Starting phenix.real_space_refine on Thu Jan 16 19:21:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.map" model { file = "/net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.071 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 280 5.16 5 C 33558 2.51 5 N 9310 2.21 5 O 10822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 53970 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "N" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "B" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "H" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "C" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "I" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "D" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "J" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "E" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "K" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "F" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "L" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "G" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "M" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Time building chain proxies: 23.85, per 1000 atoms: 0.44 Number of scatterers: 53970 At special positions: 0 Unit cell: (159.85, 161, 158.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 280 16.00 O 10822 8.00 N 9310 7.00 C 33558 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: 11.20 Conformation dependent library (CDL) restraints added in 5.8 seconds 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13272 Finding SS restraints... Secondary structure from input PDB file: 290 helices and 96 sheets defined 58.8% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.35 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 4.110A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.644A pdb=" N VAL A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 86 removed outlier: 3.790A pdb=" N LYS A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 108 Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 282 through 297 removed outlier: 3.533A pdb=" N LYS A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 338 through 355 Processing helix chain 'A' and resid 358 through 375 removed outlier: 4.287A pdb=" N GLY A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 410 Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.925A pdb=" N ILE A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 447 Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.697A pdb=" N VAL A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 497 through 516 Processing helix chain 'N' and resid 9 through 29 removed outlier: 4.202A pdb=" N VAL N 29 " --> pdb=" O ASP N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 60 removed outlier: 3.584A pdb=" N VAL N 56 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 86 removed outlier: 3.822A pdb=" N LYS N 80 " --> pdb=" O GLU N 76 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA N 81 " --> pdb=" O VAL N 77 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN N 82 " --> pdb=" O ALA N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 108 Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 140 through 152 Processing helix chain 'N' and resid 155 through 170 removed outlier: 3.541A pdb=" N GLY N 159 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 205 Processing helix chain 'N' and resid 233 through 244 Processing helix chain 'N' and resid 258 through 266 removed outlier: 3.567A pdb=" N LEU N 262 " --> pdb=" O ALA N 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 282 through 297 removed outlier: 3.558A pdb=" N LYS N 286 " --> pdb=" O GLY N 282 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 312 Processing helix chain 'N' and resid 338 through 355 Processing helix chain 'N' and resid 358 through 375 removed outlier: 4.351A pdb=" N GLY N 375 " --> pdb=" O LYS N 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 410 Processing helix chain 'N' and resid 416 through 426 removed outlier: 3.878A pdb=" N ILE N 420 " --> pdb=" O GLY N 416 " (cutoff:3.500A) Processing helix chain 'N' and resid 433 through 447 removed outlier: 3.575A pdb=" N ASN N 437 " --> pdb=" O ASN N 433 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 458 Processing helix chain 'N' and resid 461 through 472 removed outlier: 3.596A pdb=" N VAL N 465 " --> pdb=" O GLU N 461 " (cutoff:3.500A) Processing helix chain 'N' and resid 497 through 516 Processing helix chain 'B' and resid 9 through 29 removed outlier: 4.154A pdb=" N VAL B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.626A pdb=" N VAL B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 86 removed outlier: 3.835A pdb=" N LYS B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 108 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 258 through 266 Processing helix chain 'B' and resid 282 through 297 removed outlier: 3.530A pdb=" N LYS B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 338 through 355 Processing helix chain 'B' and resid 358 through 375 removed outlier: 4.275A pdb=" N GLY B 375 " --> pdb=" O LYS B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 410 Processing helix chain 'B' and resid 416 through 426 removed outlier: 3.878A pdb=" N ILE B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 447 Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 461 through 472 removed outlier: 3.699A pdb=" N VAL B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'H' and resid 9 through 29 removed outlier: 4.102A pdb=" N VAL H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 60 removed outlier: 3.612A pdb=" N VAL H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 86 removed outlier: 3.878A pdb=" N LYS H 80 " --> pdb=" O GLU H 76 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 108 Processing helix chain 'H' and resid 112 through 135 Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 155 through 170 removed outlier: 3.535A pdb=" N GLY H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 233 through 244 Processing helix chain 'H' and resid 258 through 266 Processing helix chain 'H' and resid 282 through 297 removed outlier: 3.557A pdb=" N LYS H 286 " --> pdb=" O GLY H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 312 Processing helix chain 'H' and resid 338 through 355 Processing helix chain 'H' and resid 358 through 375 removed outlier: 4.356A pdb=" N GLY H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 410 Processing helix chain 'H' and resid 416 through 426 removed outlier: 3.846A pdb=" N ILE H 420 " --> pdb=" O GLY H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 447 removed outlier: 3.623A pdb=" N ASN H 437 " --> pdb=" O ASN H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 448 through 458 Processing helix chain 'H' and resid 461 through 472 removed outlier: 3.610A pdb=" N VAL H 465 " --> pdb=" O GLU H 461 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 492 Processing helix chain 'H' and resid 497 through 516 Processing helix chain 'C' and resid 9 through 29 removed outlier: 4.097A pdb=" N VAL C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.644A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 86 removed outlier: 3.821A pdb=" N LYS C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 108 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 155 through 170 Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 258 through 266 removed outlier: 3.573A pdb=" N LEU C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 297 removed outlier: 3.519A pdb=" N LYS C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 338 through 355 Processing helix chain 'C' and resid 358 through 375 removed outlier: 4.258A pdb=" N GLY C 375 " --> pdb=" O LYS C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 410 Processing helix chain 'C' and resid 416 through 426 removed outlier: 3.823A pdb=" N ILE C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 447 Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 461 through 472 removed outlier: 3.697A pdb=" N VAL C 465 " --> pdb=" O GLU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 516 Processing helix chain 'I' and resid 9 through 29 removed outlier: 4.177A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 60 removed outlier: 3.616A pdb=" N VAL I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 86 removed outlier: 3.900A pdb=" N LYS I 80 " --> pdb=" O GLU I 76 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 108 Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 removed outlier: 3.535A pdb=" N GLY I 159 " --> pdb=" O ASP I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'I' and resid 229 through 232 removed outlier: 3.658A pdb=" N GLU I 232 " --> pdb=" O ASN I 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 229 through 232' Processing helix chain 'I' and resid 233 through 244 Processing helix chain 'I' and resid 258 through 265 removed outlier: 3.549A pdb=" N LEU I 262 " --> pdb=" O ALA I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 297 removed outlier: 3.564A pdb=" N LYS I 286 " --> pdb=" O GLY I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 312 Processing helix chain 'I' and resid 338 through 355 Processing helix chain 'I' and resid 358 through 375 removed outlier: 4.378A pdb=" N GLY I 375 " --> pdb=" O LYS I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 410 Processing helix chain 'I' and resid 416 through 426 removed outlier: 3.837A pdb=" N ILE I 420 " --> pdb=" O GLY I 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 447 removed outlier: 3.614A pdb=" N ASN I 437 " --> pdb=" O ASN I 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 448 through 458 Processing helix chain 'I' and resid 461 through 472 removed outlier: 3.628A pdb=" N VAL I 465 " --> pdb=" O GLU I 461 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 492 Processing helix chain 'I' and resid 497 through 516 Processing helix chain 'D' and resid 9 through 29 removed outlier: 4.081A pdb=" N VAL D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.620A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.876A pdb=" N LYS D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA D 81 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 108 Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 258 through 266 removed outlier: 3.530A pdb=" N LEU D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 297 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 338 through 355 Processing helix chain 'D' and resid 358 through 375 removed outlier: 4.204A pdb=" N GLY D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 410 Processing helix chain 'D' and resid 416 through 426 removed outlier: 3.965A pdb=" N ILE D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 447 Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 461 through 472 removed outlier: 3.714A pdb=" N VAL D 465 " --> pdb=" O GLU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 492 Processing helix chain 'D' and resid 497 through 516 Processing helix chain 'J' and resid 9 through 29 removed outlier: 4.129A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 60 removed outlier: 3.619A pdb=" N VAL J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 86 removed outlier: 3.842A pdb=" N LYS J 80 " --> pdb=" O GLU J 76 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA J 81 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 108 Processing helix chain 'J' and resid 112 through 135 Processing helix chain 'J' and resid 140 through 152 Processing helix chain 'J' and resid 155 through 170 removed outlier: 3.541A pdb=" N GLY J 159 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 205 Processing helix chain 'J' and resid 233 through 244 Processing helix chain 'J' and resid 258 through 266 removed outlier: 3.537A pdb=" N LEU J 262 " --> pdb=" O ALA J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 297 removed outlier: 3.567A pdb=" N LYS J 286 " --> pdb=" O GLY J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 312 Processing helix chain 'J' and resid 338 through 355 Processing helix chain 'J' and resid 358 through 375 removed outlier: 4.277A pdb=" N GLY J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 410 Processing helix chain 'J' and resid 416 through 426 removed outlier: 3.831A pdb=" N ILE J 420 " --> pdb=" O GLY J 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 447 removed outlier: 3.608A pdb=" N ASN J 437 " --> pdb=" O ASN J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 448 through 458 Processing helix chain 'J' and resid 461 through 472 removed outlier: 3.613A pdb=" N VAL J 465 " --> pdb=" O GLU J 461 " (cutoff:3.500A) Processing helix chain 'J' and resid 497 through 516 Processing helix chain 'E' and resid 9 through 29 removed outlier: 4.125A pdb=" N VAL E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 60 removed outlier: 3.590A pdb=" N VAL E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 86 removed outlier: 3.866A pdb=" N LYS E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA E 81 