Starting phenix.real_space_refine on Wed Nov 20 05:35:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0c_45079/11_2024/9c0c_45079.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0c_45079/11_2024/9c0c_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0c_45079/11_2024/9c0c_45079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0c_45079/11_2024/9c0c_45079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0c_45079/11_2024/9c0c_45079.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0c_45079/11_2024/9c0c_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): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 28.95, per 1000 atoms: 0.54 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: 12.61 Conformation dependent library (CDL) restraints added in 6.9 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: 7.35 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: 27.80 Time building geometry restraints manager: 14.61 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: 0.00 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.860 Check model and map are aligned: 0.350 Set scattering table: 0.430 Process input model: 119.490 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.330 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.000 ------------------------------------------------------------------------------- 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 : 5.933 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: 0.6438 time to fit residues: 835.2596 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 : 5.895 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 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 : 6.124 Fit side-chains REVERT: A 16 MET cc_start: 0.8275 (mtp) cc_final: 0.8027 (mtt) REVERT: A 61 GLU cc_start: 0.7060 (pt0) cc_final: 0.6806 (pt0) REVERT: A 267 MET cc_start: 0.5721 (mmm) cc_final: 0.5168 (mmm) REVERT: A 307 MET cc_start: 0.7636 (mtm) cc_final: 0.6735 (ptp) REVERT: A 321 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7746 (mmtp) REVERT: A 322 ARG cc_start: 0.7579 (ttp80) cc_final: 0.7204 (ttm110) REVERT: A 461 GLU cc_start: 0.7660 (pm20) cc_final: 0.7294 (pm20) REVERT: A 514 MET cc_start: 0.8204 (mtp) cc_final: 0.7985 (mtm) REVERT: N 69 MET cc_start: 0.6026 (mtm) cc_final: 0.5769 (mtp) REVERT: N 111 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7807 (mtt) REVERT: N 267 MET cc_start: 0.6343 (tmm) cc_final: 0.5711 (mmp) REVERT: N 321 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7541 (mmtp) REVERT: N 327 LYS cc_start: 0.8787 (tppt) cc_final: 0.8557 (tptp) REVERT: N 447 MET cc_start: 0.8033 (mtm) cc_final: 0.7795 (mtp) REVERT: B 193 MET cc_start: 0.6962 (tpt) cc_final: 0.6681 (tpt) REVERT: B 233 MET cc_start: 0.5384 (pmm) cc_final: 0.5169 (ptt) REVERT: B 267 MET cc_start: 0.6522 (tmm) cc_final: 0.5181 (mmm) REVERT: B 321 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7670 (mmtp) REVERT: B 367 GLU cc_start: 0.7616 (pp20) cc_final: 0.7321 (pp20) REVERT: H 121 ASP cc_start: 0.7092 (m-30) cc_final: 0.6810 (m-30) REVERT: H 262 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6108 (tt) REVERT: H 267 MET cc_start: 0.6074 (tmm) cc_final: 0.5181 (mmp) REVERT: H 321 LYS cc_start: 0.8336 (ttpt) cc_final: 0.7889 (mmtp) REVERT: H 327 LYS cc_start: 0.8792 (tppt) cc_final: 0.8584 (tttp) REVERT: C 102 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6507 (mt-10) REVERT: C 252 GLU cc_start: 0.6929 (tt0) cc_final: 0.6674 (tt0) REVERT: C 267 MET cc_start: 