15701/08_2025/8axl_15701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8axl_15701/08_2025/8axl_15701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8axl_15701/08_2025/8axl_15701.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8axl_15701/08_2025/8axl_15701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8axl_15701/08_2025/8axl_15701.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 23805 2.51 5 N 6510 2.21 5 O 7275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37650 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Restraints were copied for chains: O, B, C, D, E, F, G, H, I, J, K, L, M, N Time building chain proxies: 4.03, per 1000 atoms: 0.11 Number of scatterers: 37650 At special positions: 0 Unit cell: (164.659, 163.275, 125.916, 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 60 16.00 O 7275 8.00 N 6510 7.00 C 23805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 476.8 nanoseconds 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9030 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 32 sheets defined 19.1% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 209 through 218 Processing helix chain 'A' and resid 280 through 295 Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN A 497 " --> pdb=" O VAL A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR A 525 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'O' and resid 209 through 218 Processing helix chain 'O' and resid 280 through 295 Processing helix chain 'O' and resid 418 through 420 No H-bonds generated for 'chain 'O' and resid 418 through 420' Processing helix chain 'O' and resid 444 through 449 Processing helix chain 'O' and resid 488 through 492 Processing helix chain 'O' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN O 497 " --> pdb=" O VAL O 494 " (cutoff:3.500A) Processing helix chain 'O' and resid 521 through 525 removed outlier: 3.906A pdb=" N TYR O 525 " --> pdb=" O GLU O 522 " (cutoff:3.500A) Processing helix chain 'O' and resid 536 through 545 Processing helix chain 'B' and resid 209 through 218 Processing helix chain 'B' and resid 280 through 295 Processing helix chain 'B' and resid 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 494 through 499 removed outlier: 3.878A pdb=" N ASN B 497 " --> pdb=" O VAL B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR B 525 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'C' and resid 209 through 218 Processing helix chain 'C' and resid 280 through 295 Processing helix chain 'C' and resid 418 through 420 No H-bonds generated for 'chain 'C' and resid 418 through 420' Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN C 497 " --> pdb=" O VAL C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR C 525 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'D' and resid 209 through 218 Processing helix chain 'D' and resid 280 through 295 Processing helix chain 'D' and resid 418 through 420 No H-bonds generated for 'chain 'D' and resid 418 through 420' Processing helix chain 'D' and resid 444 through 449 Processing helix chain 'D' and resid 488 through 492 Processing helix chain 'D' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN D 497 " --> pdb=" O VAL D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR D 525 " --> pdb=" O GLU D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 545 Processing helix chain 'E' and resid 209 through 218 Processing helix chain 'E' and resid 280 through 295 Processing helix chain 'E' and resid 418 through 420 No H-bonds generated for 'chain 'E' and resid 418 through 420' Processing helix chain 'E' and resid 444 through 449 Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 494 through 499 removed outlier: 3.878A pdb=" N ASN E 497 " --> pdb=" O VAL E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR E 525 " --> pdb=" O GLU E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 545 Processing helix chain 'F' and resid 209 through 218 Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 418 through 420 No H-bonds generated for 'chain 'F' and resid 418 through 420' Processing helix chain 'F' and resid 444 through 449 Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN F 497 " --> pdb=" O VAL F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR F 525 " --> pdb=" O GLU F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 545 Processing helix chain 'G' and resid 209 through 218 Processing helix chain 'G' and resid 280 through 295 Processing helix chain 'G' and resid 418 through 420 No H-bonds generated for 'chain 'G' and resid 418 through 420' Processing helix chain 'G' and resid 444 through 449 Processing helix chain 'G' and resid 488 through 492 Processing helix chain 'G' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN G 497 " --> pdb=" O VAL G 494 " (cutoff:3.500A) Processing helix chain 'G' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR G 525 " --> pdb=" O GLU G 522 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 545 Processing helix chain 'H' and resid 209 through 218 Processing helix chain 'H' and resid 280 through 295 Processing helix chain 'H' and resid 418 through 420 No H-bonds generated for 'chain 'H' and resid 418 through 420' Processing helix chain 'H' and resid 444 through 449 Processing helix chain 'H' and resid 488 through 492 Processing helix chain 'H' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN H 497 " --> pdb=" O VAL H 494 " (cutoff:3.500A) Processing helix chain 'H' and resid 521 through 525 removed outlier: 3.906A pdb=" N TYR H 525 " --> pdb=" O GLU H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 536 through 545 Processing helix chain 'I' and resid 209 through 218 Processing helix chain 'I' and resid 280 through 295 Processing helix chain 'I' and resid 418 through 420 No H-bonds generated for 'chain 'I' and resid 418 through 420' Processing helix chain 'I' and resid 444 through 449 Processing helix chain 'I' and resid 488 through 492 Processing helix chain 'I' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN I 497 " --> pdb=" O VAL I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR I 525 " --> pdb=" O GLU I 522 " (cutoff:3.500A) Processing helix chain 'I' and resid 536 through 545 Processing helix chain 'J' and resid 209 through 218 Processing helix chain 'J' and resid 280 through 295 Processing helix chain 'J' and resid 418 through 420 No H-bonds generated for 'chain 'J' and resid 418 through 420' Processing helix chain 'J' and resid 444 through 449 Processing helix chain 'J' and resid 488 through 492 Processing helix chain 'J' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN J 497 " --> pdb=" O VAL J 494 " (cutoff:3.500A) Processing helix chain 'J' and resid 521 through 525 removed outlier: 3.906A pdb=" N TYR J 525 " --> pdb=" O GLU J 522 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 545 Processing helix chain 'K' and resid 209 through 218 Processing helix chain 'K' and resid 280 through 295 Processing helix chain 'K' and resid 418 through 420 No H-bonds generated for 'chain 'K' and resid 418 through 420' Processing helix chain 'K' and resid 444 through 449 Processing helix chain 'K' and resid 488 through 492 Processing helix chain 'K' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN K 497 " --> pdb=" O VAL K 494 " (cutoff:3.500A) Processing helix chain 'K' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR K 525 " --> pdb=" O GLU K 522 " (cutoff:3.500A) Processing helix chain 'K' and resid 536 through 545 Processing helix chain 'L' and resid 209 through 218 Processing helix chain 'L' and resid 280 through 295 Processing helix chain 'L' and resid 418 through 420 No H-bonds generated for 'chain 'L' and resid 418 through 420' Processing helix chain 'L' and resid 444 through 449 Processing helix chain 'L' and resid 488 through 492 Processing helix chain 'L' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN L 497 " --> pdb=" O VAL L 494 " (cutoff:3.500A) Processing helix chain 'L' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR L 525 " --> pdb=" O GLU L 522 " (cutoff:3.500A) Processing helix chain 'L' and resid 536 through 545 Processing helix chain 'M' and resid 209 through 218 Processing helix chain 'M' and resid 280 through 295 Processing helix chain 'M' and resid 418 through 420 No H-bonds generated for 'chain 'M' and resid 418 through 420' Processing helix chain 'M' and resid 444 through 449 Processing helix chain 'M' and resid 488 through 492 Processing helix chain 'M' and resid 494 through 499 removed outlier: 3.878A pdb=" N ASN M 497 " --> pdb=" O VAL M 494 " (cutoff:3.500A) Processing helix chain 'M' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR M 525 " --> pdb=" O GLU M 522 " (cutoff:3.500A) Processing helix chain 'M' and resid 536 through 545 Processing helix chain 'N' and resid 209 through 218 Processing helix chain 'N' and resid 280 through 295 Processing helix chain 'N' and resid 418 through 420 No H-bonds generated for 'chain 'N' and resid 418 through 420' Processing helix chain 'N' and resid 444 through 449 Processing helix chain 'N' and resid 488 through 492 Processing helix chain 'N' and resid 494 through 499 removed outlier: 3.878A pdb=" N ASN N 497 " --> pdb=" O VAL N 494 " (cutoff:3.500A) Processing helix chain 'N' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR N 525 " --> pdb=" O GLU N 522 " (cutoff:3.500A) Processing helix chain 'N' and resid 536 through 545 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 269 Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 198 Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.154A pdb=" N ARG A 227 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL B 185 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA A 229 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS B 187 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 300 through 328 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 332 through 336 current: chain 'A' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 501 through 519 current: chain 'O' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 332 through 336 current: chain 'O' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 501 through 519 current: chain 'B' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 332 through 336 current: chain 'B' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 501 through 519 current: chain 'C' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 332 through 336 current: chain 'C' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 501 through 519 current: chain 'D' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 332 through 336 current: chain 'D' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 501 through 519 current: chain 'E' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 332 through 336 current: chain 'E' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 501 through 519 current: chain 'F' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 332 through 336 current: chain 'F' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 501 through 519 current: chain 'G' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 332 through 336 current: chain 'G' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 501 through 519 current: chain 'H' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 332 through 336 current: chain 'H' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 501 through 519 current: chain 'I' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 332 through 336 current: chain 'I' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 501 through 519 current: chain 'J' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 332 through 336 current: chain 'J' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 501 through 519 current: chain 'K' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 332 through 336 current: chain 'K' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 501 through 519 current: chain 'L' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 332 through 336 current: chain 'L' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 501 through 519 current: chain 'M' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 332 through 336 current: chain 'M' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 501 through 519 current: chain 'N' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 332 through 336 current: chain 'N' and resid 501 through 519 Processing sheet with id=AA5, first strand: chain 'A' and resid 381 through 391 Processing sheet with id=AA6, first strand: chain 'O' and resid 265 through 269 Processing sheet with id=AA7, first strand: chain 'O' and resid 196 through 198 Processing sheet with id=AA8, first strand: chain 'B' and resid 196 through 198 Processing sheet with id=AA9, first strand: chain 'B' and resid 226 through 229 removed outlier: 6.197A pdb=" N ARG B 227 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL C 185 " --> pdb=" O ARG B 227 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 229 