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 108 Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 155 through 170 Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 258 through 265 removed outlier: 3.620A pdb=" N LEU E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 297 removed outlier: 3.533A pdb=" N LYS E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 338 through 355 Processing helix chain 'E' and resid 358 through 375 removed outlier: 4.263A pdb=" N GLY E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 410 Processing helix chain 'E' and resid 416 through 426 removed outlier: 3.916A pdb=" N ILE E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 447 Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 461 through 472 removed outlier: 3.700A pdb=" N VAL E 465 " --> pdb=" O GLU E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 497 through 516 Processing helix chain 'K' and resid 9 through 29 removed outlier: 4.165A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 60 removed outlier: 3.631A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 86 removed outlier: 3.816A pdb=" N LYS K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA K 81 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN K 82 " --> pdb=" O ALA K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 108 Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 removed outlier: 3.540A pdb=" N GLY K 159 " --> pdb=" O ASP K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 205 Processing helix chain 'K' and resid 233 through 244 Processing helix chain 'K' and resid 258 through 265 removed outlier: 3.502A pdb=" N LEU K 262 " --> pdb=" O ALA K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 297 removed outlier: 3.546A pdb=" N LYS K 286 " --> pdb=" O GLY K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 312 Processing helix chain 'K' and resid 338 through 355 Processing helix chain 'K' and resid 358 through 375 removed outlier: 4.366A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 410 Processing helix chain 'K' and resid 416 through 426 removed outlier: 3.854A pdb=" N ILE K 420 " --> pdb=" O GLY K 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 447 removed outlier: 3.552A pdb=" N ASN K 437 " --> pdb=" O ASN K 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 448 through 458 Processing helix chain 'K' and resid 461 through 472 removed outlier: 3.605A pdb=" N VAL K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 497 through 516 Processing helix chain 'F' and resid 9 through 29 removed outlier: 4.100A pdb=" N VAL F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.638A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 86 removed outlier: 3.742A pdb=" N LYS F 80 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA F 81 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 108 Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 258 through 266 removed outlier: 3.519A pdb=" N LEU F 262 " --> pdb=" O ALA F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 297 removed outlier: 3.504A pdb=" N LYS F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 312 Processing helix chain 'F' and resid 338 through 355 removed outlier: 3.503A pdb=" N ILE F 342 " --> pdb=" O GLU F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 375 removed outlier: 4.230A pdb=" N GLY F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 410 Processing helix chain 'F' and resid 416 through 426 removed outlier: 3.862A pdb=" N ILE F 420 " --> pdb=" O GLY F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 447 Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 461 through 472 removed outlier: 3.698A pdb=" N VAL F 465 " --> pdb=" O GLU F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 497 through 516 Processing helix chain 'L' and resid 9 through 29 removed outlier: 4.164A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 60 removed outlier: 3.615A pdb=" N VAL L 56 " --> pdb=" O ASP L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 86 removed outlier: 3.805A pdb=" N LYS L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA L 81 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN L 82 " --> pdb=" O ALA L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 108 Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 155 through 170 removed outlier: 3.541A pdb=" N GLY L 159 " --> pdb=" O ASP L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 201 through 205 Processing helix chain 'L' and resid 233 through 244 Processing helix chain 'L' and resid 258 through 265 removed outlier: 3.523A pdb=" N LEU L 262 " --> pdb=" O ALA L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 297 removed outlier: 3.531A pdb=" N LYS L 286 " --> pdb=" O GLY L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 312 Processing helix chain 'L' and resid 338 through 355 Processing helix chain 'L' and resid 358 through 375 removed outlier: 4.261A pdb=" N GLY L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 410 Processing helix chain 'L' and resid 416 through 426 removed outlier: 3.857A pdb=" N ILE L 420 " --> pdb=" O GLY L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 433 through 447 removed outlier: 3.572A pdb=" N ASN L 437 " --> pdb=" O ASN L 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 458 Processing helix chain 'L' and resid 461 through 472 removed outlier: 3.609A pdb=" N VAL L 465 " --> pdb=" O GLU L 461 " (cutoff:3.500A) Processing helix chain 'L' and resid 488 through 492 Processing helix chain 'L' and resid 497 through 516 Processing helix chain 'G' and resid 9 through 29 removed outlier: 4.123A pdb=" N VAL G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 60 removed outlier: 3.609A pdb=" N VAL G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 86 removed outlier: 3.791A pdb=" N LYS G 80 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 108 Processing helix chain 'G' and resid 112 through 135 Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 155 through 170 Processing helix chain 'G' and resid 201 through 205 Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 258 through 266 Processing helix chain 'G' and resid 282 through 297 removed outlier: 3.540A pdb=" N LYS G 286 " --> pdb=" O GLY G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 312 Processing helix chain 'G' and resid 338 through 355 removed outlier: 3.502A pdb=" N ILE G 342 " --> pdb=" O GLU G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 375 removed outlier: 4.250A pdb=" N GLY G 375 " --> pdb=" O LYS G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 410 Processing helix chain 'G' and resid 416 through 426 removed outlier: 3.885A pdb=" N ILE G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 447 Processing helix chain 'G' and resid 448 through 458 Processing helix chain 'G' and resid 461 through 472 removed outlier: 3.692A pdb=" N VAL G 465 " --> pdb=" O GLU G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 492 Processing helix chain 'G' and resid 497 through 516 Processing helix chain 'M' and resid 9 through 29 removed outlier: 4.141A pdb=" N VAL M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 60 removed outlier: 3.642A pdb=" N VAL M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 86 removed outlier: 3.842A pdb=" N LYS M 80 " --> pdb=" O GLU M 76 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA M 81 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN M 82 " --> pdb=" O ALA M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 108 Processing helix chain 'M' and resid 112 through 135 Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'M' and resid 155 through 170 removed outlier: 3.539A pdb=" N GLY M 159 " --> pdb=" O ASP M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 205 Processing helix chain 'M' and resid 233 through 244 Processing helix chain 'M' and resid 258 through 266 removed outlier: 3.570A pdb=" N LEU M 262 " --> pdb=" O ALA M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 297 removed outlier: 3.540A pdb=" N LYS M 286 " --> pdb=" O GLY M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 312 Processing helix chain 'M' and resid 338 through 355 Processing helix chain 'M' and resid 358 through 375 removed outlier: 4.338A pdb=" N GLY M 375 " --> pdb=" O LYS M 371 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 410 Processing helix chain 'M' and resid 416 through 426 removed outlier: 3.840A pdb=" N ILE M 420 " --> pdb=" O GLY M 416 " (cutoff:3.500A) Processing helix chain 'M' and resid 433 through 447 removed outlier: 3.506A pdb=" N ASN M 437 " --> pdb=" O ASN M 433 " (cutoff:3.500A) Processing helix chain 'M' and resid 448 through 458 Processing helix chain 'M' and resid 461 through 472 removed outlier: 3.602A pdb=" N VAL M 465 " --> pdb=" O GLU M 461 " (cutoff:3.500A) Processing helix chain 'M' and resid 497 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.097A pdb=" N ASN G 37 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS A 519 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.955A pdb=" N ASN A 37 " --> pdb=" O CYS B 519 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL B 521 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 39 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ASP B 523 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179 Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 195 Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.165A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU A 222 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.165A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA8, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 8 removed outlier: 3.505A pdb=" N LYS N 7 " --> pdb=" O MET N 520 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL H 39 " --> pdb=" O GLU N 518 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N MET N 520 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 48 through 50 removed outlier: 6.725A pdb=" N ASN N 37 " --> pdb=" O CYS M 519 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N VAL M 521 " --> pdb=" O ASN N 37 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL N 39 " --> pdb=" O VAL M 521 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ASP M 523 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 174 through 179 removed outlier: 3.558A pdb=" N VAL N 381 " --> pdb=" O GLU N 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 193 through 195 Processing sheet with id=AB4, first strand: chain 'N' and resid 273 through 277 removed outlier: 6.029A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ILE N 301 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU N 222 " --> pdb=" O ILE N 301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 273 through 277 removed outlier: 6.029A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AB7, first strand: chain 'N' and resid 476 through 479 Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 50 removed outlier: 6.843A pdb=" N ASN B 37 " --> pdb=" O CYS C 519 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL C 521 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL B 39 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ASP C 523 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 174 through 179 Processing sheet with id=AC1, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC2, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.155A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ILE B 301 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU B 222 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.155A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AC5, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AC6, first strand: chain 'H' and resid 4 through 8 removed outlier: 5.985A pdb=" N ASN I 37 " --> pdb=" O THR H 517 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS H 519 " --> pdb=" O ASN I 37 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 174 through 179 Processing sheet with id=AC8, first strand: chain 'H' and resid 193 through 195 Processing sheet with id=AC9, first strand: chain 'H' and resid 273 through 277 removed outlier: 6.037A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ILE H 301 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU H 222 " --> pdb=" O ILE H 301 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 273 through 277 removed outlier: 6.037A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AD3, first strand: chain 'H' and resid 476 through 479 Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 50 removed outlier: 7.088A pdb=" N ASN C 37 " --> pdb=" O CYS E 519 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N VAL E 521 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL C 39 " --> pdb=" O VAL E 521 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ASP E 523 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 174 through 179 Processing sheet with id=AD6, first strand: chain 'C' and resid 193 through 195 Processing sheet with