0.6769 (tmm) cc_final: 0.5916 (mmp) REVERT: C 277 LYS cc_start: 0.7985 (mttt) cc_final: 0.7668 (mmmm) REVERT: C 288 MET cc_start: 0.5831 (ptp) cc_final: 0.5572 (mtp) REVERT: C 321 LYS cc_start: 0.8402 (ttpt) cc_final: 0.7831 (mmtp) REVERT: I 5 ASP cc_start: 0.7740 (t0) cc_final: 0.7525 (t0) REVERT: I 233 MET cc_start: 0.5259 (pmm) cc_final: 0.5036 (ptt) REVERT: I 267 MET cc_start: 0.6709 (tmm) cc_final: 0.5850 (mmp) REVERT: I 321 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7528 (mmtp) REVERT: I 327 LYS cc_start: 0.8767 (tppt) cc_final: 0.8561 (tttp) REVERT: D 193 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7017 (tpt) REVERT: D 321 LYS cc_start: 0.8281 (ttpt) cc_final: 0.7633 (mmmt) REVERT: D 495 ASP cc_start: 0.7533 (m-30) cc_final: 0.7325 (m-30) REVERT: J 204 PHE cc_start: 0.7514 (m-80) cc_final: 0.7122 (m-80) REVERT: J 267 MET cc_start: 0.5935 (tmm) cc_final: 0.4910 (mmm) REVERT: J 321 LYS cc_start: 0.7826 (ttpt) cc_final: 0.7442 (mmtp) REVERT: J 351 GLN cc_start: 0.8375 (tp40) cc_final: 0.8116 (tp40) REVERT: J 461 GLU cc_start: 0.7857 (pm20) cc_final: 0.7420 (pm20) REVERT: E 252 GLU cc_start: 0.6879 (tt0) cc_final: 0.6598 (tt0) REVERT: E 321 LYS cc_start: 0.8357 (ttpt) cc_final: 0.7695 (mmpt) REVERT: E 461 GLU cc_start: 0.7573 (pm20) cc_final: 0.7317 (pm20) REVERT: E 520 MET cc_start: 0.8231 (mtt) cc_final: 0.7947 (mtt) REVERT: K 232 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6980 (pm20) REVERT: K 267 MET cc_start: 0.6593 (tmm) cc_final: 0.5397 (mmp) REVERT: K 321 LYS cc_start: 0.8086 (ttpt) cc_final: 0.7734 (mmtp) REVERT: K 351 GLN cc_start: 0.8409 (tp40) cc_final: 0.8134 (tp40) REVERT: K 461 GLU cc_start: 0.8221 (pm20) cc_final: 0.7951 (pm20) REVERT: F 160 LYS cc_start: 0.7747 (mtpp) cc_final: 0.7498 (ttmm) REVERT: F 267 MET cc_start: 0.5778 (mmm) cc_final: 0.5010 (tmm) REVERT: F 321 LYS cc_start: 0.8281 (ttpt) cc_final: 0.7732 (mmtt) REVERT: F 389 MET cc_start: 0.6376 (tmt) cc_final: 0.5866 (tmm) REVERT: L 69 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6399 (mtp) REVERT: L 121 ASP cc_start: 0.7358 (m-30) cc_final: 0.7145 (m-30) REVERT: L 193 MET cc_start: 0.6917 (tpt) cc_final: 0.6690 (tpt) REVERT: L 262 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6104 (tp) REVERT: L 267 MET cc_start: 0.6216 (tmm) cc_final: 0.5022 (mmm) REVERT: L 321 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7564 (mmtp) REVERT: L 351 GLN cc_start: 0.8359 (tp40) cc_final: 0.8056 (tp40) REVERT: G 61 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7053 (pt0) REVERT: G 160 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7623 (ptmm) REVERT: G 267 MET cc_start: 0.6110 (tmm) cc_final: 0.5199 (mmm) REVERT: G 277 LYS cc_start: 0.8023 (mttt) cc_final: 0.7629 (mmmm) REVERT: G 321 LYS cc_start: 0.8231 (ttpt) cc_final: 0.7684 (mmmt) REVERT: G 322 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7321 (mtp-110) REVERT: G 461 GLU cc_start: 0.7658 (pm20) cc_final: 0.7340 (pm20) REVERT: M 13 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.5968 (mpt-90) REVERT: M 142 LYS cc_start: 0.8198 (tppt) cc_final: 0.7905 (ttpp) REVERT: M 245 LYS cc_start: 0.6950 (mttt) cc_final: 0.6701 (mtpt) REVERT: M 267 MET cc_start: 0.6746 (tmm) cc_final: 0.5621 (mmm) REVERT: M 321 LYS cc_start: 0.7956 (ttpt) cc_final: 0.7595 (mmtp) REVERT: M 351 GLN cc_start: 0.8395 (tp40) cc_final: 0.8128 (tp40) REVERT: M 397 GLU cc_start: 0.7750 (tp30) cc_final: 0.7446 (tt0) REVERT: M 461 GLU cc_start: 0.7572 (pm20) cc_final: 0.7164 (pm20) outliers