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LYS C 187 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 196 through 198 Processing sheet with id=AB2, first strand: chain 'C' and resid 226 through 229 removed outlier: 6.188A pdb=" N ARG C 227 " --> pdb=" O PHE D 183 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL D 185 " --> pdb=" O ARG C 227 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA C 229 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LYS D 187 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 196 through 198 Processing sheet with id=AB4, first strand: chain 'D' and resid 226 through 229 removed outlier: 6.188A pdb=" N ARG D 227 " --> pdb=" O PHE E 183 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL E 185 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA D 229 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LYS E 187 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 196 through 198 Processing sheet with id=AB6, first strand: chain 'E' and resid 226 through 229 removed outlier: 6.188A pdb=" N ARG E 227 " --> pdb=" O PHE F 183 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL F 185 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA E 229 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LYS F 187 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 196 through 198 Processing sheet with id=AB8, first strand: chain 'F' and resid 226 through 229 removed outlier: 6.208A pdb=" N ARG F 227 " --> pdb=" O PHE G 183 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL G 185 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA F 229 " --> pdb=" O VAL G 185 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N LYS G 187 " --> pdb=" O ALA F 229 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 196 through 198 Processing sheet with id=AC1, first strand: chain 'G' and resid 226 through 229 removed outlier: 6.235A pdb=" N ARG G 227 " --> pdb=" O PHE H 183 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N VAL H 185 " --> pdb=" O ARG G 227 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA G 229 " --> pdb=" O VAL H 185 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N LYS H 187 " --> pdb=" O ALA G 229 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 196 through 198 Processing sheet with id=AC3, first strand: chain 'H' and resid 226 through 229 removed outlier: 6.269A pdb=" N ARG H 227 " --> pdb=" O PHE I 183 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL I 185 " --> pdb=" O ARG H 227 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA H 229 " --> pdb=" O VAL I 185 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LYS I 187 " --> pdb=" O ALA H 229 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 196 through 198 Processing sheet with id=AC5, first strand: chain 'I' and resid 226 through 229 Processing sheet with id=AC6, first strand: chain 'J' and resid 196 through 198 Processing sheet with id=AC7, first strand: chain 'J' and resid 226 through 229 removed outlier: 6.115A pdb=" N ARG J 227 " --> pdb=" O PHE K 183 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL K 185 " --> pdb=" O ARG J 227 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA J 229 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LYS K 187 " --> pdb=" O ALA J 229 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 196 through 198 Processing sheet with id=AC9, first strand: chain 'K' and resid 226 through 229 removed outlier: 6.187A pdb=" N ARG K 227 " --> pdb=" O PHE L 183 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL L 185 " --> pdb=" O ARG K 227 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA K 229 " --> pdb=" O VAL L 185 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LYS L 187 " --> pdb=" O ALA K 229 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 196 through 198 Processing sheet with id=AD2, first strand: chain 'L' and resid 226 through 229 removed outlier: 6.188A pdb=" N ARG L 227 " --> pdb=" O PHE M 183 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL M 185 " --> pdb=" O ARG L 227 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA L 229 " --> pdb=" O VAL M 185 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LYS M 187 " --> pdb=" O ALA L 229 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 196 through 198 Processing sheet with id=AD4, first strand: chain 'M' and resid 226 through 229 removed outlier: 6.188A pdb=" N ARG M 227 " --> pdb=" O PHE N 183 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL N 185 " --> pdb=" O ARG M 227 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA M 229 " --> pdb=" O VAL N 185 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LYS N 187 " --> pdb=" O ALA M 229 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 196 through 198 1323 hydrogen bonds defined for protein. 3381 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: 7.12 Time building geometry restraints manager: 3.93 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: 12438 1.34 - 1.46: 6110 1.46 - 1.57: 19492 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 38160 Sorted by residual: bond pdb=" CA ARG M 511 " pdb=" CB ARG M 511 " ideal model delta sigma weight residual 1.535 1.512 0.023 2.02e-02 2.45e+03 1.31e+00 bond pdb=" CB ASN M 411 " pdb=" CG ASN M 411 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.31e+00 bond pdb=" CB ASN E 411 " pdb=" CG ASN E 411 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.31e+00 bond pdb=" CA ARG O 511 " pdb=" CB ARG O 511 " ideal model delta sigma weight residual 1.535 1.512 0.023 2.02e-02 2.45e+03 1.31e+00 bond pdb=" CB ASN I 411 " pdb=" CG ASN I 411 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.30e+00 ... (remaining 38155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 49476 1.43 - 2.85: 1854 2.85 - 4.28: 225 4.28 - 5.70: 30 5.70 - 7.13: 30 Bond angle restraints: 51615 Sorted by residual: angle pdb=" C VAL C 296 " pdb=" N ALA C 297 " pdb=" CA ALA C 297 " ideal model delta sigma weight residual 122.15 115.02 7.13 2.83e+00 1.25e-01 6.34e+00 angle pdb=" C VAL I 296 " pdb=" N ALA I 297 " pdb=" CA ALA I 297 " ideal model delta sigma weight residual 122.15 115.03 7.12 2.83e+00 1.25e-01 6.33e+00 angle pdb=" C VAL A 296 " pdb=" N ALA A 297 " pdb=" CA ALA A 297 " ideal model delta sigma weight residual 122.15 115.04 7.11 2.83e+00 1.25e-01 6.32e+00 angle pdb=" C VAL G 296 " pdb=" N ALA G 297 " pdb=" CA ALA G 297 " ideal model delta sigma weight residual 122.15 115.04 7.11 2.83e+00 1.25e-01 6.31e+00 angle pdb=" C VAL J 296 " pdb=" N ALA J 297 " pdb=" CA ALA J 297 " ideal model delta sigma weight residual 122.15 115.05 7.10 2.83e+00 1.25e-01 6.30e+00 ... (remaining 51610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.91: 20490 11.91 - 23.82: 1800 23.82 - 35.73: 765 35.73 - 47.64: 165 47.64 - 59.55: 75 Dihedral angle restraints: 23295 sinusoidal: 9405 harmonic: 13890 Sorted by residual: dihedral pdb=" CA LYS K 351 " pdb=" C LYS K 351 " pdb=" N PHE K 352 " pdb=" CA PHE K 352 " ideal model delta harmonic sigma weight residual -180.00 -154.91 -25.09 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA LYS N 351 " pdb=" C LYS N 351 " pdb=" N PHE N 352 " pdb=" CA PHE N 352 " ideal model delta harmonic sigma weight residual -180.00 -154.94 -25.06 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA LYS M 351 " pdb=" C LYS M 351 " pdb=" N PHE M 352 " pdb=" CA PHE M 352 " ideal model delta harmonic sigma weight residual -180.00 -154.94 -25.06 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 23292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3237 0.028 - 0.056: 1826 0.056 - 0.083: 409 0.083 - 0.111: 397 0.111 - 0.139: 281 Chirality restraints: 6150 Sorted by residual: chirality pdb=" CA PRO I 487 " pdb=" N PRO I 487 " pdb=" C PRO I 487 " pdb=" CB PRO I 487 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA PRO A 487 " pdb=" N PRO A 487 " pdb=" C PRO A 487 " pdb=" CB PRO A 487 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE M 486 " pdb=" N ILE M 486 " pdb=" C ILE M 486 " pdb=" CB ILE M 486 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 6147 not shown) Planarity restraints: 6600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 370 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO L 371 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO L 371 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 371 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG N 370 " 0.037 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO N 371 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO N 371 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO N 371 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG K 370 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.10e+00 pdb=" N PRO K 371 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO K 371 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO K 371 " 0.031 5.00e-02 4.00e+02 ... (remaining 6597 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 2428 2.73 - 3.27: 36875 3.27 - 3.81: 56951 3.81 - 4.36: 67229 4.36 - 4.90: 124611 Nonbonded interactions: 288094 Sorted by model distance: nonbonded pdb=" NZ LYS I 298 " pdb=" O GLU J 271 " model vdw 2.183 3.120 nonbonded pdb=" OH TYR A 531 " pdb=" OG SER O 304 " model vdw 2.193 3.040 nonbonded pdb=" OG SER I 304 " pdb=" OH TYR J 531 " model vdw 2.197 3.040 nonbonded pdb=" OG SER H 304 " pdb=" OH TYR I 531 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR O 531 " pdb=" OG SER N 304 " model vdw 2.199 3.040 ... (remaining 288089 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 8.680 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: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 27.650 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 0.031 38160 Z= 0.277 Angle : 0.646 7.128 51615 Z= 0.371 Chirality : 0.047 0.139 6150 Planarity : 0.005 0.057 6600 Dihedral : 11.799 59.548 14265 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.47 % Allowed : 8.33 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.12), residues: 4650 helix: -0.36 (0.20), residues: 705 sheet: 0.48 (0.10), residues: 2640 loop : -2.30 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 387 TYR 0.010 0.001 TYR E 474 PHE 0.013 0.001 PHE M 513 TRP 0.006 0.001 TRP O 306 HIS 0.004 0.002 HIS H 300 Details of bonding type rmsd covalent geometry : bond 0.00627 (38160) covalent geometry : angle 0.64630 (51615) hydrogen bonds : bond 0.04953 ( 1323) hydrogen bonds : angle 5.86184 ( 3381) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 696 time to evaluate : 1.476 Fit side-chains REVERT: A 362 LYS cc_start: 0.8205 (mttt) cc_final: 0.7986 (mtmm) REVERT: A 408 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8656 (t) REVERT: O 228 GLN cc_start: 0.7033 (mt0) cc_final: 0.6676 (mt0) REVERT: O 289 ASP cc_start: 0.7560 (m-30) cc_final: 0.6834 (m-30) REVERT: O 405 THR cc_start: 0.8878 (m) cc_final: 0.8638 (t) REVERT: O 501 TYR cc_start: 0.8521 (t80) cc_final: 0.7910 (t80) REVERT: B 280 ASN cc_start: 0.7496 (m-40) cc_final: 0.7193 (m110) REVERT: B 362 LYS cc_start: 0.8141 (mttt) cc_final: 0.7887 (mtpt) REVERT: C 266 LEU cc_start: 0.8619 (tt) cc_final: 0.8332 (tt) REVERT: C 362 LYS cc_start: 0.8211 (mttt) cc_final: 0.7934 (mtmm) REVERT: C 405 THR cc_start: 0.8915 (m) cc_final: 0.8651 (t) REVERT: D 215 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7725 (tm-30) REVERT: D 266 LEU cc_start: 0.8641 (tt) cc_final: 0.8402 (tt) REVERT: D 405 THR cc_start: 0.8863 (m) cc_final: 0.8641 (t) REVERT: E 266 LEU cc_start: 0.8752 (tt) cc_final: 0.8412 (tt) REVERT: E 280 ASN cc_start: 0.7725 (m-40) cc_final: 0.7055 (m110) REVERT: E 405 THR cc_start: 0.8909 (m) cc_final: 0.8642 (t) REVERT: F 266 LEU cc_start: 0.8694 (tt) cc_final: 0.8295 (tt) REVERT: F 280 ASN cc_start: 0.7724 (m-40) cc_final: 0.7434 (m110) REVERT: F 303 LEU cc_start: 0.8984 (tp) cc_final: 0.8564 (tp) REVERT: F 405 THR cc_start: 0.8899 (m) cc_final: 0.8681 (t) REVERT: F 424 MET cc_start: 0.7552 (mtm) cc_final: 0.7244 (mtm) REVERT: G 266 LEU cc_start: 0.8389 (tt) cc_final: 0.7971 (tt) REVERT: G 269 TYR cc_start: 0.8564 (t80) cc_final: 0.8137 (t80) REVERT: G 362 LYS cc_start: 0.8253 (mttt) cc_final: 0.7987 (mttt) REVERT: G 526 TYR cc_start: 0.9152 (m-80) cc_final: 0.8899 (m-80) REVERT: G 539 GLU cc_start: 0.7862 (tp30) cc_final: 0.7591 (tp30) REVERT: H 266 LEU cc_start: 0.8591 (tt) cc_final: 0.8365 (tt) REVERT: H 280 ASN cc_start: 0.7482 (m-40) cc_final: 0.7243 (m110) REVERT: H 289 ASP cc_start: 0.7436 (m-30) cc_final: 0.6848 (m-30) REVERT: H 394 VAL cc_start: 0.7806 (m) cc_final: 0.7455 (p) REVERT: H 411 ASN cc_start: 0.8666 (p0) cc_final: 0.8036 (p0) REVERT: H 429 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7095 (mt-10) REVERT: H 471 ILE cc_start: 0.9459 (pt) cc_final: 0.9217 (pt) REVERT: I 195 ASP cc_start: 0.7993 (m-30) cc_final: 0.7712 (p0) REVERT: I 266 LEU cc_start: 0.8417 (tt) cc_final: 0.8203 (tt) REVERT: I 280 ASN cc_start: 0.7586 (m-40) cc_final: 0.7206 (m110) REVERT: I 289 ASP cc_start: 0.7437 (m-30) cc_final: 0.6894 (m-30) REVERT: I 332 PHE