id=AD7, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.060A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AD9, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AE1, first strand: chain 'I' and resid 4 through 8 removed outlier: 5.933A pdb=" N ASN K 37 " --> pdb=" O THR I 517 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS I 519 " --> pdb=" O ASN K 37 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 174 through 179 Processing sheet with id=AE3, first strand: chain 'I' and resid 193 through 195 Processing sheet with id=AE4, first strand: chain 'I' and resid 273 through 277 removed outlier: 3.513A pdb=" N ALA I 251 " --> pdb=" O VAL I 276 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ILE I 301 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU I 222 " --> pdb=" O ILE I 301 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 273 through 277 removed outlier: 3.513A pdb=" N ALA I 251 " --> pdb=" O VAL I 276 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AE7, first strand: chain 'I' and resid 476 through 479 Processing sheet with id=AE8, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.108A pdb=" N ASN E 37 " --> pdb=" O THR D 517 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N CYS D 519 " --> pdb=" O ASN E 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 48 through 50 removed outlier: 6.940A pdb=" N ASN D 37 " --> pdb=" O CYS F 519 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N VAL F 521 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL D 39 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ASP F 523 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 174 through 179 Processing sheet with id=AF2, first strand: chain 'D' and resid 193 through 195 Processing sheet with id=AF3, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.068A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ILE D 301 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU D 222 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.068A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AF6, first strand: chain 'D' and resid 476 through 479 Processing sheet with id=AF7, first strand: chain 'J' and resid 4 through 8 removed outlier: 6.017A pdb=" N ASN L 37 " --> pdb=" O THR J 517 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS J 519 " --> pdb=" O ASN L 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 48 through 50 removed outlier: 6.804A pdb=" N ASN J 37 " --> pdb=" O CYS K 519 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N VAL K 521 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL J 39 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ASP K 523 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 174 through 179 removed outlier: 3.563A pdb=" N VAL J 381 " --> pdb=" O GLU J 178 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 193 through 195 Processing sheet with id=AG2, first strand: chain 'J' and resid 273 through 277 removed outlier: 6.023A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ILE J 301 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU J 222 " --> pdb=" O ILE J 301 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 273 through 277 removed outlier: 6.023A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AG5, first strand: chain 'J' and resid 476 through 479 Processing sheet with id=AG6, first strand: chain 'E' and resid 174 through 179 Processing sheet with id=AG7, first strand: chain 'E' and resid 193 through 195 Processing sheet with id=AG8, first strand: chain 'E' and resid 273 through 277 removed outlier: 6.180A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ILE E 301 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU E 222 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 273 through 277 removed outlier: 6.180A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AH2, first strand: chain 'E' and resid 476 through 479 Processing sheet with id=AH3, first strand: chain 'K' and resid 174 through 179 Processing sheet with id=AH4, first strand: chain 'K' and resid 193 through 195 Processing sheet with id=AH5, first strand: chain 'K' and resid 273 through 277 removed outlier: 6.034A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N ILE K 301 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU K 222 " --> pdb=" O ILE K 301 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 273 through 277 removed outlier: 6.034A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AH8, first strand: chain 'K' and resid 476 through 479 Processing sheet with id=AH9, first strand: chain 'F' and resid 48 through 50 removed outlier: 6.992A pdb=" N ASN F 37 " --> pdb=" O CYS G 519 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N VAL G 521 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL F 39 " --> pdb=" O VAL G 521 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ASP G 523 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 174 through 179 Processing sheet with id=AI2, first strand: chain 'F' and resid 193 through 195 Processing sheet with id=AI3, first strand: chain 'F' and resid 273 through 277 removed outlier: 6.064A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AI5, first strand: chain 'F' and resid 476 through 479 Processing sheet with id=AI6, first strand: chain 'L' and resid 4 through 8 removed outlier: 6.008A pdb=" N ASN M 37 " --> pdb=" O THR L 517 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS L 519 " --> pdb=" O ASN M 37 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 174 through 179 Processing sheet with id=AI8, first strand: chain 'L' and resid 193 through 195 Processing sheet with id=AI9, first strand: chain 'L' and resid 273 through 277 removed outlier: 6.028A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N ILE L 301 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU L 222 " --> pdb=" O ILE L 301 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 273 through 277 removed outlier: 6.028A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AJ3, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AJ4, first strand: chain 'G' and resid 174 through 179 Processing sheet with id=AJ5, first strand: chain 'G' and resid 193 through 195 Processing sheet with id=AJ6, first strand: chain 'G' and resid 273 through 277 removed outlier: 3.516A pdb=" N ALA G 251 " --> pdb=" O VAL G 276 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE G 301 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU G 222 " --> pdb=" O ILE G 301 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'G' and resid 273 through 277 removed outlier: 3.516A pdb=" N ALA G 251 " --> pdb=" O VAL G 276 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AJ9, first strand: chain 'G' and resid 476 through 479 Processing sheet with id=AK1, first strand: chain 'M' and resid 174 through 179 Processing sheet with id=AK2, first strand: chain 'M' and resid 193 through 195 Processing sheet with id=AK3, first strand: chain 'M' and resid 273 through 277 removed outlier: 6.025A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N ILE M 301 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU M 222 " --> pdb=" O ILE M 301 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'M' and resid 273 through 277 removed outlier: 6.025A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AK6, first strand: chain 'M' and resid 476 through 479 3660 hydrogen bonds defined for protein. 10518 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: 28.07 Time building geometry restraints manager: 13.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 18774 1.34 - 1.46: 9400 1.46 - 1.58: 25670 1.58 - 1.70: 0 1.70 - 1.82: 518 Bond restraints: 54362 Sorted by residual: bond pdb=" CB VAL J 510 " pdb=" CG2 VAL J 510 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CB VAL M 510 " pdb=" CG2 VAL M 510 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CB GLU A 76 " pdb=" CG GLU A 76 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.48e+00 bond pdb=" CB VAL K 510 " pdb=" CG2 VAL K 510 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.46e+00 bond pdb=" CB VAL L 510 " pdb=" CG2 VAL L 510 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.44e+00 ... (remaining 54357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 72907 2.85 - 5.70: 441 5.70 - 8.56: 30 8.56 - 11.41: 10 11.41 - 14.26: 14 Bond angle restraints: 73402 Sorted by residual: angle pdb=" CB MET B 267 " pdb=" CG MET B 267 " pdb=" SD MET B 267 " ideal model delta sigma weight residual 112.70 126.96 -14.26 3.00e+00 1.11e-01 2.26e+01 angle pdb=" CB MET K 267 " pdb=" CG MET K 267 " pdb=" SD MET K 267 " ideal model delta sigma weight residual 112.70 126.39 -13.69 3.00e+00 1.11e-01 2.08e+01 angle pdb=" CB MET H 267 " pdb=" CG MET H 267 " pdb=" SD MET H 267 " ideal model delta sigma weight residual 112.70 125.99 -13.29 3.00e+00 1.11e-01 1.96e+01 angle pdb=" CB MET I 267 " pdb=" CG MET I 267 " pdb=" SD MET I 267 " ideal model delta sigma weight residual 112.70 125.95 -13.25 3.00e+00 1.11e-01 1.95e+01 angle pdb=" CB MET C 267 " pdb=" CG MET C 267 " pdb=" SD MET C 267 " ideal model delta sigma weight residual 112.70 125.93 -13.23 3.00e+00 1.11e-01 1.94e+01 ... (remaining 73397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 30481 18.00 - 35.99: 2512 35.99 - 53.99: 588 53.99 - 71.98: 122 71.98 - 89.98: 65 Dihedral angle restraints: 33768 sinusoidal: 13076 harmonic: 20692 Sorted by residual: dihedral pdb=" CA ARG M 231 " pdb=" C ARG M 231 " pdb=" N GLU M 232 " pdb=" CA GLU M 232 " ideal model delta harmonic sigma weight residual -180.00 -163.56 -16.44 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CG ARG H 58 " pdb=" CD ARG H 58 " pdb=" NE ARG H 58 " pdb=" CZ ARG H 58 " ideal model delta sinusoidal sigma weight residual 180.00 135.06 44.94 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG L 58 " pdb=" CD ARG L 58 " pdb=" NE ARG L 58 " pdb=" CZ ARG L 58 " ideal model delta sinusoidal sigma weight residual 90.00 134.91 -44.91 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 33765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 5611 0.029 - 0.058: 2069 0.058 - 0.087: 745 0.087 - 0.116: 445 0.116 - 0.145: 62 Chirality restraints: 8932 Sorted by residual: chirality pdb=" CA GLU A 232 " pdb=" N GLU A 232 " pdb=" C GLU A 232 " pdb=" CB GLU A 232 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA GLU D 232 " pdb=" N GLU D 232 " pdb=" C GLU D 232 " pdb=" CB GLU D 232 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA VAL F 271 " pdb=" N VAL F 271 " pdb=" C VAL F 271 " pdb=" CB VAL F 271 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 8929 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 267 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C MET B 267 " 0.035 2.00e-02 2.50e+03 pdb=" O MET B 267 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG B 268 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 267 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C MET C 267 " 0.035 2.00e-02 2.50e+03 pdb=" O MET C 267 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG C 268 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 76 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" CD GLU F 76 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU F 76 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU F 76 " 0.012 2.00e-02 2.50e+03 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 6317 2.74 - 3.28: 54878 3.28 - 3.82: 91620 3.82 - 4.36: 98267 4.36 - 4.90: 180686 Nonbonded interactions: 431768 Sorted by model distance: nonbonded pdb=" NH2 ARG J 421 " pdb=" O VAL J 469 " model vdw 2.206 3.120 nonbonded pdb=" NH2 ARG M 421 " pdb=" O VAL M 469 " model vdw 2.209 3.120 nonbonded pdb=" NH2 ARG H 421 " pdb=" O VAL H 469 " model vdw 2.209 3.120 nonbonded pdb=" O ILE A 270 " pdb=" ND2 ASN B 229 " model vdw 2.210 3.120 nonbonded pdb=" ND2 ASN A 229 " pdb=" O ILE G 270 " model vdw 2.210 3.120 ... (remaining 431763 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' 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: 0.720 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: 0.080 Extract box with map and model: 1.710 Check model and map are aligned: 0.340 Set scattering table: 0.390 Process input model: 105.630 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.320 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:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 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 : 0.003 0.042 54362 Z= 0.219 Angle : 0.581 14.260 73402 Z= 0.294 Chirality : 0.040 0.145 8932 Planarity : 0.003 0.027 9618 Dihedral : 14.856 89.981 20496 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.58 % Allowed : 9.64 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.10), residues: 7308 helix: 2.39 (0.08), residues: 4032 sheet: -0.01 (0.14), residues: 1232 loop : -0.43 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 401 PHE 0.024 0.001 PHE B 44 TYR 0.011 0.001 TYR J 478 ARG 0.005 0.000 ARG J 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 737 time to evaluate : 4.800 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8099 (ttpt) cc_final: 0.7677 (mmtp) REVERT: A 322 ARG cc_start: 0.7508 (ttp80) cc_final: 0.7201 (ttm110) REVERT: A 461 GLU cc_start: 0.7671 (pm20) cc_final: 0.7379 (pm20) REVERT: A 514 MET cc_start: 0.8393 (mtp) cc_final: 0.7936 (mtp) REVERT: N 69 MET cc_start: 0.5509 (mtm) cc_final: 0.5233 (mtp) REVERT: N 121 ASP cc_start: 0.7417 (m-30) cc_final: 0.7204 (m-30) REVERT: N 267 MET cc_start: 0.6336 (tmm) cc_final: 0.5363 (mmp) REVERT: N 321 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7490 (mmtp) REVERT: N 447 MET cc_start: 0.8065 (mtm) cc_final: 0.7828 (mtp) REVERT: B 160 LYS cc_start: 0.7755 (mtpp) cc_final: 0.7545 (ttmm) REVERT: B 193 MET cc_start: 0.6529 (tpt) cc_final: 0.6091 (tpt) REVERT: B 233 MET cc_start: 0.5060 (pmm) cc_final: 0.4814 (ptt) REVERT: B 321 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7529 (mmtp) REVERT: B 523 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7778 (m-30) REVERT: H 121 ASP cc_start: 0.7221 (m-30) cc_final: 0.6887 (m-30) REVERT: H 321 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7640 (mmtp) REVERT: H 514 MET cc_start: 0.8246 (mtp) cc_final: 0.7936 (mtp) REVERT: C 61 GLU cc_start: 0.7535 (pp20) cc_final: 0.7059 (pt0) REVERT: C 252 GLU cc_start: 0.7057 (tt0) cc_final: 0.6624 (tt0) REVERT: C 277 LYS cc_start: 0.7956 (mttt) cc_final: 0.7670 (mmmm) REVERT: C 288 MET cc_start: 0.5971 (ptp) cc_final: 0.5621 (mtp) REVERT: C 321 LYS cc_start: 0.8396 (ttpt) cc_final: 0.7892 (mmtp) REVERT: C 322 ARG cc_start: 0.7538 (ttp80) cc_final: 0.7299 (ttm110) REVERT: C 493 ILE cc_start: 0.8121 (mt) cc_final: 0.7879 (tt) REVERT: C 514 MET cc_start: 0.8550 (mtp) cc_final: 0.8179 (mtp) REVERT: C 523 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: I 121 ASP cc_start: 0.7011 (m-30) cc_final: 0.6754 (m-30) REVERT: I 193 MET cc_start: 0.6747 (tpt) cc_final: 0.6541 (tpt) REVERT: I 204 PHE cc_start: 0.7807 (m-80) cc_final: 0.7508 (m-80) REVERT: I 267 MET cc_start: 0.6556 (tmm) cc_final: 0.5466 (mmp) REVERT: I 321 LYS cc_start: 0.7674 (ttpt) cc_final: 0.7375 (mmtp) REVERT: I 336 VAL cc_start: 0.8094 (p) cc_final: 0.7718 (m) REVERT: I 351 GLN cc_start: 0.8382 (tp40) cc_final: 0.8177 (tp-100) REVERT: I 514 MET cc_start: 0.8317 (mtm) cc_final: 0.8059 (mtp) REVERT: D 321 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7499 (mmmt) REVERT: D 495 ASP cc_start: 0.7499 (m-30) cc_final: 0.7271 (m-30) REVERT: J 204 PHE cc_start: 0.7669 (m-80) cc_final: 0.7259 (m-80) REVERT: J 336 VAL cc_start: 0.7996 (p) cc_final: 0.7591 (m) REVERT: J 351 GLN cc_start: 0.8374 (tp40) cc_final: 0.8124 (tp40) REVERT: E 72 GLN cc_start: 0.7634 (mm110) cc_final: 0.7344 (mm110) REVERT: E 102 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6807 (mp0) REVERT: E 166 MET cc_start: 0.7059 (mtt) cc_final: 0.6806 (mtt) REVERT: E 233 MET cc_start: 0.5877 (ppp) cc_final: 0.5528 (ptt) REVERT: E 252 GLU cc_start: 0.7005 (tt0) cc_final: 0.6741 (tt0) REVERT: E 321 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7695 (mmpt) REVERT: E 520 MET cc_start: 0.8259 (mtt) cc_final: 0.7838 (mtt) REVERT: K 267 MET cc_start: 0.6289 (tmm) cc_final: 0.4982 (mmm) REVERT: K 351 GLN cc_start: 0.8539 (tp40) cc_final: 0.8307 (tp40) REVERT: K 514 MET cc_start: 0.8302 (mtm) cc_final: 0.7931 (mtp) REVERT: F 61 GLU cc_start: 0.7272 (pt0) cc_final: 0.6642 (pt0) REVERT: F 160 LYS cc_start: 0.7821 (mtpp) cc_final: 0.7563 (ttmm) REVERT: F 233 MET cc_start: 0.5417 (pmm) cc_final: 0.5137 (ptt) REVERT: F 321 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7603 (mmtp) REVERT: F 389 MET cc_start: 0.6298 (tmt) cc_final: 0.5841 (tmm) REVERT: L 61 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7112 (pt0) REVERT: L 69 MET cc_start: 0.6809 (mtm) cc_final: 0.6537 (mtp) REVERT: L 121 ASP cc_start: 0.7332 (m-30) cc_final: 0.7110 (m-30) REVERT: L 255 GLU cc_start: 0.7116 (pm20) cc_final: 0.6908 (pm20) REVERT: L 267 MET cc_start: 0.5973 (tmm) cc_final: 0.4831 (mmm) REVERT: L 321 LYS cc_start: 0.7875 (ttpt) cc_final: 0.7644 (mmtp) REVERT: L 351 GLN cc_start: 0.8375 (tp40) cc_final: 0.8119 (tp40) REVERT: L 433 ASN cc_start: 0.6264 (p0) cc_final: 0.5910 (p0) REVERT: G 61 GLU cc_start: 0.7409 (pp20) cc_final: 0.7063 (pt0) REVERT: G 277 LYS cc_start: 0.8069 (mttt) cc_final: 0.7691 (mmmm) REVERT: G 321 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7578 (mmmt) REVERT: G 322 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7323 (mtp-110) REVERT: G 461 GLU cc_start: 0.7787 (pm20) cc_final: 0.7513 (pm20) REVERT: M 321 LYS cc_start: 0.7806 (ttpt) cc_final: 0.7543 (mmtp) REVERT: M 351 GLN cc_start: 0.8396 (tp40) cc_final: 0.8151 (tp40) REVERT: M 397 GLU cc_start: 0.7699 (tp30) cc_final: 0.7368 (tt0) REVERT: M 433 ASN cc_start: 0.6184 (p0) cc_final: 0.5716 (p0) REVERT: M 491 MET cc_start: 0.7226 (ptm) cc_final: 0.7009 (ptm) outliers start: 33 outliers final: 21 residues processed: 763 average time/residue: 0.5011 time to fit residues: 649.6205 Evaluate side-chains 515 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 492 time to evaluate : 4.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain F residue 523 ASP Chi-restraints excluded: chain G residue 447 MET Chi-restraints excluded: chain G residue 523 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 0.3980 chunk 551 optimal weight: 20.0000 chunk 306 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 372 optimal weight: 9.9990 chunk 294 optimal weight: 9.9990 chunk 570 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 346 optimal weight: 5.9990 chunk 424 optimal weight: 1.9990 chunk 661 optimal weight: 9.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 348 GLN C 112 ASN C 146 GLN D 112 ASN D 184 GLN E 112 ASN E 184 GLN F 112 ASN F 348 GLN G 112 ASN G 348 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.153095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114207 restraints weight = 68602.183| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.74 r_work: 0.3211 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 54362 Z= 0.213 Angle : 0.527 11.519 73402 Z= 0.280 Chirality : 0.042 0.201 8932 Planarity : 0.003 0.054 9618 Dihedral : 3.998 28.800 7762 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.98 % Allowed : 11.26 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.10), residues: 7308 helix: 2.28 (0.08), residues: 4088 sheet: 0.29 (0.16), residues: 980 loop : -0.52 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS H 401 PHE 0.009 0.001 PHE H 44 TYR 0.009 0.001 TYR B 478 ARG 0.008 0.000 ARG N 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 535 time to evaluate : 4.918 Fit side-chains REVERT: A 267 MET cc_start: 0.5923 (mmm) cc_final: 0.4969 (mmm) REVERT: A 307 MET cc_start: 0.8607 (mtm) cc_final: 0.8059 (ptp) REVERT: N 69 MET cc_start: 0.7608 (mtm) cc_final: 0.7355 (mtp) REVERT: N 111 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8421 (mtt) REVERT: N 267 MET cc_start: 0.6565 (tmm) cc_final: 0.5757 (mmp) REVERT: N 442 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8798 (t) REVERT: N 447 MET cc_start: 0.9081 (mtm) cc_final: 0.8844 (mtp) REVERT: B 160 LYS cc_start: 0.8511 (mtpp) cc_final: 0.8291 (ttmm) REVERT: B 193 MET cc_start: 0.8213 (tpt) cc_final: 0.8010 (tpt) REVERT: B 233 MET cc_start: 0.5975 (pmm) cc_final: 0.5506 (ptt) REVERT: B 267 MET cc_start: 0.6371 (tmm) cc_final: 0.4962 (mmm) REVERT: B 367 GLU cc_start: 0.8453 (pp20) cc_final: 0.8160 (pp20) REVERT: H 262 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6631 (tt) REVERT: H 267 MET cc_start: 0.6273 (tmm) cc_final: 0.5284 (mmp) REVERT: C 61 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7930 (pt0) REVERT: C 267 MET cc_start: 0.6475 (tmm) cc_final: 0.5628 (mmp) REVERT: C 288 MET cc_start: 0.7170 (ptp) cc_final: 0.6548 (mtp) REVERT: C 321 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8477 (mmtp) REVERT: I 204 PHE cc_start: 0.8414 (m-80) cc_final: 0.8000 (m-80) REVERT: I 233 MET cc_start: 0.5877 (pmm) cc_final: 0.5416 (ptt) REVERT: I 267 MET cc_start: 0.7008 (tmm) cc_final: 0.5971 (mmp) REVERT: D 193 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8096 (tpt) REVERT: D 242 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7894 (mmtt) REVERT: D 321 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8447 (mmmt) REVERT: J 204 PHE cc_start: 0.8325 (m-80) cc_final: 0.7762 (m-80) REVERT: J 267 MET cc_start: 0.6267 (tmm) cc_final: 0.5007 (mmm) REVERT: J 389 MET cc_start: 0.7990 (tmt) cc_final: 0.7673 (tmm) REVERT: J 442 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8787 (t) REVERT: E 204 PHE cc_start: 0.8407 (m-80) cc_final: 0.8205 (m-80) REVERT: E 233 MET cc_start: 0.6513 (ppp) cc_final: 0.6094 (ptt) REVERT: E 252 GLU cc_start: 0.7412 (tt0) cc_final: 0.7193 (tt0) REVERT: E 321 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8417 (mmpt) REVERT: K 267 MET cc_start: 0.6893 (tmm) cc_final: 0.5409 (mmp) REVERT: F 160 LYS cc_start: 0.8603 (mtpp) cc_final: 0.8275 (ttmm) REVERT: F 233 MET cc_start: 0.6258 (pmm) cc_final: 0.5959 (ptt) REVERT: F 267 MET cc_start: 0.5952 (mmm) cc_final: 0.5145 (tmm) REVERT: F 389 MET cc_start: 0.7738 (tmt) cc_final: 0.7348 (tmm) REVERT: L 61 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8216 (tt0) REVERT: L 69 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7966 (mtp) REVERT: L 262 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6879 (tp) REVERT: L 267 MET cc_start: 0.6596 (tmm) cc_final: 0.5206 (mmm) REVERT: L 351 GLN cc_start: 0.8095 (tp40) cc_final: 0.7878 (tp40) REVERT: G 61 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7773 (pt0) REVERT: G 160 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8482 (ptmm) REVERT: G 267 MET cc_start: 0.6093 (tmm) cc_final: 0.5177 (mmm) REVERT: M 13 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7731 (mpt-90) REVERT: M 267 MET cc_start: 0.6764 (tmm) cc_final: 0.5513 (mmm) REVERT: M 351 GLN cc_start: 0.8118 (tp40) cc_final: 0.7915 (tp40) outliers start: 112 outliers final: 57 residues processed: 611 average time/residue: 0.4939 time to fit residues: 521.6042 Evaluate side-chains 518 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 450 time to evaluate : 4.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 442 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 463 SER Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain F residue 447 MET Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 69 MET Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 259 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 558 optimal weight: 4.9990 chunk 258 optimal weight: 0.8980 chunk 337 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 622 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 703 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 446 optimal weight: 2.9990 chunk 453 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN H 37 ASN C 467 ASN G 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.152356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114403 restraints weight = 68963.847| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.76 r_work: 0.3204 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 54362 Z= 0.206 Angle : 0.491 9.036 73402 Z= 0.262 Chirality : 0.042 0.152 8932 Planarity : 0.003 0.034 9618 Dihedral : 3.901 27.209 7737 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.30 % Allowed : 12.61 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.10), residues: 7308 helix: 2.26 (0.08), residues: 4088 sheet: 0.38 (0.16), residues: 980 loop : -0.50 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 401 PHE 0.009 0.001 PHE M 219 TYR 0.009 0.001 TYR K 476 ARG 0.005 0.000 ARG L 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 507 time to evaluate : 4.898 Fit side-chains revert: symmetry clash REVERT: A 267 MET cc_start: 0.5948 (mmm) cc_final: 0.5032 (mmm) REVERT: A 307 MET cc_start: 0.8645 (mtm) cc_final: 0.8150 (ptp) REVERT: A 367 GLU cc_start: 0.8548 (pp20) cc_final: 0.8239 (pp20) REVERT: A 514 MET cc_start: 0.9098 (mtm) cc_final: 0.8708 (mtp) REVERT: N 16 MET cc_start: 0.8542 (mmm) cc_final: 0.8156 (mtt) REVERT: N 111 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8422 (mtt) REVERT: N 267 MET cc_start: 0.6480 (tmm) cc_final: 0.5794 (mmp) REVERT: N 442 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8759 (t) REVERT: B 160 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8257 (ttmm) REVERT: B 193 MET cc_start: 0.8196 (tpt) cc_final: 0.7945 (ttm) REVERT: B 233 MET cc_start: 0.6227 (pmm) cc_final: 0.6005 (ptt) REVERT: B 267 MET cc_start: 0.6194 (tmm) cc_final: 0.5567 (mmp) REVERT: B 319 GLN cc_start: 0.7975 (mt0) cc_final: 0.7722 (mt0) REVERT: B 367 GLU cc_start: 0.8472 (pp20) cc_final: 0.8162 (pp20) REVERT: B 494 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8701 (pp) REVERT: H 262 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6621 (tt) REVERT: H 267 MET cc_start: 0.6718 (tmm) cc_final: 0.5146 (mmm) REVERT: C 61 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: C 267 MET cc_start: 0.6577 (tmm) cc_final: 0.5682 (mmp) REVERT: C 288 MET cc_start: 0.7112 (ptp) cc_final: 0.6508 (mtp) REVERT: C 367 GLU cc_start: 0.8568 (pp20) cc_final: 0.8230 (pp20) REVERT: C 494 