start: 112 outliers final: 57 residues processed: 611 average time/residue: 0.6035 time to fit residues: 639.5966 Evaluate side-chains 542 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 476 time to evaluate : 6.051 ------------------------------------------------------------------------------- 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 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 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 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 232 GLU 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 367 optimal weight: 1.9990 chunk 205 optimal weight: 8.9990 chunk 550 optimal weight: 0.0020 chunk 450 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 662 optimal weight: 7.9990 chunk 715 optimal weight: 6.9990 chunk 589 optimal weight: 5.9990 chunk 656 optimal weight: 0.9990 chunk 225 optimal weight: 8.9990 chunk 531 optimal weight: 2.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- 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 G 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 54362 Z= 0.236 Angle : 0.500 9.039 73402 Z= 0.266 Chirality : 0.042 0.153 8932 Planarity : 0.003 0.033 9618 Dihedral : 3.935 28.143 7737 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.39 % Allowed : 12.61 % Favored : 85.01 % 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: 1.74 (0.10), residues: 7308 helix: 2.23 (0.08), residues: 4088 sheet: 0.38 (0.16), residues: 980 loop : -0.51 (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 H 8 TYR 0.010 0.001 TYR D 478 ARG 0.005 0.000 ARG C 322 *********************** 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 662 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 527 time to evaluate : 5.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.5761 (mmm) cc_final: 0.5168 (mmm) REVERT: A 307 MET cc_start: 0.7739 (mtm) cc_final: 0.6967 (ptp) REVERT: A 321 LYS cc_start: 0.8309 (ttpt) cc_final: 0.7839 (mmtp) REVERT: A 322 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7235 (ttm110) REVERT: A 367 GLU cc_start: 0.7756 (pp20) cc_final: 0.7425 (pp20) REVERT: A 461 GLU cc_start: 0.7674 (pm20) cc_final: 0.7277 (pm20) REVERT: N 16 MET cc_start: 0.7830 (mmm) cc_final: 0.7441 (mtt) REVERT: N 76 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7968 (tm-30) REVERT: N 111 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7854 (mtt) REVERT: N 267 MET cc_start: 0.6286 (tmm) cc_final: 0.5675 (mmp) REVERT: N 321 LYS cc_start: 0.8108 (ttpt) cc_final: 0.7568 (mmtp) REVERT: N 327 LYS cc_start: 0.8899 (tppt) cc_final: 0.8674 (tttp) REVERT: N 461 GLU cc_start: 0.7633 (pm20) cc_final: 0.7418 (pm20) REVERT: B 193 MET cc_start: 0.6987 (tpt) cc_final: 0.6671 (ttm) REVERT: B 267 MET cc_start: 0.6449 (tmm) cc_final: 0.5649 (mmp) REVERT: B 319 GLN cc_start: 0.7282 (mt0) cc_final: 0.7061 (mt0) REVERT: B 321 LYS cc_start: 0.8138 (ttpt) cc_final: 0.7658 (mmtp) REVERT: B 367 GLU cc_start: 0.7633 (pp20) cc_final: 0.7314 (pp20) REVERT: B 494 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7529 (pp) REVERT: H 121 ASP cc_start: 0.7088 (m-30) cc_final: 0.6865 (m-30) REVERT: H 262 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6093 (tt) REVERT: H 267 MET cc_start: 0.6632 (tmm) cc_final: 0.5145 (mmm) REVERT: H 321 LYS cc_start: 0.8371 (ttpt) cc_final: 0.7902 (mmtp) REVERT: H 327 LYS cc_start: 0.8861 (tppt) cc_final: 0.8646 (tttp) REVERT: H 461 GLU cc_start: 0.7787 (pm20) cc_final: 0.7305 (pm20) REVERT: H 514 MET cc_start: 