cc_start: 0.7989 (t80) cc_final: 0.7775 (t80) REVERT: I 357 MET cc_start: 0.6931 (tpp) cc_final: 0.6375 (mpp) REVERT: J 194 SER cc_start: 0.9108 (m) cc_final: 0.8396 (p) REVERT: J 195 ASP cc_start: 0.8159 (m-30) cc_final: 0.7901 (p0) REVERT: J 408 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8594 (p) REVERT: J 451 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7628 (mt-10) REVERT: K 181 VAL cc_start: 0.7219 (t) cc_final: 0.7015 (p) REVERT: K 302 GLU cc_start: 0.8111 (tt0) cc_final: 0.7858 (tt0) REVERT: K 338 MET cc_start: 0.7628 (mmm) cc_final: 0.7328 (mmm) REVERT: K 362 LYS cc_start: 0.8127 (mttt) cc_final: 0.7827 (mttt) REVERT: K 405 THR cc_start: 0.8732 (m) cc_final: 0.8463 (t) REVERT: K 410 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8888 (pt) REVERT: K 526 TYR cc_start: 0.9225 (m-80) cc_final: 0.8931 (m-80) REVERT: K 539 GLU cc_start: 0.7915 (tp30) cc_final: 0.7417 (tp30) REVERT: L 405 THR cc_start: 0.8910 (m) cc_final: 0.8662 (t) REVERT: M 266 LEU cc_start: 0.8826 (tt) cc_final: 0.8579 (tt) REVERT: M 282 GLN cc_start: 0.7417 (mt0) cc_final: 0.7207 (mt0) REVERT: M 286 ILE cc_start: 0.8306 (pt) cc_final: 0.7990 (pt) REVERT: M 289 ASP cc_start: 0.7322 (m-30) cc_final: 0.6818 (m-30) REVERT: M 303 LEU cc_start: 0.8987 (tp) cc_final: 0.8701 (tp) REVERT: M 539 GLU cc_start: 0.7772 (tp30) cc_final: 0.7505 (tp30) REVERT: N 405 THR cc_start: 0.8887 (m) cc_final: 0.8658 (t) REVERT: N 539 GLU cc_start: 0.7925 (tp30) cc_final: 0.7696 (tp30) outliers start: 150 outliers final: 75 residues processed: 817 average time/residue: 0.2048 time to fit residues: 275.4807 Evaluate side-chains 590 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 512 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain O residue 408 THR Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 514 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 408 THR Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 430 ASP Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 430 ASP Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain H residue 514 LEU Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 460 ILE Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain J residue 408 THR Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 430 ASP Chi-restraints excluded: chain J residue 460 ILE Chi-restraints excluded: chain K residue 408 THR Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 430 ASP Chi-restraints excluded: chain K residue 460 ILE Chi-restraints excluded: chain K residue 514 LEU Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 393 LEU Chi-restraints excluded: chain L residue 408 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 430 ASP Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain M residue 393 LEU Chi-restraints excluded: chain M residue 408 THR Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 514 LEU Chi-restraints excluded: chain N residue 356 VAL Chi-restraints excluded: chain N residue 408 THR Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 489 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.5980 chunk 470 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN A 465 GLN B 361 GLN C 361 GLN C 465 GLN D 361 GLN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 GLN E 465 GLN G 280 ASN G 361 GLN H 361 GLN ** H 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 GLN L 361 GLN ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN N 361 GLN N 465 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.148542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104664 restraints weight = 43581.083| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.38 r_work: 0.3180 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 38160 Z= 0.188 Angle : 0.592 6.924 51615 Z= 0.319 Chirality : 0.049 0.156 6150 Planarity : 0.005 0.051 6600 Dihedral : 7.261 59.711 5221 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.96 % Allowed : 12.36 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.12), residues: 4650 helix: -0.38 (0.19), residues: 705 sheet: 0.61 (0.10), residues: 2610 loop : -2.23 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 419 TYR 0.015 0.002 TYR H 501 PHE 0.015 0.001 PHE N 332 TRP 0.009 0.001 TRP L 306 HIS 0.005 0.002 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00432 (38160) covalent geometry : angle 0.59191 (51615) hydrogen bonds : bond 0.04478 ( 1323) hydrogen bonds : angle 5.71348 ( 3381) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 601 time to evaluate : 1.285 Fit side-chains REVERT: A 303 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8492 (tt) REVERT: O 228 GLN cc_start: 0.6844 (mt0) cc_final: 0.6263 (mt0) REVERT: O 289 ASP cc_start: 0.7735 (m-30) cc_final: 0.6880 (m-30) REVERT: O 328 PHE cc_start: 0.7185 (m-80) cc_final: 0.6945 (m-10) REVERT: O 332 PHE cc_start: 0.7944 (t80) cc_final: 0.7596 (t80) REVERT: O 405 THR cc_start: 0.8952 (m) cc_final: 0.8699 (t) REVERT: B 362 LYS cc_start: 0.8746 (mttt) cc_final: 0.8491 (mtpt) REVERT: C 227 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.5567 (mmt-90) REVERT: C 266 LEU cc_start: 0.8522 (tt) cc_final: 0.8215 (tt) REVERT: C 357 MET cc_start: 0.8071 (tpp) cc_final: 0.7464 (mtp) REVERT: C 405 THR cc_start: 0.9052 (m) cc_final: 0.8792 (t) REVERT: D 215 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7777 (tm-30) REVERT: D 227 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.5760 (mmt-90) REVERT: D 266 LEU cc_start: 0.8616 (tt) cc_final: 0.8381 (tt) REVERT: D 328 PHE cc_start: 0.7228 (m-80) cc_final: 0.7006 (m-10) REVERT: D 332 PHE cc_start: 0.7741 (t80) cc_final: 0.7491 (t80) REVERT: D 405 THR cc_start: 0.9005 (m) cc_final: 0.8784 (t) REVERT: D 423 GLU cc_start: 0.8700 (tt0) cc_final: 0.8451 (tt0) REVERT: E 266 LEU cc_start: 0.8827 (tt) cc_final: 0.8535 (tt) REVERT: E 271 GLU cc_start: 0.8832 (tt0) cc_final: 0.8516 (tt0) REVERT: E 405 THR cc_start: 0.9103 (m) cc_final: 0.8794 (t) REVERT: F 227 ARG cc_start: 0.6424 (OUTLIER) cc_final: 0.5436 (mmt-90) REVERT: F 266 LEU cc_start: 0.8681 (tt) cc_final: 0.8184 (tt) REVERT: F 303 LEU cc_start: 0.9263 (tp) cc_final: 0.8826 (tp) REVERT: F 357 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8023 (tpp) REVERT: F 501 TYR cc_start: 0.8978 (t80) cc_final: 0.8738 (t80) REVERT: G 266 LEU cc_start: 0.8549 (tt) cc_final: 0.8137 (tt) REVERT: G 352 PHE cc_start: 0.7868 (m-80) cc_final: 0.7630 (m-80) REVERT: G 362 LYS cc_start: 0.8822 (mttt) cc_final: 0.8589 (mttt) REVERT: G 526 TYR cc_start: 0.9437 (m-80) cc_final: 0.8851 (m-80) REVERT: G 539 GLU cc_start: 0.8622 (tp30) cc_final: 0.8225 (tp30) REVERT: H 266 LEU cc_start: 0.8601 (tt) cc_final: 0.8279 (tt) REVERT: H 289 ASP cc_start: 0.8011 (m-30) cc_final: 0.7682 (t70) REVERT: H 411 ASN cc_start: 0.8939 (p0) cc_final: 0.8380 (p0) REVERT: I 266 LEU cc_start: 0.8394 (tt) cc_final: 0.8093 (tt) REVERT: I 303 LEU cc_start: 0.9265 (tp) cc_final: 0.8989 (tp) REVERT: I 332 PHE cc_start: 0.8156 (t80) cc_final: 0.7827 (t80) REVERT: J 194 SER cc_start: 0.9091 (m) cc_final: 0.8315 (p) REVERT: J 332 PHE cc_start: 0.7938 (t80) cc_final: 0.7640 (t80) REVERT: K 227 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.6169 (mmt180) REVERT: K 303 LEU cc_start: 0.9203 (tp) cc_final: 0.8892 (tp) REVERT: K 338 MET cc_start: 0.7791 (mmm) cc_final: 0.7495 (mmm) REVERT: K 362 LYS cc_start: 0.8882 (mttt) cc_final: 0.8649 (mttt) REVERT: K 405 THR cc_start: 0.8974 (m) cc_final: 0.8755 (t) REVERT: K 526 TYR cc_start: 0.9432 (m-80) cc_final: 0.9001 (m-80) REVERT: K 539 GLU cc_start: 0.8685 (tp30) cc_final: 0.8299 (tp30) REVERT: L 227 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.5740 (mmt-90) REVERT: L 338 MET cc_start: 0.8305 (mmm) cc_final: 0.7763 (mmm) REVERT: L 405 THR cc_start: 0.9059 (m) cc_final: 0.8827 (t) REVERT: L 423 GLU cc_start: 0.8807 (tt0) cc_final: 0.8546 (tt0) REVERT: L 474 TYR cc_start: 0.8354 (t80) cc_final: 0.8059 (t80) REVERT: L 537 GLU cc_start: 0.8580 (tp30) cc_final: 0.8291 (tp30) REVERT: M 266 LEU cc_start: 0.8953 (tt) cc_final: 0.8626 (tt) REVERT: M 539 GLU cc_start: 0.8623 (tp30) cc_final: 0.8208 (tp30) REVERT: N 227 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.5921 (mmt-90) REVERT: N 357 MET cc_start: 0.8106 (tpp) cc_final: 0.7841 (tpp) REVERT: N 377 GLU cc_start: 0.8965 (pt0) cc_final: 0.8623 (pt0) REVERT: N 501 TYR cc_start: 0.9057 (t80) cc_final: 0.8806 (t80) REVERT: N 539 GLU cc_start: 0.8756 (tp30) cc_final: 0.8294 (tp30) outliers start: 171 outliers final: 132 residues processed: 713 average time/residue: 0.2292 time to fit residues: 268.4155 Evaluate side-chains 659 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 519 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 335 SER Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 408 THR Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 408 THR Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 430 ASP Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 474 TYR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 430 ASP Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 460 ILE Chi-restraints excluded: chain I residue 474 TYR Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 275 ILE Chi-restraints excluded: chain J residue 408 THR Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 430 ASP Chi-restraints excluded: chain J residue 460 ILE Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 408 THR Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 430 ASP Chi-restraints excluded: chain K residue 460 ILE Chi-restraints excluded: chain K residue 471 ILE Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 401 LEU Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 408 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 430 ASP Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 362 LYS Chi-restraints excluded: chain M residue 404 VAL Chi-restraints excluded: chain M residue 408 THR Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain N residue 227 ARG Chi-restraints excluded: chain N residue 316 ASN Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 408 THR Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 489 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 289 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 271 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 130 optimal weight: 0.0570 chunk 120 optimal weight: 0.5980 chunk 362 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN B 465 GLN B 476 HIS D 476 HIS F 361 GLN G 476 HIS H 280 ASN J 361 GLN ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 ASN L 280 ASN ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.148323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.104633 restraints weight = 43514.233| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.36 r_work: 0.3183 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 38160 Z= 0.177 Angle : 0.577 8.051 51615 Z= 0.310 Chirality : 0.048 0.165 6150 Planarity : 0.004 0.050 6600 Dihedral : 6.707 55.939 5194 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.37 % Allowed : 13.87 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.12), residues: 4650 helix: -0.27 (0.20), residues: 705 sheet: 0.66 (0.11), residues: 2550 loop : -2.21 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 419 TYR 0.014 0.001 TYR M 390 PHE 0.020 0.001 PHE G 328 TRP 0.006 0.001 TRP B 306 HIS 0.005 0.002 HIS H 300 Details of bonding type rmsd covalent geometry : bond 0.00405 (38160) covalent geometry : angle 0.57659 (51615) hydrogen bonds : bond 0.04417 ( 1323) hydrogen bonds : angle 5.59152 ( 3381) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 547 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.8448 (tpp) cc_final: 0.8117 (tpp) REVERT: O 289 ASP cc_start: 0.7684 (m-30) cc_final: 0.7104 (m-30) REVERT: O 405 THR cc_start: 0.8922 (m) cc_final: 0.8678 (t) REVERT: B 266 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8166 (tt) REVERT: B 362 LYS cc_start: 0.8791 (mttt) cc_final: 0.8561 (mtpt) REVERT: B 411 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8291 (p0) REVERT: C 227 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.5525 (mmt-90) REVERT: C 266 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8206 (tt) REVERT: C 357 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7669 (mtt) REVERT: C 401 LEU cc_start: 0.8325 (tp) cc_final: 0.8071 (tt) REVERT: C 405 THR cc_start: 0.9028 (m) cc_final: 0.8792 (t) REVERT: D 215 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7746 (tm-30) REVERT: D 227 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.5765 (mmt-90) REVERT: D 266 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8398 (tt) REVERT: D 352 PHE cc_start: 0.7348 (m-80) cc_final: 0.7104 (m-80) REVERT: D 357 MET cc_start: 0.8139 (tpp) cc_final: 0.7922 (tpp) REVERT: D 405 THR cc_start: 0.8982 (m) cc_final: 0.8773 (t) REVERT: D 423 GLU cc_start: 0.8649 (tt0) cc_final: 0.8369 (tt0) REVERT: D 539 GLU cc_start: 0.8240 (tp30) cc_final: 0.8025 (tp30) REVERT: E 215 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8119 (tm-30) REVERT: E 266 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8443 (tt) REVERT: E 271 GLU cc_start: 0.8852 (tt0) cc_final: 0.8569 (tt0) REVERT: E 405 THR cc_start: 0.9092 (m) cc_final: 0.8796 (t) REVERT: F 227 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.5714 (mmt-90) REVERT: F 266 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8062 (tt) REVERT: F 501 TYR cc_start: 0.9079 (t80) cc_final: 0.8876 (t80) REVERT: G 266 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8124 (tt) REVERT: G 352 PHE cc_start: 0.7924 (m-80) cc_final: 0.7585 (m-80) REVERT: G 362 LYS cc_start: 0.8857 (mttt) cc_final: 0.8623 (mttt) REVERT: G 424 MET cc_start: 0.9011 (mtm) cc_final: 0.8752 (ptp) REVERT: G 526 TYR cc_start: 0.9417 (m-80) cc_final: 0.8729 (m-80) REVERT: G 539 GLU cc_start: 0.8633 (tp30) cc_final: 0.8223 (tp30) REVERT: H 266 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8365 (tt) REVERT: H 289 ASP cc_start: 0.7934 (m-30) cc_final: 0.7573 (t70) REVERT: H 411 ASN cc_start: 0.8717 (p0) cc_final: 0.8502 (p0) REVERT: I 227 ARG cc_start: 0.6122 (OUTLIER) cc_final: 0.5293 (mmt-90) REVERT: I 266 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8122 (tt) REVERT: I 303 LEU cc_start: 0.9225 (tp) cc_final: 0.8914 (tp) REVERT: I 332 PHE cc_start: 0.8206 (t80) cc_final: 0.7891 (t80) REVERT: J 194 SER cc_start: 0.9114 (m) cc_final: 0.8352 (p) REVERT: J 338 MET cc_start: 0.7863 (mmm) cc_final: 0.7652 (mtp) REVERT: J 352 PHE cc_start: 0.7450 (m-80) cc_final: 0.7162 (m-80) REVERT: K 227 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.6047 (mmt180) REVERT: K 303 LEU cc_start: 0.9264 (tp) cc_final: 0.8949 (tp) REVERT: K 338 MET cc_start: 0.7715 (mmm) cc_final: 0.7438 (mmm) REVERT: K 357 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8117 (tpp) REVERT: K 362 LYS cc_start: 0.8897 (mttt) cc_final: 0.8632 (mttt) REVERT: K 410 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8951 (pt) REVERT: K 424 MET cc_start: 0.8855 (mtm) cc_final: 0.8476 (ptp) REVERT: K 455 THR cc_start: 0.8576 (m) cc_final: 0.8220 (m) REVERT: K 526 TYR cc_start: 0.9394 (m-80) cc_final: 0.8957 (m-80) REVERT: K 539 GLU cc_start: 0.8692 (tp30) cc_final: 0.8306 (tp30) REVERT: L 227 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.5727 (mmt-90) REVERT: L 266 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8343 (tt) REVERT: L 338 MET cc_start: 0.8237 (mmm) cc_final: 0.7697 (mmm) REVERT: L 405 THR cc_start: 0.9006 (m) cc_final: 0.8792 (t) REVERT: L 423 GLU cc_start: 0.8663 (tt0) cc_final: 0.8306 (tt0) REVERT: L 474 TYR cc_start: 0.8350 (t80) cc_final: 0.8011 (t80) REVERT: M 266 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8607 (tt) REVERT: M 352 PHE cc_start: 0.7559 (m-80) cc_final: 0.7311 (m-80) REVERT: M 359 LEU cc_start: 0.8989 (tt) cc_final: 0.8711 (tt) REVERT: M 424 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8667 (ptp) REVERT: M 539 GLU cc_start: 0.8614 (tp30) cc_final: 0.8195 (tp30) REVERT: N 227 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.5847 (mmt-90) REVERT: N 266 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8487 (tt) REVERT: N 501 TYR cc_start: 0.8980 (t80) cc_final: 0.8762 (t80) REVERT: N 539 GLU cc_start: 0.8779 (tp30) cc_final: 0.8315 (tp30) outliers start: 232 outliers final: 152 residues processed: 693 average time/residue: 0.2357 time to fit residues: 268.8958 Evaluate side-chains 692 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 517 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 227 ARG Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 335 SER Chi-restraints excluded: chain O residue 408 THR Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 316 ASN Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 408 THR Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 430 ASP Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 474 TYR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 280 ASN Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 430 ASP Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 316 ASN Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 460 ILE Chi-restraints excluded: chain I residue 474 TYR Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 275 ILE Chi-restraints excluded: chain J residue 316 ASN Chi-restraints excluded: chain J residue 408 THR Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 430 ASP Chi-restraints excluded: chain J residue 460 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 357 MET Chi-restraints excluded: chain K residue 408 THR Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 429 GLU Chi-restraints excluded: chain K residue 430 ASP Chi-restraints excluded: chain K residue 460 ILE Chi-restraints excluded: chain K residue 471 ILE Chi-restraints excluded: chain K residue 474 TYR Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 408 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 430 ASP Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 408 THR Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 424 MET Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 227 ARG Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 275 ILE Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain N residue 316 ASN Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 408 THR Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 474 TYR Chi-restraints excluded: chain N residue 489 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 82 optimal weight: 0.9980 chunk 395 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 186 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 301 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 516 GLN ** C 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 GLN E 476 HIS F 476 HIS H 516 GLN ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 476 HIS J 516 GLN K 280 ASN K 516 GLN ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 476 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107035 restraints weight = 42348.570| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.18 r_work: 0.3168 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 38160 Z= 0.198 Angle : 0.593 8.283 51615 Z= 0.318 Chirality : 0.048 0.158 6150 Planarity : 0.004 0.052 6600 Dihedral : 6.593 53.341 5191 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.12 % Allowed : 15.09 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.12), residues: 4650 helix: -0.35 (0.19), residues: 720 sheet: 0.58 (0.11), residues: 2550 loop : -2.16 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 419 TYR 0.015 0.001 TYR M 390 PHE 0.015 0.001 PHE H 332 TRP 0.006 0.001 TRP B 306 HIS 0.005 0.002 HIS N 300 Details of bonding type rmsd covalent geometry : bond 0.00454 (38160) covalent geometry : angle 0.59289 (51615) hydrogen bonds : bond 0.04512 ( 1323) hydrogen bonds : angle 5.56930 ( 3381) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 536 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 352 PHE cc_start: 0.7694 (m-80) cc_final: 0.7357 (m-80) REVERT: O 405 THR cc_start: 0.8999 (m) cc_final: 0.8720 (t) REVERT: O 539 GLU cc_start: 0.8309 (tp30) cc_final: 0.8005 (tp30) REVERT: B 266 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8272 (tt) REVERT: B 411 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8435 (p0) REVERT: C 227 ARG cc_start: 0.6740 (OUTLIER) cc_final: 0.5569 (mmt-90) REVERT: C 266 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8316 (tt) REVERT: C 357 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7691 (mtt) REVERT: C 394 VAL cc_start: 0.7625 (m) cc_final: 0.7324 (p) REVERT: C 405 THR cc_start: 0.9080 (m) cc_final: 0.8864 (t) REVERT: D 215 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7771 (tm-30) REVERT: D 227 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.5847 (mmt-90) REVERT: D 266 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8418 (tt) REVERT: D 352 PHE cc_start: 0.7563 (m-80) cc_final: 0.7301 (m-80) REVERT: D 405 THR cc_start: 0.9024 (m) cc_final: 0.8793 (t) REVERT: D 423 GLU cc_start: 0.8527 (tt0) cc_final: 0.8257 (tt0) REVERT: D 539 GLU cc_start: 0.8238 (tp30) cc_final: 0.7978 (tp30) REVERT: E 215 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8160 (tm-30) REVERT: E 266 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8437 (tt) REVERT: E 271 GLU cc_start: 0.8851 (tt0) cc_final: 0.8543 (tt0) REVERT: E 405 THR cc_start: 0.9102 (m) cc_final: 0.8816 (t) REVERT: E 474 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.8092 (t80) REVERT: F 227 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.5727 (mmt-90) REVERT: F 266 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8091 (tt) REVERT: F 359 LEU cc_start: 0.8837 (tt) cc_final: 0.8511 (tt) REVERT: G 266 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8164 (tt) REVERT: G 526 TYR cc_start: 0.9419 (m-80) cc_final: 0.8737 (m-80) REVERT: G 539 GLU cc_start: 0.8497 (tp30) cc_final: 0.8165 (tp30) REVERT: H 289 ASP cc_start: 0.8023 (m-30) cc_final: 0.7628 (t70) REVERT: I 227 ARG cc_start: 0.6191 (OUTLIER) cc_final: 0.5321 (mmt-90) REVERT: I 266 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8202 (tt) REVERT: I 303 LEU cc_start: 0.9160 (tp) cc_final: 0.8865 (tp) REVERT: I 332 PHE cc_start: 0.8248 (t80) cc_final: 0.7972 (t80) REVERT: J 194 SER cc_start: 0.9128 (m) cc_final: 0.8328 (p) REVERT: J 303 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9065 (tp) REVERT: K 227 ARG cc_start: 0.6740 (OUTLIER) cc_final: 0.6108 (mmt180) REVERT: K 303 LEU cc_start: 0.9269 (tp) cc_final: 0.8952 (tp) REVERT: K 362 LYS cc_start: 0.8955 (mttt) cc_final: 0.8696 (mttt) REVERT: K 410 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9047 (pt) REVERT: K 424 MET cc_start: 0.8835 (mtm) cc_final: 0.8456 (ptp) REVERT: K 526 TYR cc_start: 0.9384 (m-80) cc_final: 0.9048 (m-80) REVERT: K 539 GLU cc_start: 0.8555 (tp30) cc_final: 0.8252 (tp30) REVERT: L 227 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.5748 (mmt-90) REVERT: L 266 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8362 (tt) REVERT: L 359 LEU cc_start: 0.8990 (tt) cc_final: 0.8719 (tt) REVERT: L 405 THR cc_start: 0.9094 (m) cc_final: 0.8851 (t) REVERT: L 423 GLU cc_start: 0.8591 (tt0) cc_final: 0.8250 (tt0) REVERT: L 474 TYR cc_start: 0.8055 (t80) cc_final: 0.7685 (t80) REVERT: M 227 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6069 (mmt-90) REVERT: M 266 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8671 (tt) REVERT: M 352 PHE cc_start: 0.7546 (m-80) cc_final: 0.7283 (m-80) REVERT: M 359 LEU cc_start: 0.9090 (tt) cc_final: 0.8775 (tt) REVERT: M 424 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8568 (ptp) REVERT: M 539 GLU cc_start: 0.8459 (tp30) cc_final: 0.8093 (tp30) REVERT: N 227 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.5886 (mmt-90) REVERT: N 266 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8410 (tt) REVERT: N 501 TYR cc_start: 0.9011 (t80) cc_final: 0.8801 (t80) REVERT: N 539 GLU cc_start: 0.8722 (tp30) cc_final: 0.8305 (tp30) outliers start: 221 outliers final: 170 residues processed: 675 average time/residue: 0.2387 time to fit residues: 263.9774 Evaluate side-chains 709 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 515 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 474 TYR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 227 ARG Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 316 ASN Chi-restraints excluded: chain O residue 335 SER Chi-restraints excluded: chain O residue 408 THR Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 516 GLN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 316 ASN Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 474 TYR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 316 ASN Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 408 THR Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 430 ASP Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 474 TYR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 316 ASN Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 430 ASP Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain H residue 474 TYR Chi-restraints excluded: chain H residue 516 GLN Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 316 ASN Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 411 ASN Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 460 ILE Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain I residue 474 TYR Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 275 ILE Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 316 ASN Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 430 ASP Chi-restraints excluded: chain J residue 460 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 316 ASN Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 408 THR Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 429 GLU Chi-restraints excluded: chain K residue 430 ASP Chi-restraints excluded: chain K residue 460 ILE Chi-restraints excluded: chain K residue 471 ILE Chi-restraints excluded: chain K residue 474 TYR Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 