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8772 (pp) REVERT: I 193 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8203 (ttm) REVERT: I 204 PHE cc_start: 0.8437 (m-80) cc_final: 0.8038 (m-80) REVERT: I 267 MET cc_start: 0.6685 (tmm) cc_final: 0.5870 (mmp) REVERT: I 351 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8121 (pp30) REVERT: D 242 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7827 (mmmt) REVERT: D 267 MET cc_start: 0.5543 (tmm) cc_final: 0.5206 (mmp) REVERT: D 321 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8528 (mmmt) REVERT: D 367 GLU cc_start: 0.8580 (pp20) cc_final: 0.8327 (pp20) REVERT: J 204 PHE cc_start: 0.8366 (m-80) cc_final: 0.7922 (m-80) REVERT: J 267 MET cc_start: 0.6044 (tmm) cc_final: 0.4935 (mmm) REVERT: J 442 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8753 (t) REVERT: E 111 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8147 (mtt) REVERT: E 233 MET cc_start: 0.6358 (ppp) cc_final: 0.6016 (ptt) REVERT: E 252 GLU cc_start: 0.7387 (tt0) cc_final: 0.7108 (tt0) REVERT: E 267 MET cc_start: 0.6061 (tmm) cc_final: 0.5397 (mmp) REVERT: E 447 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8889 (mtp) REVERT: E 494 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8838 (pp) REVERT: K 267 MET cc_start: 0.6809 (tmm) cc_final: 0.5469 (mmp) REVERT: F 102 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7320 (mp0) REVERT: F 160 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8362 (ptmm) REVERT: F 204 PHE cc_start: 0.8418 (m-80) cc_final: 0.8101 (m-80) REVERT: F 367 GLU cc_start: 0.8436 (pp20) cc_final: 0.8144 (pp20) REVERT: L 61 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8297 (tt0) REVERT: L 69 MET cc_start: 0.8435 (mtm) cc_final: 0.8050 (mtp) REVERT: L 267 MET cc_start: 0.6435 (tmm) cc_final: 0.5242 (mmm) REVERT: L 288 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.6757 (mpp) REVERT: L 351 GLN cc_start: 0.8125 (tp40) cc_final: 0.7908 (tp40) REVERT: L 389 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7493 (tmm) REVERT: G 61 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7926 (pt0) REVERT: G 160 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8450 (ptmm) REVERT: G 267 MET cc_start: 0.6205 (tmm) cc_final: 0.5349 (mmm) REVERT: G 322 ARG cc_start: 0.8732 (mtp-110) cc_final: 0.8405 (ttm110) REVERT: G 367 GLU cc_start: 0.8529 (pp20) cc_final: 0.8238 (pp20) REVERT: G 491 MET cc_start: 0.9036 (mtt) cc_final: 0.8800 (mtt) REVERT: G 494 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8833 (pp) REVERT: M 267 MET cc_start: 0.6691 (tmm) cc_final: 0.5542 (mmm) REVERT: M 351 GLN cc_start: 0.8161 (tp40) cc_final: 0.7925 (tp40) outliers start: 130 outliers final: 72 residues processed: 601 average time/residue: 0.4758 time to fit residues: 500.5399 Evaluate side-chains 552 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 463 time to evaluate : 6.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 442 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain J residue 232 GLU Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 388 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 447 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain K residue 463 SER Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 389 MET Chi-restraints excluded: chain L residue 442 VAL Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 463 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 315 optimal weight: 2.9990 chunk 389 optimal weight: 9.9990 chunk 510 optimal weight: 0.9980 chunk 398 optimal weight: 10.0000 chunk 657 optimal weight: 0.7980 chunk 331 optimal weight: 20.0000 chunk 514 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 554 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN C 112 ASN C 467 ASN I 319 GLN D 112 ASN E 112 ASN K 37 ASN F 112 ASN M 37 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.150754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112011 restraints weight = 68645.911| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.76 r_work: 0.3161 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 54362 Z= 0.250 Angle : 0.505 7.912 73402 Z= 0.268 Chirality : 0.042 0.167 8932 Planarity : 0.003 0.031 9618 Dihedral : 3.937 27.072 7736 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.20 % Allowed : 12.89 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.10), residues: 7308 helix: 2.21 (0.08), residues: 4088 sheet: 0.63 (0.17), residues: 938 loop : -0.46 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 401 PHE 0.011 0.001 PHE J 66 TYR 0.010 0.001 TYR I 478 ARG 0.006 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 511 time to evaluate : 4.878 Fit side-chains revert: symmetry clash REVERT: A 267 MET cc_start: 0.6065 (mmm) cc_final: 0.5086 (mmm) REVERT: A 367 GLU cc_start: 0.8525 (pp20) cc_final: 0.8231 (pp20) REVERT: N 16 MET cc_start: 0.8605 (mmm) cc_final: 0.8329 (mtt) REVERT: N 111 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8453 (mtt) REVERT: N 201 SER cc_start: 0.8378 (t) cc_final: 0.8081 (m) REVERT: N 267 MET cc_start: 0.6415 (tmm) cc_final: 0.5849 (mmp) REVERT: N 442 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8784 (t) REVERT: N 494 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8868 (pp) REVERT: B 160 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8195 (ptmm) REVERT: B 233 MET cc_start: 0.6457 (pmm) cc_final: 0.6215 (ptt) REVERT: B 267 MET cc_start: 0.6143 (tmm) cc_final: 0.5560 (mmp) REVERT: B 319 GLN cc_start: 0.8005 (mt0) cc_final: 0.7744 (mt0) REVERT: B 367 GLU cc_start: 0.8484 (pp20) cc_final: 0.8151 (pp20) REVERT: B 389 MET cc_start: 0.8311 (tmm) cc_final: 0.8055 (ttp) REVERT: B 494 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8703 (pp) REVERT: H 267 MET cc_start: 0.6670 (tmm) cc_final: 0.5377 (mmm) REVERT: H 514 MET cc_start: 0.9065 (mtp) cc_final: 0.8789 (mtm) REVERT: C 61 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8118 (pt0) REVERT: C 69 MET cc_start: 0.8489 (mtp) cc_final: 0.8195 (ttm) REVERT: C 102 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7408 (mp0) REVERT: C 267 MET cc_start: 0.6556 (tmm) cc_final: 0.5788 (mmp) REVERT: C 288 MET cc_start: 0.7050 (ptp) cc_final: 0.6631 (mtp) REVERT: C 367 GLU cc_start: 0.8512 (pp20) cc_final: 0.8163 (pp20) REVERT: C 514 MET cc_start: 0.9070 (mtp) cc_final: 0.8780 (mtm) REVERT: I 193 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8201 (ttm) REVERT: I 204 PHE cc_start: 0.8433 (m-80) cc_final: 0.8059 (m-80) REVERT: I 267 MET cc_start: 0.6634 (tmm) cc_final: 0.5947 (mmp) REVERT: I 351 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8152 (pp30) REVERT: I 494 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8864 (pp) REVERT: D 242 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7814 (mmmt) REVERT: D 267 MET cc_start: 0.6347 (tmm) cc_final: 0.5553 (mmm) REVERT: D 321 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8519 (mmmt) REVERT: D 367 GLU cc_start: 0.8670 (pp20) cc_final: 0.8389 (pp20) REVERT: J 16 MET cc_start: 0.8691 (mtp) cc_final: 0.8396 (mtm) REVERT: J 204 PHE cc_start: 0.8334 (m-80) cc_final: 0.7972 (m-80) REVERT: J 267 MET cc_start: 0.6017 (tmm) cc_final: 0.5028 (mmm) REVERT: J 442 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8762 (t) REVERT: J 494 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8819 (pp) REVERT: E 111 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8210 (mtt) REVERT: E 267 MET cc_start: 0.6482 (tmm) cc_final: 0.5757 (mmp) REVERT: E 367 GLU cc_start: 0.8613 (pp20) cc_final: 0.8329 (pp20) REVERT: E 447 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8885 (mtp) REVERT: E 494 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8847 (pp) REVERT: E 514 MET cc_start: 0.9207 (ttm) cc_final: 0.8813 (mtp) REVERT: K 267 MET cc_start: 0.6682 (tmm) cc_final: 0.5391 (mmp) REVERT: F 160 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8364 (ptmm) REVERT: F 367 GLU cc_start: 0.8418 (pp20) cc_final: 0.8098 (pp20) REVERT: L 61 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8232 (tm-30) REVERT: L 69 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8117 (mtp) REVERT: L 262 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6953 (tp) REVERT: L 267 MET cc_start: 0.6339 (tmm) cc_final: 0.5332 (mmm) REVERT: L 288 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.6783 (mpp) REVERT: L 351 GLN cc_start: 0.8182 (tp40) cc_final: 0.7951 (tp40) REVERT: G 61 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: G 160 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8499 (ptmm) REVERT: G 166 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8007 (mtt) REVERT: G 267 MET cc_start: 0.6203 (tmm) cc_final: 0.5319 (mmp) REVERT: G 367 GLU cc_start: 0.8608 (pp20) cc_final: 0.8274 (pp20) REVERT: G 494 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8866 (pp) REVERT: M 13 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7949 (mpt-90) REVERT: M 267 MET cc_start: 0.6677 (tmm) cc_final: 0.5780 (mmt) outliers start: 181 outliers final: 109 residues processed: 647 average time/residue: 0.4766 time to fit residues: 542.2480 Evaluate side-chains 591 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 461 time to evaluate : 5.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 442 VAL Chi-restraints excluded: chain N residue 494 LEU Chi-restraints excluded: chain N residue 517 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 146 GLN Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 232 GLU Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 388 GLU Chi-restraints excluded: chain J residue 433 ASN Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 447 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 146 GLN Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 307 MET Chi-restraints excluded: chain K residue 463 SER Chi-restraints excluded: chain K residue 517 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 69 MET Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 442 VAL Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 489 ILE Chi-restraints excluded: chain M residue 517 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 164 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 470 optimal weight: 0.7980 chunk 455 optimal weight: 2.9990 chunk 353 optimal weight: 4.9990 chunk 334 optimal weight: 9.9990 chunk 578 optimal weight: 6.9990 chunk 673 optimal weight: 5.9990 chunk 565 optimal weight: 1.9990 chunk 558 optimal weight: 8.9990 chunk 644 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 319 GLN E 348 GLN L 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.150147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.108103 restraints weight = 68456.092| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.74 r_work: 0.3142 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 54362 Z= 0.202 Angle : 0.485 12.007 73402 Z= 0.256 Chirality : 0.041 0.165 8932 Planarity : 0.003 0.030 9618 Dihedral : 3.865 26.099 7733 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.69 % Allowed : 14.14 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.10), residues: 7308 helix: 2.25 (0.08), residues: 4088 sheet: 0.63 (0.17), residues: 938 loop : -0.43 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS N 401 PHE 0.011 0.001 PHE G 204 TYR 0.010 0.001 TYR K 476 ARG 0.004 0.000 ARG L 345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 503 time to evaluate : 4.912 Fit side-chains revert: symmetry clash REVERT: A 267 MET cc_start: 0.6120 (mmm) cc_final: 0.5147 (mmm) REVERT: A 367 GLU cc_start: 0.8419 (pp20) cc_final: 0.8122 (pp20) REVERT: A 514 MET cc_start: 0.9247 (mtm) cc_final: 0.8909 (mtp) REVERT: N 16 MET cc_start: 0.8627 (mmm) cc_final: 0.8334 (mtt) REVERT: N 69 MET cc_start: 0.7984 (mtm) cc_final: 0.7608 (mtp) REVERT: N 111 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8461 (mtt) REVERT: N 201 SER cc_start: 0.8365 (t) cc_final: 0.8070 (m) REVERT: N 267 MET cc_start: 0.6330 (tmm) cc_final: 0.5930 (mmp) REVERT: N 442 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8784 (t) REVERT: N 494 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8855 (pp) REVERT: B 160 LYS cc_start: 0.8558 (mtpp) cc_final: 0.8229 (ptmm) REVERT: B 204 PHE cc_start: 0.8472 (m-80) cc_final: 0.8148 (m-80) REVERT: B 267 MET cc_start: 0.6083 (tmm) cc_final: 0.5540 (mmp) REVERT: B 367 GLU cc_start: 0.8465 (pp20) cc_final: 0.8124 (pp20) REVERT: B 389 MET cc_start: 0.8255 (tmm) cc_final: 0.8042 (ttp) REVERT: B 494 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8668 (pp) REVERT: H 267 MET cc_start: 0.6340 (tmm) cc_final: 0.5311 (mmm) REVERT: H 514 MET cc_start: 0.9087 (mtp) cc_final: 0.8836 (mtp) REVERT: C 61 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8131 (pt0) REVERT: C 267 MET cc_start: 0.6492 (tmm) cc_final: 0.5791 (mmp) REVERT: C 288 MET cc_start: 0.7001 (ptp) cc_final: 0.6661 (mtp) REVERT: C 322 ARG cc_start: 0.8926 (mtp-110) cc_final: 0.8690 (ttm110) REVERT: C 367 GLU cc_start: 0.8487 (pp20) cc_final: 0.8109 (pp20) REVERT: C 488 MET cc_start: 0.9039 (tpt) cc_final: 0.8651 (mmt) REVERT: C 514 MET cc_start: 0.9104 (mtp) cc_final: 0.8881 (mtm) REVERT: I 193 MET cc_start: 0.8463 (tpt) cc_final: 0.8230 (ttm) REVERT: I 204 PHE cc_start: 0.8451 (m-80) cc_final: 0.8150 (m-80) REVERT: I 267 MET cc_start: 0.6678 (tmm) cc_final: 0.5812 (mmp) REVERT: I 351 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8146 (pp30) REVERT: I 494 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8830 (pp) REVERT: D 242 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7777 (mmmt) REVERT: D 267 MET cc_start: 0.6286 (tmm) cc_final: 0.5507 (mmm) REVERT: D 321 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8516 (mmmt) REVERT: D 367 GLU cc_start: 0.8674 (pp20) cc_final: 0.8369 (pp20) REVERT: J 16 MET cc_start: 0.8800 (mtp) cc_final: 0.8536 (mtm) REVERT: J 204 PHE cc_start: 0.8325 (m-80) cc_final: 0.7978 (m-80) REVERT: J 267 MET cc_start: 0.5962 (tmm) cc_final: 0.5042 (mmm) REVERT: J 442 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8725 (t) REVERT: J 494 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8817 (pp) REVERT: E 102 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7401 (mp0) REVERT: E 111 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8310 (mtt) REVERT: E 267 MET cc_start: 0.6500 (tmm) cc_final: 0.5822 (mmp) REVERT: E 367 GLU cc_start: 0.8540 (pp20) cc_final: 0.8241 (pp20) REVERT: E 447 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8912 (mtp) REVERT: E 494 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8821 (pp) REVERT: E 514 MET cc_start: 0.9132 (ttm) cc_final: 0.8919 (mtp) REVERT: K 267 MET cc_start: 0.6683 (tmm) cc_final: 0.5483 (mmp) REVERT: K 514 MET cc_start: 0.9241 (ttm) cc_final: 0.8859 (mtp) REVERT: F 102 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: F 160 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8387 (ptmm) REVERT: F 321 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8402 (mmtp) REVERT: F 367 GLU cc_start: 0.8382 (pp20) cc_final: 0.8097 (pp20) REVERT: L 61 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8256 (tm-30) REVERT: L 69 MET cc_start: 0.8483 (mtm) cc_final: 0.8057 (mtp) REVERT: L 262 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7018 (tp) REVERT: L 267 MET cc_start: 0.6174 (tmm) cc_final: 0.5243 (mmm) REVERT: L 288 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.6810 (mpp) REVERT: L 351 GLN cc_start: 0.8179 (tp40) cc_final: 0.7942 (tp40) REVERT: L 461 GLU cc_start: 0.7906 (pm20) cc_final: 0.7528 (pm20) REVERT: G 61 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: G 160 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8464 (ptmm) REVERT: G 204 PHE cc_start: 0.8487 (m-80) cc_final: 0.8218 (m-80) REVERT: G 267 MET cc_start: 0.6258 (tmm) cc_final: 0.5412 (mmp) REVERT: G 367 GLU cc_start: 0.8508 (pp20) cc_final: 0.8148 (pp20) REVERT: G 494 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8889 (pp) REVERT: M 13 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7979 (mpt-90) REVERT: M 267 MET cc_start: 0.6541 (tmm) cc_final: 0.5749 (mmm) outliers start: 152 outliers final: 108 residues processed: 622 average time/residue: 0.5013 time to fit residues: 551.3913 Evaluate side-chains 590 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 463 time to evaluate : 4.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 442 VAL Chi-restraints excluded: chain N residue 494 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 146 GLN Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 232 GLU Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 388 GLU Chi-restraints excluded: chain J residue 433 ASN Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 348 GLN Chi-restraints excluded: chain E residue 447 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 307 MET Chi-restraints excluded: chain K residue 463 SER Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 442 VAL Chi-restraints excluded: chain M residue 463 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 505 optimal weight: 0.8980 chunk 379 optimal weight: 4.9990 chunk 549 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 690 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 679 optimal weight: 4.9990 chunk 691 optimal weight: 5.9990 chunk 421 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 GLN J 351 GLN M 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.148829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106590 restraints weight = 68515.929| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.74 r_work: 0.3112 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 54362 Z= 0.259 Angle : 0.506 10.738 73402 Z= 0.267 Chirality : 0.042 0.176 8932 Planarity : 0.003 0.035 9618 Dihedral : 3.882 19.159 7730 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.18 % Allowed : 14.48 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.10), residues: 7308 helix: 2.19 (0.08), residues: 4088 sheet: 0.60 (0.17), residues: 938 loop : -0.45 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 401 PHE 0.008 0.001 PHE L 8 TYR 0.010 0.001 TYR I 478 ARG 0.005 0.000 ARG E 345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 484 time to evaluate : 4.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.6167 (mmm) cc_final: 0.5188 (mmm) REVERT: A 367 GLU cc_start: 0.8407 (pp20) cc_final: 0.8110 (pp20) REVERT: N 111 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8482 (mtt) REVERT: N 201 SER cc_start: 0.8378 (t) cc_final: 0.8081 (m) REVERT: N 267 MET cc_start: 0.6330 (tmm) cc_final: 0.5948 (mmp) REVERT: N 442 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8813 (t) REVERT: N 494 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8850 (pp) REVERT: N 514 MET cc_start: 0.9174 (ttm) cc_final: 0.8743 (mtp) REVERT: N 520 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8523 (mmt) REVERT: B 160 LYS cc_start: 0.8559 (mtpp) cc_final: 0.8216 (ptmm) REVERT: B 204 PHE cc_start: 0.8493 (m-80) cc_final: 0.8173 (m-80) REVERT: B 267 MET cc_start: 0.6544 (tmm) cc_final: 0.5404 (mmp) REVERT: B 367 GLU cc_start: 0.8461 (pp20) cc_final: 0.8149 (pp20) REVERT: B 389 MET cc_start: 0.8253 (tmm) cc_final: 0.8049 (ttp) REVERT: B 494 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8661 (pp) REVERT: H 267 MET cc_start: 0.6409 (tmm) cc_final: 0.5349 (mmp) REVERT: H 514 MET cc_start: 0.9120 (mtp) cc_final: 0.8850 (mtm) REVERT: C 61 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: C 69 MET cc_start: 0.8486 (mtp) cc_final: 0.8071 (ttm) REVERT: C 267 MET cc_start: 0.6425 (tmm) cc_final: 0.5775 (mmp) REVERT: C 288 MET cc_start: 0.7011 (ptp) cc_final: 0.6776 (mtp) REVERT: C 322 ARG cc_start: 0.8929 (mtp-110) cc_final: 0.8724 (ttm110) REVERT: C 367 GLU cc_start: 0.8471 (pp20) cc_final: 0.8080 (pp20) REVERT: C 494 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8747 (pp) REVERT: C 514 MET cc_start: 0.9097 (mtp) cc_final: 0.8832 (mtm) REVERT: I 193 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8273 (ttm) REVERT: I 204 PHE cc_start: 0.8457 (m-80) cc_final: 0.8136 (m-80) REVERT: I 267 MET cc_start: 0.6650 (tmm) cc_final: 0.5870 (mmp) REVERT: I 351 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8152 (pp30) REVERT: I 494 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8809 (pp) REVERT: I 514 MET cc_start: 0.9197 (ttm) cc_final: 0.8827 (mtp) REVERT: D 242 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7780 (mmmt) REVERT: D 267 MET cc_start: 0.6631 (tmm) cc_final: 0.5863 (mmm) REVERT: D 321 LYS cc_start: 0.8823 (ttpt) cc_final: 0.8499 (mmmt) REVERT: D 367 GLU cc_start: 0.8619 (pp20) cc_final: 0.8287 (pp20) REVERT: J 16 MET cc_start: 0.8850 (mtp) cc_final: 0.8598 (mtm) REVERT: J 204 PHE cc_start: 0.8350 (m-80) cc_final: 0.8014 (m-80) REVERT: J 267 MET cc_start: 0.6001 (tmm) cc_final: 0.5109 (mmm) REVERT: J 442 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8759 (t) REVERT: J 494 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8852 (pp) REVERT: E 102 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7461 (mp0) REVERT: E 111 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8354 (mtt) REVERT: E 267 MET cc_start: 0.6799 (tmm) cc_final: 0.5817 (mmp) REVERT: E 367 GLU cc_start: 0.8546 (pp20) cc_final: 0.8231 (pp20) REVERT: E 389 MET cc_start: 0.7922 (tmm) cc_final: 0.7653 (tmt) REVERT: E 447 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8920 (mtp) REVERT: E 494 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8839 (pp) REVERT: E 514 MET cc_start: 0.9178 (ttm) cc_final: 0.8949 (mtp) REVERT: K 142 LYS cc_start: 0.8604 (tppt) cc_final: 0.8338 (ttpp) REVERT: K 267 MET cc_start: 0.6660 (tmm) cc_final: 0.5508 (mmp) REVERT: K 514 MET cc_start: 0.9237 (ttm) cc_final: 0.8946 (mtp) REVERT: F 102 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7390 (mp0) REVERT: F 111 MET cc_start: 0.8995 (mtp) cc_final: 0.8667 (mtt) REVERT: F 160 LYS cc_start: 0.8674 (mtpp) cc_final: 0.8390 (ptmm) REVERT: F 321 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8408 (mmtp) REVERT: F 367 GLU cc_start: 0.8382 (pp20) cc_final: 0.8062 (pp20) REVERT: L 69 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8118 (mtp) REVERT: L 262 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6947 (tp) REVERT: L 267 MET cc_start: 0.6194 (tmm) cc_final: 0.5319 (mmm) REVERT: L 288 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6720 (mpp) REVERT: L 351 GLN cc_start: 0.8221 (tp40) cc_final: 0.7978 (tp40) REVERT: G 61 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8091 (pt0) REVERT: G 160 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8496 (ptmm) REVERT: G 166 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.7990 (mtt) REVERT: G 204 PHE cc_start: 0.8545 (m-80) cc_final: 0.8242 (m-80) REVERT: G 267 MET cc_start: 0.6266 (tmm) cc_final: 0.5479 (mmp) REVERT: G 367 GLU cc_start: 0.8491 (pp20) cc_final: 0.8119 (pp20) REVERT: G 494 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8891 (pp) REVERT: M 13 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7959 (mpt-90) REVERT: M 267 MET cc_start: 0.6483 (tmm) cc_final: 0.5678 (mmm) outliers start: 180 outliers final: 134 residues processed: 631 average time/residue: 0.4580 time to fit residues: 509.8252 Evaluate side-chains 613 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 456 time to evaluate : 4.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 442 VAL Chi-restraints excluded: chain N residue 494 LEU Chi-restraints excluded: chain N residue 517 THR Chi-restraints excluded: chain N residue 520 MET Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 146 GLN Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain I residue 517 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 232 GLU Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain J residue 388 GLU Chi-restraints excluded: chain J residue 433 ASN Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 447 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 146 GLN Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 307 MET Chi-restraints excluded: chain K residue 463 SER Chi-restraints excluded: chain K residue 517 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 69 MET Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain M residue 205 ILE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 442 VAL Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 489 ILE Chi-restraints excluded: chain M residue 517 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 683 optimal weight: 0.7980 chunk 420 optimal weight: 0.7980 chunk 280 optimal weight: 0.4980 chunk 214 optimal weight: 4.9990 chunk 536 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 chunk 498 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 241 optimal weight: 10.0000 chunk 351 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN C 467 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.150581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.109638 restraints weight = 68254.565| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.79 r_work: 0.3145 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 54362 Z= 0.172 Angle : 0.482 10.095 73402 Z= 0.254 Chirality : 0.041 0.172 8932 Planarity : 0.003 0.033 9618 Dihedral : 3.815 18.675 7729 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.72 % Allowed : 15.33 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.10), residues: 7308 helix: 2.27 (0.08), residues: 4088 sheet: 0.63 (0.17), residues: 938 loop : -0.41 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS N 401 PHE 0.008 0.001 PHE L 204 TYR 0.010 0.001 TYR J 476 ARG 0.006 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 497 time to evaluate : 4.820 Fit side-chains revert: symmetry clash REVERT: A 267 MET cc_start: 0.6163 (mmm) cc_final: 0.5192 (mmm) REVERT: A 367 GLU cc_start: 0.8417 (pp20) cc_final: 0.8121 (pp20) REVERT: N 69 MET cc_start: 0.7911 (mtm) cc_final: 0.7549 (mtp) REVERT: N 111 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8423 (mtt) REVERT: N 201 SER cc_start: 0.8331 (t) cc_final: 0.8011 (m) REVERT: N 267 MET cc_start: 0.6218 (tmm) cc_final: 0.5971 (mmp) REVERT: N 442 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8767 (t) REVERT: N 494 