0.8230 (mtp) cc_final: 0.7952 (mtp) REVERT: C 102 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6548 (mt-10) REVERT: C 267 MET cc_start: 0.7019 (tmm) cc_final: 0.6024 (mmp) REVERT: C 288 MET cc_start: 0.5807 (ptp) cc_final: 0.5601 (mtp) REVERT: C 321 LYS cc_start: 0.8350 (ttpt) cc_final: 0.7898 (mmtp) REVERT: C 367 GLU cc_start: 0.7788 (pp20) cc_final: 0.7471 (pp20) REVERT: I 5 ASP cc_start: 0.7631 (t0) cc_final: 0.7413 (t0) REVERT: I 193 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6946 (ttm) REVERT: I 267 MET cc_start: 0.6515 (tmm) cc_final: 0.5701 (mmp) REVERT: I 321 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7562 (mmtp) REVERT: I 351 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8286 (pp30) REVERT: I 461 GLU cc_start: 0.7877 (pm20) cc_final: 0.7350 (pm20) REVERT: I 514 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8147 (mtp) REVERT: D 267 MET cc_start: 0.5786 (tmm) cc_final: 0.5334 (mmp) REVERT: D 321 LYS cc_start: 0.8381 (ttpt) cc_final: 0.7711 (mmmt) REVERT: D 367 GLU cc_start: 0.7809 (pp20) cc_final: 0.7546 (pp20) REVERT: J 204 PHE cc_start: 0.7583 (m-80) cc_final: 0.7281 (m-80) REVERT: J 267 MET cc_start: 0.5762 (tmm) cc_final: 0.4790 (mmm) REVERT: J 321 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7429 (mmtp) REVERT: J 351 GLN cc_start: 0.8362 (tp40) cc_final: 0.8083 (tp40) REVERT: J 397 GLU cc_start: 0.7812 (tp30) cc_final: 0.7504 (tt0) REVERT: J 461 GLU cc_start: 0.7742 (pm20) cc_final: 0.7269 (pm20) REVERT: E 111 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7929 (mtt) REVERT: E 252 GLU cc_start: 0.6866 (tt0) cc_final: 0.6490 (tt0) REVERT: E 267 MET cc_start: 0.5944 (tmm) cc_final: 0.5372 (mmp) REVERT: E 321 LYS cc_start: 0.8460 (ttpt) cc_final: 0.7838 (mmtp) REVERT: E 447 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8003 (mtp) REVERT: E 461 GLU cc_start: 0.7607 (pm20) cc_final: 0.7339 (pm20) REVERT: E 494 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7986 (pp) REVERT: E 520 MET cc_start: 0.8327 (mtt) cc_final: 0.8106 (mtt) REVERT: K 267 MET cc_start: 0.6528 (tmm) cc_final: 0.5408 (mmp) REVERT: K 321 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7705 (mmtp) REVERT: K 461 GLU cc_start: 0.8221 (pm20) cc_final: 0.7857 (pm20) REVERT: F 160 LYS cc_start: 0.7744 (mtpp) cc_final: 0.7484 (ptmm) REVERT: F 321 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7738 (mmtp) REVERT: F 367 GLU cc_start: 0.7779 (pp20) cc_final: 0.7475 (pp20) REVERT: F 389 MET cc_start: 0.6548 (tmt) cc_final: 0.6323 (tmm) REVERT: L 69 MET cc_start: 0.6896 (mtm) cc_final: 0.6412 (mtp) REVERT: L 76 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7801 (tm-30) REVERT: L 262 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6241 (tp) REVERT: L 267 MET cc_start: 0.6105 (tmm) cc_final: 0.5016 (mmm) REVERT: L 288 MET cc_start: 0.6085 (OUTLIER) cc_final: 0.5296 (mpp) REVERT: L 321 LYS cc_start: 0.7984 (ttpt) cc_final: 0.7581 (mmtp) REVERT: L 351 GLN cc_start: 0.8392 (tp40) cc_final: 0.8088 (tp40) REVERT: L 389 MET cc_start: 0.6370 (OUTLIER) cc_final: 0.5985 (tmm) REVERT: L 461 GLU cc_start: 0.7771 (pm20) cc_final: 0.7382 (pm20) REVERT: G 61 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7201 (pt0) REVERT: G 160 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7629 (ptmm) REVERT: G 267 MET cc_start: 0.6251 (tmm) cc_final: 0.5375 (mmp) REVERT: G 277 LYS cc_start: 0.7951 (mttt) cc_final: 0.7579 (mmmm) REVERT: G 321 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7783 (mmmt) REVERT: G 322 ARG cc_start: 0.7680 (ttp80) cc_final: 0.7333 (mtp-110) REVERT: G 367 GLU cc_start: 0.7664 (pp20) cc_final: 0.7393 (pp20) REVERT: G 461 GLU cc_start: 0.7673 (pm20) cc_final: 0.7352 (pm20) REVERT: M 142 LYS cc_start: 0.8263 (tppt) cc_final: 0.7989 (ttpp) REVERT: M 245 LYS cc_start: 0.6790 (mttt) cc_final: 0.6552 (mtpt) REVERT: M 267 MET cc_start: 0.6878 (tmm) cc_final: 0.5741 (mmm) REVERT: M 307 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7521 (ptp) REVERT: M 321 LYS cc_start: 0.7983 (ttpt) cc_final: 0.7601 (mmtp) REVERT: M 351 GLN cc_start: 0.8449 (tp40) cc_final: 0.8141 (tp40) REVERT: M 461 GLU cc_start: 0.7599 (pm20) cc_final: 0.7154 (pm20) outliers start: 135 outliers final: 81 residues processed: 624 average time/residue: 0.6066 time to fit residues: 655.3029 Evaluate side-chains 590 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 494 time to evaluate : 5.842 ------------------------------------------------------------------------------- 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 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 160 LYS 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 146 GLN 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 169 VAL Chi-restraints excluded: chain C residue 213 VAL 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 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 201 SER 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 514 MET 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 193 MET 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 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 307 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 169 VAL 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 50 THR Chi-restraints excluded: chain L residue 262 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 M residue 61 GLU Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 307 MET 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 654 optimal weight: 9.9990 chunk 497 optimal weight: 10.0000 chunk 343 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 316 optimal weight: 0.0870 chunk 444 optimal weight: 10.0000 chunk 664 optimal weight: 5.9990 chunk 703 optimal weight: 6.9990 chunk 347 optimal weight: 7.9990 chunk 629 optimal weight: 6.9990 chunk 189 optimal weight: 20.0000 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN H 72 GLN C 112 ASN I 37 ASN I 319 GLN D 112 ASN J 37 ASN E 112 ASN K 37 ASN F 112 ASN M 37 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 54362 Z= 0.466 Angle : 0.619 7.900 73402 Z= 0.329 Chirality : 0.047 0.169 8932 Planarity : 0.004 0.036 9618 Dihedral : 4.337 34.182 7737 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.75 % Allowed : 13.19 % Favored : 83.06 % 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: 1.38 (0.10), residues: 7308 helix: 1.88 (0.08), residues: 4046 sheet: 0.50 (0.16), residues: 938 loop : -0.60 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 401 PHE 0.014 0.001 PHE L 8 TYR 0.014 0.002 TYR E 478 ARG 0.007 0.001 ARG K 421 *********************** 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 728 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 516 time to evaluate : 5.