316 ASN Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 408 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 411 ASN Chi-restraints excluded: chain L residue 430 ASP Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 267 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 404 VAL Chi-restraints excluded: chain M residue 408 THR Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 424 MET Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 227 ARG Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 275 ILE Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain N residue 316 ASN Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 405 THR Chi-restraints excluded: chain N residue 408 THR Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 474 TYR Chi-restraints excluded: chain N residue 489 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 22 optimal weight: 0.6980 chunk 451 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 454 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 322 optimal weight: 0.0980 chunk 326 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 349 optimal weight: 0.9980 chunk 478 optimal weight: 0.7980 chunk 258 optimal weight: 0.0020 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN B 465 GLN ** C 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 GLN ** I 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.150655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108940 restraints weight = 42059.929| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.17 r_work: 0.3196 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 38160 Z= 0.142 Angle : 0.567 8.043 51615 Z= 0.303 Chirality : 0.048 0.160 6150 Planarity : 0.004 0.049 6600 Dihedral : 6.127 50.245 5188 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.75 % Allowed : 15.76 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.12), residues: 4650 helix: -0.20 (0.20), residues: 720 sheet: 0.61 (0.11), residues: 2550 loop : -2.14 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 419 TYR 0.015 0.001 TYR I 406 PHE 0.019 0.001 PHE N 328 TRP 0.004 0.001 TRP B 306 HIS 0.003 0.001 HIS H 476 Details of bonding type rmsd covalent geometry : bond 0.00318 (38160) covalent geometry : angle 0.56746 (51615) hydrogen bonds : bond 0.04249 ( 1323) hydrogen bonds : angle 5.48023 ( 3381) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 537 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.5164 (mmt-90) REVERT: O 227 ARG cc_start: 0.6196 (OUTLIER) cc_final: 0.5458 (mmt-90) REVERT: B 266 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8265 (tt) REVERT: B 411 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8282 (p0) REVERT: C 227 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.5621 (mmt-90) REVERT: C 266 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8286 (tt) REVERT: C 357 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7541 (mtt) REVERT: C 405 THR cc_start: 0.9041 (m) cc_final: 0.8823 (t) REVERT: D 215 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7699 (tm-30) REVERT: D 227 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.5809 (mmt-90) REVERT: D 266 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8417 (tt) REVERT: D 332 PHE cc_start: 0.7745 (t80) cc_final: 0.7340 (t80) REVERT: D 357 MET cc_start: 0.8427 (tpp) cc_final: 0.8115 (tpp) REVERT: D 405 THR cc_start: 0.8983 (m) cc_final: 0.8753 (t) REVERT: D 423 GLU cc_start: 0.8535 (tt0) cc_final: 0.8267 (tt0) REVERT: E 215 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8073 (tm-30) REVERT: E 266 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8415 (tt) REVERT: E 271 GLU cc_start: 0.8817 (tt0) cc_final: 0.8529 (tt0) REVERT: E 405 THR cc_start: 0.9061 (m) cc_final: 0.8783 (t) REVERT: E 474 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.8009 (t80) REVERT: F 200 MET cc_start: 0.8508 (mmp) cc_final: 0.8034 (mmp) REVERT: F 227 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6022 (mmt-90) REVERT: F 266 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8055 (tt) REVERT: F 357 MET cc_start: 0.8260 (tpp) cc_final: 0.8023 (tpp) REVERT: F 359 LEU cc_start: 0.8805 (tt) cc_final: 0.8473 (tt) REVERT: G 266 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8175 (tt) REVERT: G 359 LEU cc_start: 0.8947 (tt) cc_final: 0.8697 (tp) REVERT: G 539 GLU cc_start: 0.8442 (tp30) cc_final: 0.8218 (tp30) REVERT: H 266 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8508 (tt) REVERT: H 289 ASP cc_start: 0.8013 (m-30) cc_final: 0.7601 (t70) REVERT: H 357 MET cc_start: 0.8334 (tpp) cc_final: 0.8087 (tpp) REVERT: I 227 ARG cc_start: 0.6293 (OUTLIER) cc_final: 0.5395 (mmt-90) REVERT: I 266 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8257 (tt) REVERT: I 303 LEU cc_start: 0.9157 (tp) cc_final: 0.8857 (tp) REVERT: I 332 PHE cc_start: 0.8230 (t80) cc_final: 0.7970 (t80) REVERT: I 359 LEU cc_start: 0.8875 (tt) cc_final: 0.8612 (tt) REVERT: J 194 SER cc_start: 0.9039 (m) cc_final: 0.8312 (p) REVERT: K 227 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6326 (mmt180) REVERT: K 362 LYS cc_start: 0.8951 (mttt) cc_final: 0.8689 (mttt) REVERT: K 526 TYR cc_start: 0.9353 (m-80) cc_final: 0.8831 (m-80) REVERT: K 539 GLU cc_start: 0.8524 (tp30) cc_final: 0.8228 (tp30) REVERT: L 227 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.5458 (mmt-90) REVERT: L 266 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8343 (tt) REVERT: L 405 THR cc_start: 0.9033 (m) cc_final: 0.8808 (t) REVERT: L 423 GLU cc_start: 0.8542 (tt0) cc_final: 0.8169 (tt0) REVERT: M 227 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.5973 (mmt-90) REVERT: M 266 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8649 (tt) REVERT: M 359 LEU cc_start: 0.9047 (tt) cc_final: 0.8754 (tt) REVERT: M 539 GLU cc_start: 0.8430 (tp30) cc_final: 0.8087 (tp30) REVERT: N 227 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.5819 (mmt-90) REVERT: N 266 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8388 (tt) REVERT: N 501 TYR cc_start: 0.8996 (t80) cc_final: 0.8782 (t80) outliers start: 205 outliers final: 164 residues processed: 660 average time/residue: 0.2344 time to fit residues: 254.7171 Evaluate side-chains 694 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 506 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 474 TYR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 227 ARG Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 335 SER Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 408 THR Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 316 ASN Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 474 TYR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 430 ASP Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 474 TYR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 430 ASP Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain H residue 474 TYR Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 316 ASN Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 411 ASN Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 460 ILE Chi-restraints excluded: chain I residue 474 TYR Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 267 ILE Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 316 ASN Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 430 ASP Chi-restraints excluded: chain J residue 460 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 316 ASN Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 408 THR Chi-restraints excluded: chain K residue 430 ASP Chi-restraints excluded: chain K residue 460 ILE Chi-restraints excluded: chain K residue 471 ILE Chi-restraints excluded: chain K residue 474 TYR Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 408 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 411 ASN Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 430 ASP Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 267 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 404 VAL Chi-restraints excluded: chain M residue 408 THR Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 227 ARG Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 275 ILE Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain N residue 316 ASN Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 405 THR Chi-restraints excluded: chain N residue 408 THR Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 474 TYR Chi-restraints excluded: chain N residue 489 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 81 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 281 optimal weight: 0.6980 chunk 353 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 434 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 185 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 113 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 HIS ** O 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 ASN D 516 GLN ** I 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 ASN ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.150288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108570 restraints weight = 42163.751| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.17 r_work: 0.3192 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 38160 Z= 0.158 Angle : 0.570 7.788 51615 Z= 0.305 Chirality : 0.048 0.165 6150 Planarity : 0.004 0.051 6600 Dihedral : 5.980 48.129 5185 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.95 % Allowed : 16.74 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.12), residues: 4650 helix: -0.15 (0.20), residues: 720 sheet: 0.58 (0.11), residues: 2550 loop : -2.08 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 419 TYR 0.014 0.001 TYR F 390 PHE 0.013 0.001 PHE F 328 TRP 0.004 0.001 TRP L 306 HIS 0.003 0.001 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00359 (38160) covalent geometry : angle 0.57041 (51615) hydrogen bonds : bond 0.04312 ( 1323) hydrogen bonds : angle 5.46232 ( 3381) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 533 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.5218 (mmt-90) REVERT: O 195 ASP cc_start: 0.8505 (m-30) cc_final: 0.8272 (m-30) REVERT: O 227 ARG cc_start: 0.6293 (OUTLIER) cc_final: 0.5479 (mmt-90) REVERT: B 266 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8243 (tt) REVERT: B 352 PHE cc_start: 0.8071 (m-80) cc_final: 0.7658 (m-80) REVERT: C 227 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.5586 (mmt-90) REVERT: C 266 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8195 (tt) REVERT: C 357 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7822 (mtp) REVERT: C 405 THR cc_start: 0.9047 (m) cc_final: 0.8833 (t) REVERT: D 215 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7689 (tm-30) REVERT: D 227 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.5907 (mmt-90) REVERT: D 266 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8400 (tt) REVERT: D 332 PHE cc_start: 0.7714 (t80) cc_final: 0.7333 (t80) REVERT: D 405 THR cc_start: 0.8981 (m) cc_final: 0.8755 (t) REVERT: D 423 GLU cc_start: 0.8527 (tt0) cc_final: 0.8268 (tt0) REVERT: D 539 GLU cc_start: 0.8320 (tp30) cc_final: 0.8017 (tp30) REVERT: E 215 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8085 (tm-30) REVERT: E 266 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8401 (tt) REVERT: E 269 TYR cc_start: 0.8978 (t80) cc_final: 0.8662 (t80) REVERT: E 271 GLU cc_start: 0.8806 (tt0) cc_final: 0.8422 (tt0) REVERT: E 405 THR cc_start: 0.9068 (m) cc_final: 0.8785 (t) REVERT: E 474 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.8051 (t80) REVERT: F 227 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.5939 (mmt-90) REVERT: F 266 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8014 (tt) REVERT: F 357 MET cc_start: 0.8333 (tpp) cc_final: 0.8099 (tpp) REVERT: F 359 LEU cc_start: 0.8858 (tt) cc_final: 0.8537 (tt) REVERT: G 266 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8044 (tt) REVERT: G 352 PHE cc_start: 0.8004 (m-10) cc_final: 0.7736 (m-80) REVERT: G 539 GLU cc_start: 0.8461 (tp30) cc_final: 0.8236 (tp30) REVERT: H 266 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8538 (tt) REVERT: H 289 ASP cc_start: 0.8016 (m-30) cc_final: 0.7591 (t70) REVERT: H 357 MET cc_start: 0.8313 (tpp) cc_final: 0.8089 (tpp) REVERT: I 227 ARG cc_start: 0.6428 (OUTLIER) cc_final: 0.5505 (mmt-90) REVERT: I 228 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6256 (mt0) REVERT: I 266 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8406 (tt) REVERT: I 303 LEU cc_start: 0.9165 (tp) cc_final: 0.8854 (tp) REVERT: I 332 PHE cc_start: 0.8210 (t80) cc_final: 0.7972 (t80) REVERT: J 194 SER cc_start: 0.9043 (m) cc_final: 0.8332 (p) REVERT: J 215 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7716 (tm-30) REVERT: J 227 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6111 (mmt-90) REVERT: J 228 GLN cc_start: 0.6853 (mt0) cc_final: 0.6327 (mt0) REVERT: K 227 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.6289 (mmt180) REVERT: K 280 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7826 (p0) REVERT: K 362 LYS cc_start: 0.8953 (mttt) cc_final: 0.8720 (mttt) REVERT: K 526 TYR cc_start: 0.9352 (m-80) cc_final: 0.8705 (m-80) REVERT: K 539 GLU cc_start: 0.8520 (tp30) cc_final: 0.8227 (tp30) REVERT: L 227 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.5302 (mmt-90) REVERT: L 266 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8284 (tt) REVERT: L 405 THR cc_start: 0.9046 (m) cc_final: 0.8831 (t) REVERT: L 423 GLU cc_start: 0.8532 (tt0) cc_final: 0.8178 (tt0) REVERT: L 474 TYR cc_start: 0.8027 (t80) cc_final: 0.7620 (t80) REVERT: M 227 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.5973 (mmt-90) REVERT: M 266 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8653 (tt) REVERT: M 359 LEU cc_start: 0.9071 (tt) cc_final: 0.8793 (tt) REVERT: M 408 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8709 (t) REVERT: N 227 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.5802 (mmt-90) REVERT: N 266 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8289 (tt) outliers start: 214 outliers final: 181 residues processed: 665 average time/residue: 0.2292 time to fit residues: 250.6998 Evaluate side-chains 722 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 514 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 474 TYR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 227 ARG Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 316 ASN Chi-restraints excluded: chain O residue 335 SER Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 408 THR Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 471 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 516 GLN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 316 ASN Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 474 TYR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 316 ASN Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 430 ASP Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 474 TYR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 316 ASN Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 430 ASP Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain H residue 474 TYR Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 316 ASN Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 411 ASN Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 460 ILE Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain I residue 474 TYR Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 267 ILE Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 316 ASN Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain J residue 408 THR Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 430 ASP Chi-restraints excluded: chain J residue 460 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 280 ASN Chi-restraints excluded: chain K residue 316 ASN Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 408 THR Chi-restraints excluded: chain K residue 429 GLU Chi-restraints excluded: chain K residue 430 ASP Chi-restraints excluded: chain K residue 460 ILE Chi-restraints excluded: chain K residue 471 ILE Chi-restraints excluded: chain K residue 474 TYR Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 316 ASN Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 408 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 411 ASN Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 430 ASP Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 267 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 404 VAL Chi-restraints excluded: chain M residue 408 THR Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 474 TYR Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 227 ARG Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 275 ILE Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain N residue 316 ASN Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 405 THR Chi-restraints excluded: chain N residue 408 THR Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 474 TYR Chi-restraints excluded: chain N residue 489 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 424 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 245 optimal weight: 0.7980 chunk 403 optimal weight: 0.5980 chunk 240 optimal weight: 1.9990 chunk 399 optimal weight: 0.9990 chunk 395 optimal weight: 0.9990 chunk 423 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 412 optimal weight: 0.7980 chunk 409 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 378 ASN O 476 HIS D 516 GLN ** I 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 ASN ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.149116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107372 restraints weight = 42470.865| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.17 r_work: 0.3176 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 38160 Z= 0.190 Angle : 0.593 7.466 51615 Z= 0.317 Chirality : 0.048 0.172 6150 Planarity : 0.004 0.055 6600 Dihedral : 6.079 48.274 5185 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 5.23 % Allowed : 17.55 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.12), residues: 4650 helix: -0.17 (0.20), residues: 720 sheet: 0.47 (0.10), residues: 2550 loop : -2.02 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 419 TYR 0.014 0.001 TYR I 406 PHE 0.020 0.001 PHE A 336 TRP 0.006 0.001 TRP L 306 HIS 0.005 0.001 HIS F 300 Details of bonding type rmsd covalent geometry : bond 0.00437 (38160) covalent geometry : angle 0.59272 (51615) hydrogen bonds : bond 0.04453 ( 1323) hydrogen bonds : angle 5.49139 ( 3381) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 510 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.5224 (mmt-90) REVERT: O 195 ASP cc_start: 0.8508 (m-30) cc_final: 0.8268 (m-30) REVERT: O 227 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5503 (mmt-90) REVERT: O 289 ASP cc_start: 0.7903 (m-30) cc_final: 0.7208 (m-30) REVERT: O 303 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8888 (tp) REVERT: B 266 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8144 (tt) REVERT: B 411 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8301 (p0) REVERT: C 227 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.5771 (mmt-90) REVERT: C 266 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8197 (tt) REVERT: C 357 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7837 (mtp) REVERT: C 405 THR cc_start: 0.9072 (m) cc_final: 0.8862 (t) REVERT: D 195 ASP cc_start: 0.8394 (m-30) cc_final: 0.8194 (m-30) REVERT: D 215 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7689 (tm-30) REVERT: D 227 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.5925 (mmt-90) REVERT: D 266 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8334 (tt) REVERT: D 332 PHE cc_start: 0.7806 (t80) cc_final: 0.7420 (t80) REVERT: D 352 PHE cc_start: 0.7535 (m-80) cc_final: 0.7269 (m-80) REVERT: D 357 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8098 (tpp) REVERT: D 405 THR cc_start: 0.9005 (m) cc_final: 0.8787 (t) REVERT: D 423 GLU cc_start: 0.8556 (tt0) cc_final: 0.8305 (tt0) REVERT: D 539 GLU cc_start: 0.8355 (tp30) cc_final: 0.8045 (tp30) REVERT: E 215 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8078 (tm-30) REVERT: E 266 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8433 (tt) REVERT: E 405 THR cc_start: 0.9094 (m) cc_final: 0.8806 (t) REVERT: E 474 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.8041 (t80) REVERT: F 227 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.5950 (mmt-90) REVERT: F 266 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8054 (tt) REVERT: F 357 MET cc_start: 0.8377 (tpp) cc_final: 0.8120 (tpp) REVERT: F 359 LEU cc_start: 0.8873 (tt) cc_final: 0.8570 (tt) REVERT: G 266 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8061 (tt) REVERT: G 352 PHE cc_start: 0.8026 (m-10) cc_final: 0.7738 (m-80) REVERT: G 539 GLU cc_start: 0.8487 (tp30) cc_final: 0.8255 (tp30) REVERT: H 266 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8555 (tt) REVERT: H 289 ASP cc_start: 0.8041 (m-30) cc_final: 0.7681 (t70) REVERT: H 357 MET cc_start: 0.8294 (tpp) cc_final: 0.8064 (tpp) REVERT: I 227 ARG cc_start: 0.6151 (OUTLIER) cc_final: 0.5201 (mmt-90) REVERT: I 228 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6315 (mt0) REVERT: I 266 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8347 (tt) REVERT: I 303 LEU cc_start: 0.9158 (tp) cc_final: 0.8854 (tp) REVERT: J 194 SER cc_start: 0.8983 (m) cc_final: 0.8330 (p) REVERT: J 215 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7739 (tm-30) REVERT: J 227 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6149 (mmt-90) REVERT: J 228 GLN cc_start: 0.6834 (mt0) cc_final: 0.6270 (mt0) REVERT: K 181 VAL cc_start: 0.7969 (t) cc_final: 0.7700 (p) REVERT: K 227 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6350 (mmt180) REVERT: K 303 LEU cc_start: 0.9271 (tp) cc_final: 0.9043 (tp) REVERT: K 362 LYS cc_start: 0.8965 (mttt) cc_final: 0.8733 (mttt) REVERT: K 424 MET cc_start: 0.8713 (ptp) cc_final: 0.8470 (ptp) REVERT: K 526 TYR cc_start: 0.9380 (m-80) cc_final: 0.8718 (m-80) REVERT: L 227 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.5336 (mmt-90) REVERT: L 266 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8274 (tt) REVERT: L 405 THR cc_start: 0.9084 (m) cc_final: 0.8862 (t) REVERT: L 423 GLU cc_start: 0.8548 (tt0) cc_final: 0.8205 (tt0) REVERT: L 474 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7630 (t80) REVERT: M 227 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.5813 (mmt-90) REVERT: M 266 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8647 (tt) REVERT: N 227 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.5563 (mmt-90) REVERT: N 266 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8285 (tt) outliers start: 226 outliers final: 181 residues processed: 651 average time/residue: 0.2210 time to fit residues: 238.0909 Evaluate side-chains 710 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 500 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 474 TYR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 227 ARG Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 303 LEU Chi-restraints excluded: chain O residue 316 ASN Chi-restraints excluded: chain O residue 335 SER Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 408 THR Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 471 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 316 ASN Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 474 TYR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 316 ASN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 430 ASP Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 474 TYR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 316 ASN Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 430 ASP Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain H residue 474 TYR Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 316 ASN Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 411 ASN Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 460 ILE Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain I residue 474 TYR Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 275 ILE Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 316 ASN Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain J residue 408 THR Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 430 ASP Chi-restraints excluded: chain J residue 460 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 316 ASN Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 408 THR Chi-restraints excluded: chain K residue 429 GLU Chi-restraints excluded: chain K residue 430 ASP Chi-restraints excluded: chain K residue 460 ILE Chi-restraints excluded: chain K residue 471 ILE Chi-restraints excluded: chain K residue 474 TYR Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 316 ASN Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 408 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 411 ASN Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 430 ASP Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain L residue 474 TYR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 267 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 404 VAL Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 424 MET Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 474 TYR Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 227 ARG Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 275 ILE Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain N residue 316 ASN Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 405 THR Chi-restraints excluded: chain N residue 408 THR Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 474 TYR Chi-restraints excluded: chain N residue 489 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 464 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 339 optimal weight: 0.4980 chunk 327 optimal weight: 2.9990 chunk 365 optimal weight: 5.9990 chunk 343 optimal weight: 0.6980 chunk 405 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 chunk 70 optimal