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8861 (pp) REVERT: N 520 MET cc_start: 0.8774 (mmt) cc_final: 0.8546 (mmt) REVERT: B 160 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8257 (ptmm) REVERT: B 204 PHE cc_start: 0.8456 (m-80) cc_final: 0.8092 (m-80) REVERT: B 267 MET cc_start: 0.6527 (tmm) cc_final: 0.5406 (mmp) REVERT: B 367 GLU cc_start: 0.8409 (pp20) cc_final: 0.8101 (pp20) REVERT: B 494 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8659 (pp) REVERT: H 267 MET cc_start: 0.6298 (tmm) cc_final: 0.5341 (mmp) REVERT: C 61 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8076 (pt0) REVERT: C 69 MET cc_start: 0.8358 (mtp) cc_final: 0.8015 (ttm) REVERT: C 267 MET cc_start: 0.6422 (tmm) cc_final: 0.5745 (mmp) REVERT: C 322 ARG cc_start: 0.8961 (mtp-110) cc_final: 0.8688 (ttm110) REVERT: C 367 GLU cc_start: 0.8429 (pp20) cc_final: 0.8026 (pp20) REVERT: C 514 MET cc_start: 0.9092 (mtp) cc_final: 0.8865 (mtm) REVERT: I 193 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8231 (ttm) REVERT: I 204 PHE cc_start: 0.8421 (m-80) cc_final: 0.8144 (m-80) REVERT: I 267 MET cc_start: 0.6536 (tmm) cc_final: 0.5793 (mmp) REVERT: I 351 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8157 (pp30) REVERT: I 494 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8797 (pp) REVERT: I 514 MET cc_start: 0.9201 (ttm) cc_final: 0.8907 (mtp) REVERT: D 242 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7778 (mmmt) REVERT: D 267 MET cc_start: 0.6600 (tmm) cc_final: 0.5816 (mmm) REVERT: D 321 LYS cc_start: 0.8820 (ttpt) cc_final: 0.8480 (mmmt) REVERT: D 367 GLU cc_start: 0.8616 (pp20) cc_final: 0.8271 (pp20) REVERT: J 16 MET cc_start: 0.8813 (mtp) cc_final: 0.8592 (mtm) REVERT: J 204 PHE cc_start: 0.8305 (m-80) cc_final: 0.7980 (m-80) REVERT: J 267 MET cc_start: 0.5697 (tmm) cc_final: 0.4914 (mmm) REVERT: J 442 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8706 (t) REVERT: E 267 MET cc_start: 0.6737 (tmm) cc_final: 0.5859 (mmp) REVERT: E 351 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7939 (tp-100) REVERT: E 367 GLU cc_start: 0.8548 (pp20) cc_final: 0.8204 (pp20) REVERT: E 389 MET cc_start: 0.7908 (tmm) cc_final: 0.7598 (tmt) REVERT: E 447 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8919 (mtp) REVERT: E 494 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8801 (pp) REVERT: E 514 MET cc_start: 0.9145 (ttm) cc_final: 0.8732 (mtp) REVERT: K 238 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6898 (mm-30) REVERT: K 267 MET cc_start: 0.6531 (tmm) cc_final: 0.5425 (mmp) REVERT: K 514 MET cc_start: 0.9165 (ttm) cc_final: 0.8913 (mtp) REVERT: F 102 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7292 (mp0) REVERT: F 111 MET cc_start: 0.8973 (mtp) cc_final: 0.8635 (mtt) REVERT: F 160 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8383 (ptmm) REVERT: F 321 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8377 (mmtp) REVERT: F 367 GLU cc_start: 0.8360 (pp20) cc_final: 0.8054 (pp20) REVERT: L 61 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8408 (tm-30) REVERT: L 69 MET cc_start: 0.8469 (mtm) cc_final: 0.8035 (mtp) REVERT: L 262 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7033 (tp) REVERT: L 267 MET cc_start: 0.6129 (tmm) cc_final: 0.5373 (mmm) REVERT: L 288 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.6727 (mpp) REVERT: L 351 GLN cc_start: 0.8219 (tp40) cc_final: 0.7969 (tp40) REVERT: G 61 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8071 (pt0) REVERT: G 166 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7914 (mtt) REVERT: G 204 PHE cc_start: 0.8541 (m-80) cc_final: 0.8212 (m-80) REVERT: G 267 MET cc_start: 0.6185 (tmm) cc_final: 0.5487 (mmp) REVERT: G 367 GLU cc_start: 0.8470 (pp20) cc_final: 0.8095 (pp20) REVERT: G 494 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8842 (pp) REVERT: M 267 MET cc_start: 0.6367 (tmm) cc_final: 0.5690 (mmm) outliers start: 154 outliers final: 118 residues processed: 624 average time/residue: 0.4663 time to fit residues: 513.3552 Evaluate side-chains 593 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 458 time to evaluate : 4.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 442 VAL Chi-restraints excluded: chain N residue 494 LEU Chi-restraints excluded: chain N residue 499 VAL Chi-restraints excluded: chain N residue 517 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 146 GLN Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain I residue 499 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 232 GLU Chi-restraints excluded: chain J residue 388 GLU Chi-restraints excluded: chain J residue 433 ASN Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 447 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 146 GLN Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 307 MET Chi-restraints excluded: chain K residue 463 SER Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 442 VAL Chi-restraints excluded: chain M residue 463 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 86 optimal weight: 2.9990 chunk 554 optimal weight: 9.9990 chunk 274 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 465 optimal weight: 4.9990 chunk 412 optimal weight: 6.9990 chunk 483 optimal weight: 0.0010 chunk 594 optimal weight: 20.0000 chunk 604 optimal weight: 10.0000 chunk 579 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 351 GLN K 351 GLN G 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.150346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.108384 restraints weight = 68509.381| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.79 r_work: 0.3132 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 54362 Z= 0.193 Angle : 0.488 9.616 73402 Z= 0.256 Chirality : 0.041 0.172 8932 Planarity : 0.003 0.035 9618 Dihedral : 3.811 18.585 7729 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.90 % Allowed : 15.22 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.10), residues: 7308 helix: 2.26 (0.08), residues: 4088 sheet: 0.62 (0.17), residues: 938 loop : -0.41 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS N 401 PHE 0.007 0.001 PHE L 8 TYR 0.010 0.001 TYR J 476 ARG 0.004 0.000 ARG I 345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 484 time to evaluate : 5.633 Fit side-chains REVERT: A 267 MET cc_start: 0.6053 (mmm) cc_final: 0.5121 (mmm) REVERT: A 367 GLU cc_start: 0.8398 (pp20) cc_final: 0.8083 (pp20) REVERT: N 69 MET cc_start: 0.7954 (mtm) cc_final: 0.7588 (mtp) REVERT: N 111 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8443 (mtt) REVERT: N 201 SER cc_start: 0.8324 (t) cc_final: 0.8013 (m) REVERT: N 267 MET cc_start: 0.6682 (tmm) cc_final: 0.5882 (mmp) REVERT: N 442 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8801 (t) REVERT: N 494 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8870 (pp) REVERT: B 160 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8268 (ptmm) REVERT: B 204 PHE cc_start: 0.8466 (m-80) cc_final: 0.8099 (m-80) REVERT: B 267 MET cc_start: 0.6605 (tmm) cc_final: 0.5535 (mmp) REVERT: B 367 GLU cc_start: 0.8417 (pp20) cc_final: 0.8105 (pp20) REVERT: B 494 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8607 (pp) REVERT: H 69 MET cc_start: 0.8705 (mtp) cc_final: 0.8502 (mtt) REVERT: H 267 MET cc_start: 0.6226 (tmm) cc_final: 0.5202 (mmp) REVERT: C 61 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: C 69 MET cc_start: 0.8362 (mtp) cc_final: 0.8020 (ttm) REVERT: C 267 MET cc_start: 0.6679 (tmm) cc_final: 0.6023 (mmp) REVERT: C 322 ARG cc_start: 0.8973 (mtp-110) cc_final: 0.8599 (ttm110) REVERT: C 367 GLU cc_start: 0.8424 (pp20) cc_final: 0.8011 (pp20) REVERT: C 514 MET cc_start: 0.9076 (mtp) cc_final: 0.8842 (mtm) REVERT: I 193 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8272 (ttm) REVERT: I 204 PHE cc_start: 0.8412 (m-80) cc_final: 0.8156 (m-80) REVERT: I 267 MET cc_start: 0.6535 (tmm) cc_final: 0.5847 (mmp) REVERT: I 351 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8185 (pp30) REVERT: I 494 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8803 (pp) REVERT: I 514 MET cc_start: 0.9208 (ttm) cc_final: 0.8918 (mtp) REVERT: D 242 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7781 (mmmt) REVERT: D 267 MET cc_start: 0.6576 (tmm) cc_final: 0.5764 (mmm) REVERT: D 321 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8462 (mmmt) REVERT: D 367 GLU cc_start: 0.8591 (pp20) cc_final: 0.8239 (pp20) REVERT: J 16 MET cc_start: 0.8826 (mtp) cc_final: 0.8615 (mtm) REVERT: J 204 PHE cc_start: 0.8305 (m-80) cc_final: 0.7989 (m-80) REVERT: J 267 MET cc_start: 0.5661 (tmm) cc_final: 0.4908 (mmm) REVERT: J 389 MET cc_start: 0.8229 (tmm) cc_final: 0.7983 (tmm) REVERT: E 267 MET cc_start: 0.6582 (tmm) cc_final: 0.5812 (mmp) REVERT: E 351 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8110 (mm110) REVERT: E 367 GLU cc_start: 0.8537 (pp20) cc_final: 0.8266 (pp20) REVERT: E 389 MET cc_start: 0.7907 (tmm) cc_final: 0.7704 (tmm) REVERT: E 447 MET cc_start: 0.9204 (mtm) cc_final: 0.8936 (mtp) REVERT: E 494 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8851 (pp) REVERT: E 514 MET cc_start: 0.9154 (ttm) cc_final: 0.8717 (mtp) REVERT: K 142 LYS cc_start: 0.8621 (tppt) cc_final: 0.8356 (ttpp) REVERT: K 267 MET cc_start: 0.6539 (tmm) cc_final: 0.5476 (mmp) REVERT: F 102 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7265 (mp0) REVERT: F 111 MET cc_start: 0.8996 (mtp) cc_final: 0.8651 (mtt) REVERT: F 160 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8383 (ptmm) REVERT: F 234 LEU cc_start: 0.7871 (tp) cc_final: 0.7641 (tp) REVERT: F 321 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8390 (mmtp) REVERT: F 367 GLU cc_start: 0.8362 (pp20) cc_final: 0.8057 (pp20) REVERT: L 61 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8376 (tm-30) REVERT: L 69 MET cc_start: 0.8511 (mtm) cc_final: 0.8068 (mtp) REVERT: L 267 MET cc_start: 0.6114 (tmm) cc_final: 0.5370 (mmm) REVERT: L 288 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6654 (mpp) REVERT: L 351 GLN cc_start: 0.8222 (tp40) cc_final: 0.7974 (tp40) REVERT: G 61 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8085 (pt0) REVERT: G 166 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.7900 (mtt) REVERT: G 204 PHE cc_start: 0.8500 (m-80) cc_final: 0.8172 (m-80) REVERT: G 267 MET cc_start: 0.6346 (tmm) cc_final: 0.5823 (mmp) REVERT: G 367 GLU cc_start: 0.8486 (pp20) cc_final: 0.8113 (pp20) REVERT: G 494 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8861 (pp) REVERT: M 13 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7858 (mpt-90) REVERT: M 267 MET cc_start: 0.6355 (tmm) cc_final: 0.5714 (mmm) outliers start: 164 outliers final: 136 residues processed: 620 average time/residue: 0.4745 time to fit residues: 521.3993 Evaluate side-chains 620 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 469 time to evaluate : 5.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 442 VAL Chi-restraints excluded: chain N residue 494 LEU Chi-restraints excluded: chain N residue 499 VAL Chi-restraints excluded: chain N residue 517 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 146 GLN Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain I residue 499 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 388 GLU Chi-restraints excluded: chain J residue 433 ASN Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 146 GLN Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 307 MET Chi-restraints excluded: chain K residue 463 SER Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 494 LEU Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 205 ILE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 442 VAL Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 517 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 581 optimal weight: 1.9990 chunk 646 optimal weight: 6.9990 chunk 253 optimal weight: 0.9980 chunk 543 optimal weight: 0.0970 chunk 334 optimal weight: 20.0000 chunk 255 optimal weight: 4.9990 chunk 600 optimal weight: 1.9990 chunk 371 optimal weight: 0.8980 chunk 381 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.151666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109829 restraints weight = 68309.399| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.74 r_work: 0.3161 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 54362 Z= 0.161 Angle : 0.488 13.079 73402 Z= 0.255 Chirality : 0.040 0.170 8932 Planarity : 0.003 0.037 9618 Dihedral : 3.771 18.721 7729 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.63 % Allowed : 15.51 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.10), residues: 7308 helix: 2.31 (0.08), residues: 4088 sheet: 0.65 (0.17), residues: 938 loop : -0.41 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS N 401 PHE 0.007 0.001 PHE N 195 TYR 0.010 0.001 TYR J 476 ARG 0.004 0.000 ARG I 345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 501 time to evaluate : 4.852 Fit side-chains REVERT: A 238 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6870 (mm-30) REVERT: A 267 MET cc_start: 0.6010 (mmm) cc_final: 0.5058 (mmm) REVERT: A 367 GLU cc_start: 0.8366 (pp20) cc_final: 0.8056 (pp20) REVERT: N 69 MET cc_start: 0.7900 (mtm) cc_final: 0.7472 (mtp) REVERT: N 111 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8372 (mtt) REVERT: N 201 SER cc_start: 0.8109 (t) cc_final: 0.7807 (m) REVERT: N 267 MET cc_start: 0.6702 (tmm) cc_final: 0.5921 (mmp) REVERT: N 494 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8878 (pp) REVERT: N 514 MET cc_start: 0.9126 (ttm) cc_final: 0.8742 (mtp) REVERT: N 520 MET cc_start: 0.8805 (mmm) cc_final: 0.8429 (mtt) REVERT: B 160 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8269 (ptmm) REVERT: B 204 PHE cc_start: 0.8461 (m-80) cc_final: 0.8080 (m-80) REVERT: B 267 MET cc_start: 0.6479 (tmm) cc_final: 0.5467 (mmp) REVERT: B 367 GLU cc_start: 0.8429 (pp20) cc_final: 0.8196 (pp20) REVERT: B 494 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8629 (pp) REVERT: H 238 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6736 (mm-30) REVERT: H 267 MET cc_start: 0.6264 (tmm) cc_final: 0.5335 (mmp) REVERT: H 514 MET cc_start: 0.9052 (mtp) cc_final: 0.8803 (mtm) REVERT: C 61 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8120 (pt0) REVERT: C 69 MET cc_start: 0.8271 (mtp) cc_final: 0.7987 (ttm) REVERT: C 267 MET cc_start: 0.6577 (tmm) cc_final: 0.5931 (mmp) REVERT: C 322 ARG cc_start: 0.8957 (mtp-110) cc_final: 0.8701 (ttm110) REVERT: C 367 GLU cc_start: 0.8435 (pp20) cc_final: 0.8024 (pp20) REVERT: I 193 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8246 (ttm) REVERT: I 204 PHE cc_start: 0.8412 (m-80) cc_final: 0.8133 (m-80) REVERT: I 267 MET cc_start: 0.6457 (tmm) cc_final: 0.5900 (mmp) REVERT: I 288 MET cc_start: 0.7784 (mmp) cc_final: 0.7581 (mmp) REVERT: I 351 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8108 (pp30) REVERT: I 494 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8771 (pp) REVERT: I 514 MET cc_start: 0.9172 (ttm) cc_final: 0.8904 (mtp) REVERT: D 267 MET cc_start: 0.6526 (tmm) cc_final: 0.5726 (mmm) REVERT: D 321 LYS cc_start: 0.8799 (ttpt) cc_final: 0.8495 (mmmt) REVERT: D 367 GLU cc_start: 0.8600 (pp20) cc_final: 0.8251 (pp20) REVERT: J 204 PHE cc_start: 0.8296 (m-80) cc_final: 0.7971 (m-80) REVERT: J 267 MET cc_start: 0.5577 (tmm) cc_final: 0.4896 (mmm) REVERT: J 389 MET cc_start: 0.8179 (tmm) cc_final: 0.7928 (tmm) REVERT: E 267 MET cc_start: 0.6471 (tmm) cc_final: 0.5853 (mmp) REVERT: E 367 GLU cc_start: 0.8487 (pp20) cc_final: 0.8194 (pp20) REVERT: E 389 MET cc_start: 0.7886 (tmm) cc_final: 0.7671 (tmm) REVERT: E 447 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8894 (mtp) REVERT: E 494 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8839 (pp) REVERT: E 514 MET cc_start: 0.9086 (ttm) cc_final: 0.8719 (mtp) REVERT: K 204 PHE cc_start: 0.8283 (m-80) cc_final: 0.7892 (m-80) REVERT: K 267 MET cc_start: 0.6451 (tmm) cc_final: 0.5518 (mmp) REVERT: F 102 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7174 (mp0) REVERT: F 111 MET cc_start: 0.8945 (mtp) cc_final: 0.8640 (mtt) REVERT: F 160 LYS cc_start: 0.8645 (mtpp) cc_final: 0.8372 (ptmm) REVERT: F 234 LEU cc_start: 0.7904 (tp) cc_final: 0.7671 (tp) REVERT: F 321 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8425 (mmtp) REVERT: F 367 GLU cc_start: 0.8359 (pp20) cc_final: 0.8157 (pp20) REVERT: L 61 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8436 (tm-30) REVERT: L 69 MET cc_start: 0.8379 (mtm) cc_final: 0.7940 (mtp) REVERT: L 76 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8558 (tm-30) REVERT: L 267 MET cc_start: 0.6067 (tmm) cc_final: 0.5379 (mmm) REVERT: L 288 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6650 (mpp) REVERT: L 351 GLN cc_start: 0.8188 (tp40) cc_final: 0.7951 (tp40) REVERT: G 61 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8062 (pt0) REVERT: G 166 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7910 (mtt) REVERT: G 204 PHE cc_start: 0.8488 (m-80) cc_final: 0.8213 (m-80) REVERT: G 267 MET cc_start: 0.6191 (tmm) cc_final: 0.5856 (mmp) REVERT: G 367 GLU cc_start: 0.8487 (pp20) cc_final: 0.8194 (pp20) REVERT: G 494 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8861 (pp) REVERT: M 267 MET cc_start: 0.6288 (tmm) cc_final: 0.5727 (mmm) outliers start: 149 outliers final: 121 residues processed: 624 average time/residue: 0.4669 time to fit residues: 516.4114 Evaluate side-chains 606 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 472 time to evaluate : 5.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 494 LEU Chi-restraints excluded: chain N residue 499 VAL Chi-restraints excluded: chain N residue 517 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain I residue 499 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 388 GLU Chi-restraints excluded: chain J residue 433 ASN Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 447 MET Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 307 MET Chi-restraints excluded: chain K residue 463 SER Chi-restraints excluded: chain K residue 517 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 494 LEU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 205 ILE Chi-restraints excluded: chain M residue 442 VAL Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 517 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 50 optimal weight: 5.9990 chunk 387 optimal weight: 0.9980 chunk 478 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 583 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 317 optimal weight: 3.9990 chunk 543 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 327 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN J 351 GLN E 351 GLN G 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.149426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107173 restraints weight = 68619.065| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.74 r_work: 0.3122 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 54362 Z= 0.254 Angle : 0.524 11.678 73402 Z= 0.273 Chirality : 0.042 0.155 8932 Planarity : 0.003 0.041 9618 Dihedral : 3.847 19.209 7729 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.62 % Allowed : 15.61 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.10), residues: 7308 helix: 2.27 (0.08), residues: 4060 sheet: 0.62 (0.17), residues: 938 loop : -0.44 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 401 PHE 0.009 0.001 PHE H 8 TYR 0.010 0.001 TYR J 476 ARG 0.004 0.000 ARG I 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 478 time to evaluate : 4.848 Fit side-chains REVERT: A 267 MET cc_start: 0.5966 (mmm) cc_final: 0.5054 (mmm) REVERT: A 367 GLU cc_start: 0.8398 (pp20) cc_final: 0.8088 (pp20) REVERT: N 111 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8443 (mtt) REVERT: N 201 SER cc_start: 0.8213 (t) cc_final: 0.7899 (m) REVERT: N 267 MET cc_start: 0.6759 (tmm) cc_final: 0.5953 (mmp) REVERT: N 494 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8881 (pp) REVERT: B 160 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8276 (ptmm) REVERT: B 204 PHE cc_start: 0.8456 (m-80) cc_final: 0.8083 (m-80) REVERT: B 267 MET cc_start: 0.6605 (tmm) cc_final: 0.5588 (mmp) REVERT: B 367 GLU cc_start: 0.8449 (pp20) cc_final: 0.8177 (pp20) REVERT: B 494 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8679 (pp) REVERT: H 69 MET cc_start: 0.8611 (mtp) cc_final: 0.8373 (mtt) REVERT: H 267 MET cc_start: 0.6315 (tmm) cc_final: 0.5342 (mmp) REVERT: H 514 MET cc_start: 0.9160 (mtp) cc_final: 0.8884 (mtm) REVERT: C 61 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8054 (pt0) REVERT: C 69 MET cc_start: 0.8401 (mtp) cc_final: 0.8009 (ttm) REVERT: C 267 MET cc_start: 0.6650 (tmm) cc_final: 0.6007 (mmp) REVERT: C 322 ARG cc_start: 0.8918 (mtp-110) cc_final: 0.8708 (ttm110) REVERT: C 367 GLU cc_start: 0.8416 (pp20) cc_final: 0.7997 (pp20) REVERT: I 193 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8268 (ttm) REVERT: I 204 PHE cc_start: 0.8439 (m-80) cc_final: 0.8233 (m-80) REVERT: I 267 MET cc_start: 0.6433 (tmm) cc_final: 0.5882 (mmp) REVERT: I 288 MET cc_start: 0.7822 (mmp) cc_final: 0.7605 (mmp) REVERT: I 351 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8118 (pp30) REVERT: I 494 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8816 (pp) REVERT: I 514 MET cc_start: 0.9157 (ttm) cc_final: 0.8894 (mtp) REVERT: D 267 MET cc_start: 0.6564 (tmm) cc_final: 0.5769 (mmp) REVERT: D 321 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8503 (mmmt) REVERT: D 367 GLU cc_start: 0.8589 (pp20) cc_final: 0.8235 (pp20) REVERT: J 204 PHE cc_start: 0.8326 (m-80) cc_final: 0.8015 (m-80) REVERT: J 267 MET cc_start: 0.5615 (tmm) cc_final: 0.4921 (mmm) REVERT: J 389 MET cc_start: 0.8303 (tmm) cc_final: 0.8072 (tmm) REVERT: E 267 MET cc_start: 0.6439 (tmm) cc_final: 0.5840 (mmp) REVERT: E 367 GLU cc_start: 0.8482 (pp20) cc_final: 0.8193 (pp20) REVERT: E 389 MET cc_start: 0.7918 (tmm) cc_final: 0.7688 (tmm) REVERT: E 447 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8918 (mtp) REVERT: E 514 MET cc_start: 0.9108 (ttm) cc_final: 0.8741 (mtp) REVERT: K 142 LYS cc_start: 0.8632 (tppt) cc_final: 0.8377 (ttpp) REVERT: K 204 PHE cc_start: 0.8320 (m-80) cc_final: 0.7921 (m-80) REVERT: K 267 MET cc_start: 0.6462 (tmm) cc_final: 0.5487 (mmp) REVERT: F 102 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7241 (mp0) REVERT: F 111 MET cc_start: 0.8974 (mtp) cc_final: 0.8656 (mtt) REVERT: F 160 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8394 (ptmm) REVERT: F 234 LEU cc_start: 0.7909 (tp) cc_final: 0.7681 (tp) REVERT: F 321 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8381 (mmtp) REVERT: F 367 GLU cc_start: 0.8366 (pp20) cc_final: 0.8160 (pp20) REVERT: L 61 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8377 (tm-30) REVERT: L 69 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8095 (mtp) REVERT: L 76 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8599 (tm-30) REVERT: L 267 MET cc_start: 0.6114 (tmm) cc_final: 0.5393 (mmm) REVERT: L 288 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.6640 (mpp) REVERT: L 351 GLN cc_start: 0.8215 (tp40) cc_final: 0.7966 (tp40) REVERT: G 61 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7905 (pt0) REVERT: G 166 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.7968 (mtt) REVERT: G 204 PHE cc_start: 0.8506 (m-80) cc_final: 0.8199 (m-80) REVERT: G 267 MET cc_start: 0.6180 (tmm) cc_final: 0.5813 (mmp) REVERT: G 367 GLU cc_start: 0.8477 (pp20) cc_final: 0.8178 (pp20) REVERT: G 494 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8873 (pp) REVERT: M 13 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7889 (mpt-90) REVERT: M 76 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8727 (tm-30) REVERT: M 267 MET cc_start: 0.6369 (tmm) cc_final: 0.5863 (mmm) outliers start: 148 outliers final: 124 residues processed: 603 average time/residue: 0.5119 time to fit residues: 548.2854 Evaluate side-chains 601 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 463 time to evaluate : 4.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 494 LEU Chi-restraints excluded: chain N residue 499 VAL Chi-restraints excluded: chain N residue 517 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain I residue 499 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 388 GLU Chi-restraints excluded: chain J residue 433 ASN Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 447 MET Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 146 GLN Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 307 MET Chi-restraints excluded: chain K residue 463 SER Chi-restraints excluded: chain K residue 517 THR Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 69 MET Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 494 LEU Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 205 ILE Chi-restraints excluded: chain M residue 442 VAL Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 517 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 250 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 546 optimal weight: 30.0000 chunk 389 optimal weight: 20.0000 chunk 473 optimal weight: 0.9980 chunk 477 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 725 optimal weight: 0.0770 chunk 207 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 430 optimal weight: 0.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.151799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.111953 restraints weight = 68658.860| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.77 r_work: 0.3187 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 54362 Z= 0.155 Angle : 0.489 11.779 73402 Z= 0.254 Chirality : 0.040 0.182 8932 Planarity : 0.003 0.042 9618 Dihedral : 3.771 17.999 7728 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.35 % Allowed : 16.00 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.10), residues: 7308 helix: 2.33 (0.08), residues: 4088 sheet: 0.65 (0.17), residues: 938 loop : -0.41 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS N 401 PHE 0.007 0.001 PHE N 195 TYR 0.010 0.001 TYR C 476 ARG 0.004 0.000 ARG I 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23076.01 seconds wall clock time: 397 minutes 40.00 seconds (23860.00 seconds total)