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.5722 (mmm) cc_final: 0.5056 (mmm) REVERT: A 321 LYS cc_start: 0.8350 (ttpt) cc_final: 0.7870 (mmtp) REVERT: A 322 ARG cc_start: 0.7553 (ttp80) cc_final: 0.7225 (ttm110) REVERT: A 367 GLU cc_start: 0.7771 (pp20) cc_final: 0.7471 (pp20) REVERT: A 461 GLU cc_start: 0.7758 (pm20) cc_final: 0.7376 (pm20) REVERT: A 514 MET cc_start: 0.8582 (mtp) cc_final: 0.8113 (mtp) REVERT: A 520 MET cc_start: 0.8892 (mtp) cc_final: 0.8649 (mtm) REVERT: N 16 MET cc_start: 0.7900 (mmm) cc_final: 0.7691 (mtt) REVERT: N 111 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7863 (mtt) REVERT: N 142 LYS cc_start: 0.8158 (tppt) cc_final: 0.7863 (ttpp) REVERT: N 201 SER cc_start: 0.8144 (t) cc_final: 0.7927 (m) REVERT: N 267 MET cc_start: 0.6347 (tmm) cc_final: 0.5790 (mmp) REVERT: N 321 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7538 (mmtp) REVERT: N 327 LYS cc_start: 0.8869 (tppt) cc_final: 0.8599 (tttm) REVERT: N 447 MET cc_start: 0.8098 (mtm) cc_final: 0.7860 (mtp) REVERT: N 461 GLU cc_start: 0.7931 (pm20) cc_final: 0.7691 (pm20) REVERT: N 494 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8001 (pp) REVERT: B 111 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7888 (mtt) REVERT: B 193 MET cc_start: 0.7184 (tpt) cc_final: 0.6905 (ttm) REVERT: B 204 PHE cc_start: 0.7836 (m-80) cc_final: 0.7623 (m-80) REVERT: B 267 MET cc_start: 0.6405 (tmm) cc_final: 0.5572 (mmp) REVERT: B 321 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7665 (mmtp) REVERT: B 367 GLU cc_start: 0.7719 (pp20) cc_final: 0.7360 (pp20) REVERT: B 461 GLU cc_start: 0.7946 (pm20) cc_final: 0.7703 (pm20) REVERT: B 494 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7531 (pp) REVERT: H 184 GLN cc_start: 0.8519 (mp10) cc_final: 0.8292 (mm-40) REVERT: H 262 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6202 (tp) REVERT: H 267 MET cc_start: 0.6685 (tmm) cc_final: 0.5334 (mmp) REVERT: H 321 LYS cc_start: 0.8348 (ttpt) cc_final: 0.7902 (mmpt) REVERT: H 389 MET cc_start: 0.6472 (tmm) cc_final: 0.6100 (tmm) REVERT: H 461 GLU cc_start: 0.7732 (pm20) cc_final: 0.7479 (pm20) REVERT: H 514 MET cc_start: 0.8700 (mtp) cc_final: 0.8410 (mtm) REVERT: C 102 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6669 (mt-10) REVERT: C 267 MET cc_start: 0.6985 (tmm) cc_final: 0.6041 (mmp) REVERT: C 321 LYS cc_start: 0.8331 (ttpt) cc_final: 0.7932 (mmtp) REVERT: C 367 GLU cc_start: 0.7716 (pp20) cc_final: 0.7392 (pp20) REVERT: C 461 GLU cc_start: 0.7829 (pm20) cc_final: 0.7525 (pm20) REVERT: C 514 MET cc_start: 0.8728 (mtp) cc_final: 0.8368 (mtm) REVERT: I 193 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.7030 (ttm) REVERT: I 267 MET cc_start: 0.6541 (tmm) cc_final: 0.5784 (mmp) REVERT: I 321 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7556 (mmtt) REVERT: I 461 GLU cc_start: 0.7869 (pm20) cc_final: 0.7648 (pm20) REVERT: I 494 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7672 (pp) REVERT: D 193 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7216 (ttm) REVERT: D 262 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6287 (tm) REVERT: D 267 MET cc_start: 0.6778 (tmm) cc_final: 0.5772 (mmm) REVERT: D 321 LYS cc_start: 0.8237 (ttpt) cc_final: 0.7578 (mmmt) REVERT: D 367 GLU cc_start: 0.7977 (pp20) cc_final: 0.7693 (pp20) REVERT: J 16 MET cc_start: 0.8188 (mtp) cc_final: 0.7974 (mtm) REVERT: J 267 MET cc_start: 0.5962 (tmm) cc_final: 0.5068 (mmm) REVERT: J 321 LYS cc_start: 0.7911 (ttpt) cc_final: 0.7525 (mmtp) REVERT: J 351 GLN cc_start: 0.8411 (tp40) cc_final: 0.8090 (tp40) REVERT: J 397 GLU cc_start: 0.7849 (tp30) cc_final: 0.7512 (tt0) REVERT: J 461 GLU cc_start: 0.7586 (pm20) cc_final: 0.7223 (pm20) REVERT: E 111 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7933 (mtt) REVERT: E 166 MET cc_start: 0.6968 (mtt) cc_final: 0.6573 (mtt) REVERT: E 267 MET cc_start: 0.6612 (tmm) cc_final: 0.5893 (mmp) REVERT: E 321 LYS cc_start: 0.8422 (ttpt) cc_final: 0.7848 (mmtt) REVERT: E 367 GLU cc_start: 0.7888 (pp20) cc_final: 0.7595 (pp20) REVERT: E 447 MET cc_start: 0.8248 (mtm) cc_final: 0.7997 (mtp) REVERT: E 461 GLU cc_start: 0.7697 (pm20) cc_final: 0.7446 (pm20) REVERT: E 473 ASP cc_start: 0.8059 (t70) cc_final: 0.7828 (t0) REVERT: E 520 MET cc_start: 0.8618 (mtt) cc_final: 0.8408 (mtt) REVERT: K 69 MET cc_start: 0.6836 (mtp) cc_final: 0.6628 (mtp) REVERT: K 142 LYS cc_start: 0.8004 (tppt) cc_final: 0.7678 (ttpp) REVERT: K 267 MET cc_start: 0.6547 (tmm) cc_final: 0.5432 (mmp) REVERT: K 321 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7764 (mmtp) REVERT: K 351 GLN cc_start: 0.8450 (tp40) cc_final: 0.8202 (tp40) REVERT: K 397 GLU cc_start: 0.7736 (tp30) cc_final: 0.7347 (tt0) REVERT: K 461 GLU cc_start: 0.8300 (pm20) cc_final: 0.7940 (pm20) REVERT: F 61 GLU cc_start: 0.7288 (pt0) cc_final: 0.6948 (pt0) REVERT: F 111 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7828 (mtp) REVERT: F 160 LYS cc_start: 0.7838 (mtpp) cc_final: 0.7540 (ptmm) REVERT: F 321 LYS cc_start: 0.8304 (ttpt) cc_final: 0.7808 (mmtp) REVERT: F 367 GLU cc_start: 0.7728 (pp20) cc_final: 0.7434 (pp20) REVERT: F 389 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.6335 (tmm) REVERT: L 69 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6794 (mtp) REVERT: L 76 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7745 (tm-30) REVERT: L 262 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6150 (tp) REVERT: L 267 MET cc_start: 0.6252 (tmm) cc_final: 0.5267 (mmm) REVERT: L 321 LYS cc_start: 0.8018 (ttpt) cc_final: 0.7611 (mmtp) REVERT: L 351 GLN cc_start: 0.8367 (tp40) cc_final: 0.8007 (tp40) REVERT: L 389 MET cc_start: 0.6381 (OUTLIER) cc_final: 0.6017 (tmm) REVERT: L 461 GLU cc_start: 0.7557 (pm20) cc_final: 0.7208 (pm20) REVERT: G 61 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7157 (pt0) REVERT: G 160 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7656 (ptmm) REVERT: G 166 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6326 (mtt) REVERT: G 262 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6418 (tm) REVERT: G 267 MET cc_start: 0.6607 (tmm) cc_final: 0.5547 (mmp) REVERT: G 321 LYS cc_start: 0.8265 (ttpt) cc_final: 0.7782 (mmtt) REVERT: G 322 ARG cc_start: 0.7747 (ttp80) cc_final: 0.7466 (mtp-110) REVERT: G 367 GLU cc_start: 0.7721 (pp20) cc_final: 0.7417 (pp20) REVERT: G 461 GLU cc_start: 0.7687 (pm20) cc_final: 0.7378 (pm20) REVERT: M 13 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6449 (mpt-90) REVERT: M 142 LYS cc_start: 0.8284 (tppt) cc_final: 0.8015 (ttpp) REVERT: M 267 MET cc_start: 0.6915 (tmm) cc_final: 0.5923 (mmt) REVERT: M 307 MET cc_start: 0.7467 (mtm) cc_final: 0.7123 (ptp) REVERT: M 321 LYS cc_start: 0.8033 (ttpt) cc_final: 0.7589 (mmtt) REVERT: M 461 GLU cc_start: 0.7538 (pm20) cc_final: 0.7322 (pm20) outliers start: 212 outliers final: 147 residues processed: 684 average time/residue: 0.6005 time to fit residues: 715.4978 Evaluate side-chains 645 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 478 time to evaluate : 5.935 ------------------------------------------------------------------------------- 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 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 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 