weight: 0.0770 chunk 299 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 GLN ** H 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 516 GLN M 516 GLN ** N 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.150954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109234 restraints weight = 41971.020| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.17 r_work: 0.3205 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 38160 Z= 0.140 Angle : 0.570 8.344 51615 Z= 0.304 Chirality : 0.048 0.162 6150 Planarity : 0.004 0.054 6600 Dihedral : 5.750 47.262 5183 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.02 % Allowed : 18.19 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.13), residues: 4650 helix: -0.07 (0.20), residues: 720 sheet: 0.51 (0.11), residues: 2550 loop : -1.97 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 419 TYR 0.015 0.001 TYR I 406 PHE 0.021 0.001 PHE M 328 TRP 0.005 0.001 TRP B 306 HIS 0.003 0.001 HIS H 476 Details of bonding type rmsd covalent geometry : bond 0.00316 (38160) covalent geometry : angle 0.56962 (51615) hydrogen bonds : bond 0.04210 ( 1323) hydrogen bonds : angle 5.42355 ( 3381) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 514 time to evaluate : 1.341 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 227 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.6358 (mmt180) REVERT: O 195 ASP cc_start: 0.8550 (m-30) cc_final: 0.8317 (m-30) REVERT: O 227 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.5413 (mmt-90) REVERT: B 266 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8142 (tt) REVERT: C 227 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6338 (mpt180) REVERT: C 228 GLN cc_start: 0.7093 (mt0) cc_final: 0.6712 (mt0) REVERT: C 266 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8167 (tt) REVERT: C 405 THR cc_start: 0.9037 (m) cc_final: 0.8816 (t) REVERT: D 215 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7604 (tm-30) REVERT: D 227 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.5894 (mmt-90) REVERT: D 266 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8332 (tt) REVERT: D 332 PHE cc_start: 0.7901 (t80) cc_final: 0.7572 (t80) REVERT: D 405 THR cc_start: 0.8867 (m) cc_final: 0.8652 (t) REVERT: D 423 GLU cc_start: 0.8509 (tt0) cc_final: 0.8257 (tt0) REVERT: D 539 GLU cc_start: 0.8340 (tp30) cc_final: 0.8036 (tp30) REVERT: E 215 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7971 (tm-30) REVERT: E 227 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.5363 (mmt-90) REVERT: E 266 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8415 (tt) REVERT: E 405 THR cc_start: 0.9051 (m) cc_final: 0.8760 (t) REVERT: E 423 GLU cc_start: 0.8695 (tt0) cc_final: 0.8445 (tt0) REVERT: E 474 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7981 (t80) REVERT: F 200 MET cc_start: 0.8543 (mmp) cc_final: 0.8050 (mmp) REVERT: F 266 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7963 (tt) REVERT: F 357 MET cc_start: 0.8362 (tpp) cc_final: 0.8104 (tpp) REVERT: F 359 LEU cc_start: 0.8860 (tt) cc_final: 0.8549 (tt) REVERT: G 266 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7969 (tt) REVERT: H 266 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8562 (tt) REVERT: H 289 ASP cc_start: 0.8013 (m-30) cc_final: 0.7580 (t70) REVERT: H 357 MET cc_start: 0.8198 (tpp) cc_final: 0.7998 (tpp) REVERT: I 227 ARG cc_start: 0.6421 (OUTLIER) cc_final: 0.5488 (mmt-90) REVERT: I 228 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6303 (mt0) REVERT: I 266 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8331 (tt) REVERT: I 303 LEU cc_start: 0.9121 (tp) cc_final: 0.8826 (tp) REVERT: J 194 SER cc_start: 0.8965 (m) cc_final: 0.8351 (p) REVERT: J 215 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7702 (tm-30) REVERT: J 227 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.5976 (mmt-90) REVERT: J 228 GLN cc_start: 0.6847 (mt0) cc_final: 0.6309 (mt0) REVERT: K 227 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6355 (mmt180) REVERT: K 303 LEU cc_start: 0.9291 (tp) cc_final: 0.9062 (tp) REVERT: K 357 MET cc_start: 0.8206 (tpp) cc_final: 0.7926 (tpp) REVERT: K 362 LYS cc_start: 0.8928 (mttt) cc_final: 0.8694 (mttt) REVERT: K 424 MET cc_start: 0.8695 (ptp) cc_final: 0.8463 (ptp) REVERT: K 455 THR cc_start: 0.8615 (m) cc_final: 0.8288 (m) REVERT: K 526 TYR cc_start: 0.9334 (m-80) cc_final: 0.8697 (m-80) REVERT: L 227 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5010 (mmt-90) REVERT: L 266 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8285 (tt) REVERT: L 423 GLU cc_start: 0.8502 (tt0) cc_final: 0.8141 (tt0) REVERT: L 474 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7596 (t80) REVERT: M 227 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.5733 (mmt-90) REVERT: M 266 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8625 (tt) REVERT: M 282 GLN cc_start: 0.7581 (mt0) cc_final: 0.7298 (mt0) REVERT: N 227 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.5535 (mmt-90) REVERT: N 266 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8288 (tt) REVERT: N 538 ARG cc_start: 0.8793 (ttt-90) cc_final: 0.8569 (tpp80) outliers start: 217 outliers final: 175 residues processed: 650 average time/residue: 0.2153 time to fit residues: 231.1428 Evaluate side-chains 698 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 498 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 474 TYR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 227 ARG Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 335 SER Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 471 ILE Chi-restraints excluded: chain O residue 474 TYR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 316 ASN Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 474 TYR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 316 ASN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 430 ASP Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 474 TYR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 316 ASN Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 430 ASP Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain H residue 474 TYR Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 316 ASN Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 411 ASN Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 460 ILE Chi-restraints excluded: chain I residue 474 TYR Chi-restraints excluded: chain I residue 534 LEU Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 267 ILE Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 316 ASN Chi-restraints excluded: chain J residue 408 THR Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 430 ASP Chi-restraints excluded: chain J residue 460 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 430 ASP Chi-restraints excluded: chain K residue 460 ILE Chi-restraints excluded: chain K residue 471 ILE Chi-restraints excluded: chain K residue 474 TYR Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 316 ASN Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 408 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 411 ASN Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 430 ASP Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain L residue 474 TYR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 267 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 287 ILE Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 404 VAL Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 474 TYR Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 227 ARG Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 275 ILE Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain N residue 316 ASN Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 405 THR Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 474 TYR Chi-restraints excluded: chain N residue 489 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 333 optimal weight: 5.9990 chunk 448 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 179 optimal weight: 0.5980 chunk 266 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN D 516 GLN H 378 ASN I 465 GLN ** I 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106148 restraints weight = 42886.889| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.17 r_work: 0.3163 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 38160 Z= 0.226 Angle : 0.619 12.900 51615 Z= 0.331 Chirality : 0.049 0.175 6150 Planarity : 0.005 0.058 6600 Dihedral : 6.151 52.677 5177 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.00 % Allowed : 18.63 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.12), residues: 4650 helix: -0.18 (0.20), residues: 720 sheet: 0.33 (0.10), residues: 2550 loop : -1.93 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 419 TYR 0.016 0.001 TYR K 390 PHE 0.018 0.002 PHE B 499 TRP 0.008 0.001 TRP L 306 HIS 0.005 0.001 HIS F 300 Details of bonding type rmsd covalent geometry : bond 0.00521 (38160) covalent geometry : angle 0.61889 (51615) hydrogen bonds : bond 0.04599 ( 1323) hydrogen bonds : angle 5.52092 ( 3381) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 512 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.6368 (mmt180) REVERT: O 195 ASP cc_start: 0.8509 (m-30) cc_final: 0.8265 (m-30) REVERT: O 289 ASP cc_start: 0.7932 (m-30) cc_final: 0.7233 (m-30) REVERT: O 303 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8913 (tp) REVERT: O 539 GLU cc_start: 0.8493 (tp30) cc_final: 0.8139 (tp30) REVERT: B 266 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8154 (tt) REVERT: B 411 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8401 (p0) REVERT: C 227 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.5833 (mmt-90) REVERT: C 266 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8232 (tt) REVERT: C 357 MET cc_start: 0.8443 (tpp) cc_final: 0.7988 (mtp) REVERT: C 405 THR cc_start: 0.9104 (m) cc_final: 0.8896 (t) REVERT: C 419 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7377 (mtm-85) REVERT: D 215 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7733 (tm-30) REVERT: D 227 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.5909 (mmt-90) REVERT: D 266 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8351 (tt) REVERT: D 332 PHE cc_start: 0.7978 (t80) cc_final: 0.7650 (t80) REVERT: D 357 MET cc_start: 0.8516 (tpp) cc_final: 0.8088 (tpp) REVERT: D 405 THR cc_start: 0.9025 (m) cc_final: 0.8810 (t) REVERT: D 539 GLU cc_start: 0.8411 (tp30) cc_final: 0.8093 (tp30) REVERT: E 215 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8064 (tm-30) REVERT: E 227 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.5354 (mmt-90) REVERT: E 266 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8477 (tt) REVERT: E 271 GLU cc_start: 0.8798 (tt0) cc_final: 0.8588 (tt0) REVERT: E 405 THR cc_start: 0.9109 (m) cc_final: 0.8821 (t) REVERT: E 474 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7971 (t80) REVERT: F 266 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8058 (tt) REVERT: F 357 MET cc_start: 0.8427 (tpp) cc_final: 0.8154 (tpp) REVERT: F 359 LEU cc_start: 0.8895 (tt) cc_final: 0.8605 (tt) REVERT: G 266 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8038 (tt) REVERT: G 539 GLU cc_start: 0.8513 (tp30) cc_final: 0.8276 (tp30) REVERT: H 266 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8588 (tt) REVERT: H 289 ASP cc_start: 0.8025 (m-30) cc_final: 0.7602 (t70) REVERT: I 227 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.5524 (mmt-90) REVERT: I 228 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6291 (mt0) REVERT: I 266 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8367 (tt) REVERT: I 303 LEU cc_start: 0.9178 (tp) cc_final: 0.8877 (tp) REVERT: J 194 SER cc_start: 0.9008 (m) cc_final: 0.8399 (p) REVERT: J 215 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7770 (tm-30) REVERT: J 227 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6022 (mmt-90) REVERT: J 228 GLN cc_start: 0.6912 (mt0) cc_final: 0.6376 (mt0) REVERT: J 451 GLU cc_start: 0.8660 (tp30) cc_final: 0.8400 (tp30) REVERT: K 227 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6372 (mmt180) REVERT: K 357 MET cc_start: 0.8170 (tpp) cc_final: 0.7813 (tpp) REVERT: K 424 MET cc_start: 0.8712 (ptp) cc_final: 0.8482 (ptp) REVERT: K 526 TYR cc_start: 0.9377 (m-80) cc_final: 0.8760 (m-80) REVERT: L 227 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.5240 (mmt-90) REVERT: L 266 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8301 (tt) REVERT: L 423 GLU cc_start: 0.8562 (tt0) cc_final: 0.8236 (tt0) REVERT: L 474 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7641 (t80) REVERT: L 539 GLU cc_start: 0.8474 (tp30) cc_final: 0.8144 (tp30) REVERT: M 227 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.5879 (mmt-90) REVERT: M 266 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8649 (tt) REVERT: N 227 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.5550 (mmt-90) REVERT: N 266 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8299 (tt) REVERT: N 538 ARG cc_start: 0.8835 (ttt-90) cc_final: 0.8616 (tpp80) outliers start: 216 outliers final: 180 residues processed: 640 average time/residue: 0.1982 time to fit residues: 209.7827 Evaluate side-chains 708 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 502 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 474 TYR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 227 ARG Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 303 LEU Chi-restraints excluded: chain O residue 335 SER Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 471 ILE Chi-restraints excluded: chain O residue 474 TYR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 316 ASN Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 474 TYR Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 316 ASN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 429 GLU Chi-restraints excluded: chain G residue 430 ASP Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 474 TYR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 316 ASN Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 430 ASP Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain H residue 474 TYR Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 316 ASN Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 411 ASN Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 460 ILE Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain I residue 474 TYR Chi-restraints excluded: chain I residue 534 LEU Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 267 ILE Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 316 ASN Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain J residue 408 THR Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 430 ASP Chi-restraints excluded: chain J residue 460 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 316 ASN Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 429 GLU Chi-restraints excluded: chain K residue 430 ASP Chi-restraints excluded: chain K residue 460 ILE Chi-restraints excluded: chain K residue 471 ILE Chi-restraints excluded: chain K residue 474 TYR Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 316 ASN Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 377 GLU Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 430 ASP Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain L residue 474 TYR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 267 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 287 ILE Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 404 VAL Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 411 ASN Chi-restraints excluded: chain M residue 424 MET Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 471 ILE Chi-restraints excluded: chain M residue 474 TYR Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 227 ARG Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 275 ILE Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain N residue 316 ASN Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 405 THR Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 474 TYR Chi-restraints excluded: chain N residue 489 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 146 optimal weight: 0.9990 chunk 413 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 154 optimal weight: 0.0470 chunk 93 optimal weight: 0.8980 chunk 386 optimal weight: 0.7980 chunk 471 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 245 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 GLN I 465 GLN ** I 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.149265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107575 restraints weight = 42200.630| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.17 r_work: 0.3179 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 38160 Z= 0.174 Angle : 0.599 13.229 51615 Z= 0.319 Chirality : 0.048 0.189 6150 Planarity : 0.004 0.056 6600 Dihedral : 5.959 51.423 5176 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.81 % Allowed : 19.05 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.13), residues: 4650 helix: -0.12 (0.20), residues: 720 sheet: 0.34 (0.10), residues: 2550 loop : -1.89 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 419 TYR 0.015 0.001 TYR K 390 PHE 0.017 0.001 PHE A 336 TRP 0.006 0.001 TRP L 306 HIS 0.004 0.001 HIS K 476 Details of bonding type rmsd covalent geometry : bond 0.00398 (38160) covalent geometry : angle 0.59889 (51615) hydrogen bonds : bond 0.04390 ( 1323) hydrogen bonds : angle 5.48465 ( 3381) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 501 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.7713 (m110) cc_final: 0.7397 (p0) REVERT: O 195 ASP cc_start: 0.8476 (m-30) cc_final: 0.8226 (m-30) REVERT: O 227 ARG cc_start: 0.6333 (OUTLIER) cc_final: 0.5518 (mmt-90) REVERT: O 289 ASP cc_start: 0.7923 (m-30) cc_final: 0.7552 (t70) REVERT: O 303 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8879 (tp) REVERT: O 539 GLU cc_start: 0.8428 (tp30) cc_final: 0.8089 (tp30) REVERT: B 266 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8138 (tt) REVERT: C 227 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6358 (mpt180) REVERT: C 228 GLN cc_start: 0.7104 (mt0) cc_final: 0.6677 (mt0) REVERT: C 266 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8208 (tt) REVERT: C 357 MET cc_start: 0.8480 (tpp) cc_final: 0.7877 (mtp) REVERT: C 405 THR cc_start: 0.9078 (m) cc_final: 0.8857 (t) REVERT: D 215 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7684 (tm-30) REVERT: D 227 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.5874 (mmt-90) REVERT: D 266 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8314 (tt) REVERT: D 332 PHE cc_start: 0.7977 (t80) cc_final: 0.7646 (t80) REVERT: D 357 MET cc_start: 0.8458 (tpp) cc_final: 0.8038 (tpp) REVERT: D 405 THR cc_start: 0.8991 (m) cc_final: 0.8773 (t) REVERT: D 423 GLU cc_start: 0.8528 (tt0) cc_final: 0.8289 (tt0) REVERT: D 539 GLU cc_start: 0.8399 (tp30) cc_final: 0.8088 (tp30) REVERT: E 215 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8018 (tm-30) REVERT: E 227 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.5012 (mmt-90) REVERT: E 266 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8434 (tt) REVERT: E 405 THR cc_start: 0.9075 (m) cc_final: 0.8790 (t) REVERT: E 474 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7936 (t80) REVERT: F 266 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.7972 (tt) REVERT: F 357 MET cc_start: 0.8424 (tpp) cc_final: 0.8154 (tpp) REVERT: F 359 LEU cc_start: 0.8889 (tt) cc_final: 0.8594 (tt) REVERT: G 266 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8041 (tt) REVERT: G 539 GLU cc_start: 0.8489 (tp30) cc_final: 0.8260 (tp30) REVERT: H 266 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8556 (tt) REVERT: H 289 ASP cc_start: 0.8013 (m-30) cc_final: 0.7588 (t70) REVERT: H 357 MET cc_start: 0.8244 (tpp) cc_final: 0.7989 (tpp) REVERT: I 227 ARG cc_start: 0.6445 (OUTLIER) cc_final: 0.5510 (mmt-90) REVERT: I 228 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6256 (mt0) REVERT: I 266 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8353 (tt) REVERT: I 303 LEU cc_start: 0.9129 (tp) cc_final: 0.8828 (tp) REVERT: J 194 SER cc_start: 0.8915 (m) cc_final: 0.8332 (p) REVERT: J 215 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7754 (tm-30) REVERT: J 227 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6005 (mmt-90) REVERT: J 228 GLN cc_start: 0.6895 (mt0) cc_final: 0.6368 (mt0) REVERT: K 227 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6378 (mmt180) REVERT: K 357 MET cc_start: 0.8120 (tpp) cc_final: 0.7761 (tpp) REVERT: K 455 THR cc_start: 0.8665 (m) cc_final: 0.8404 (m) REVERT: K 526 TYR cc_start: 0.9374 (m-80) cc_final: 0.8751 (m-80) REVERT: L 227 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.5256 (mmt-90) REVERT: L 266 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8288 (tt) REVERT: L 423 GLU cc_start: 0.8546 (tt0) cc_final: 0.8211 (tt0) REVERT: L 474 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7549 (t80) REVERT: M 227 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.5703 (mmt-90) REVERT: M 266 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8640 (tt) REVERT: N 227 ARG cc_start: 0.6575 (OUTLIER) cc_final: 0.5775 (mmt-90) REVERT: N 266 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8277 (tt) REVERT: N 538 ARG cc_start: 0.8842 (ttt-90) cc_final: 0.8624 (tpp80) outliers start: 208 outliers final: 177 residues processed: 631 average time/residue: 0.2149 time to fit residues: 224.0945 Evaluate side-chains 697 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 495 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 474 TYR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 227 ARG Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 303 LEU Chi-restraints excluded: chain O residue 335 SER Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 471 ILE Chi-restraints excluded: chain O residue 474 TYR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 516 GLN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 316 ASN Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 474 TYR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 316 ASN Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 430 ASP Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 474 TYR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 316 ASN Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 430 ASP Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain H residue 474 TYR Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 316 ASN Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 411 ASN Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 460 ILE Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain I residue 474 TYR Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 267 ILE Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 316 ASN Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain J residue 408 THR Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 430 ASP Chi-restraints excluded: chain J residue 460 ILE Chi-restraints excluded: chain J residue 474 TYR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 316 ASN Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 429 GLU Chi-restraints excluded: chain K residue 430 ASP Chi-restraints excluded: chain K residue 460 ILE Chi-restraints excluded: chain K residue 471 ILE Chi-restraints excluded: chain K residue 474 TYR Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 316 ASN Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 430 ASP Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain L residue 474 TYR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 267 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 287 ILE Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 404 VAL Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 411 ASN Chi-restraints excluded: chain M residue 424 MET Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 471 ILE Chi-restraints excluded: chain M residue 474 TYR Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 227 ARG Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 275 ILE Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain N residue 316 ASN Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 405 THR Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 474 TYR Chi-restraints excluded: chain N residue 489 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 45 optimal weight: 4.9990 chunk 387 optimal weight: 0.0770 chunk 340 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 chunk 256 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 417 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 418 optimal weight: 0.2980 chunk 401 optimal weight: 0.4980 chunk 410 optimal weight: 0.0970 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN D 411 ASN D 516 GLN ** H 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 516 GLN L 280 ASN ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 465 GLN ** N 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109802 restraints weight = 42004.482| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.17 r_work: 0.3211 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 38160 Z= 0.124 Angle : 0.580 13.268 51615 Z= 0.308 Chirality : 0.048 0.202 6150 Planarity : 0.004 0.052 6600 Dihedral : 5.658 49.799 5175 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.33 % Allowed : 19.56 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.13), residues: 4650 helix: -0.03 (0.20), residues: 720 sheet: 0.48 (0.11), residues: 2550 loop : -1.88 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 419 TYR 0.016 0.001 TYR I 406 PHE 0.018 0.001 PHE M 328 TRP 0.004 0.001 TRP G 306 HIS 0.003 0.001 HIS K 476 Details of bonding type rmsd covalent geometry : bond 0.00278 (38160) covalent geometry : angle 0.58050 (51615) hydrogen bonds : bond 0.04116 ( 1323) hydrogen bonds : angle 5.43026 ( 3381) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9319.00 seconds wall clock time: 160 minutes 28.52 seconds (9628.52 seconds total)