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 61 GLU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 160 LYS 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 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 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 228 SER Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 262 LEU 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 11 ASP 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 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 330 THR 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 I residue 514 MET 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 193 MET Chi-restraints excluded: chain D residue 205 ILE 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 262 LEU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 314 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 43 SER 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 261 THR 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 517 THR 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 187 LEU 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 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 442 VAL 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 111 MET Chi-restraints excluded: chain F residue 124 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 331 THR Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 389 MET 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 389 MET Chi-restraints excluded: chain L residue 517 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 213 VAL Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 307 MET 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 234 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 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 586 optimal weight: 4.9990 chunk 399 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 523 optimal weight: 2.9990 chunk 290 optimal weight: 6.9990 chunk 600 optimal weight: 10.0000 chunk 486 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 359 optimal weight: 4.9990 chunk 631 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 348 GLN L 319 GLN G 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 54362 Z= 0.237 Angle : 0.508 10.937 73402 Z= 0.269 Chirality : 0.042 0.152 8932 Planarity : 0.003 0.032 9618 Dihedral : 4.133 32.448 7736 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.85 % Allowed : 15.08 % Favored : 82.07 % 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: 1.63 (0.10), residues: 7308 helix: 2.14 (0.08), residues: 4046 sheet: 0.51 (0.16), residues: 938 loop : -0.56 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS N 401 PHE 0.008 0.001 PHE B 195 TYR 0.010 0.001 TYR I 478 ARG 0.004 0.000 ARG C 421 *********************** 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 671 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 510 time to evaluate : 5.977 Fit side-chains revert: symmetry clash REVERT: A 267 MET cc_start: 0.5677 (mmm) cc_final: 0.5012 (mmm) REVERT: A 321 LYS cc_start: 0.8355 (ttpt) cc_final: 0.7869 (mmtp) REVERT: A 322 ARG cc_start: 0.7555 (ttp80) cc_final: 0.7183 (ttm110) REVERT: A 367 GLU cc_start: 0.7741 (pp20) cc_final: 0.7428 (pp20) REVERT: A 461 GLU cc_start: 0.7737 (pm20) cc_final: 0.7361 (pm20) REVERT: A 520 MET cc_start: 0.8828 (mtp) cc_final: 0.8602 (mtm) REVERT: N 16 MET cc_start: 0.7886 (mmm) cc_final: 0.7584 (mtt) REVERT: N 61 GLU cc_start: 0.6919 (tt0) cc_final: 0.6712 (tt0) REVERT: N 69 MET cc_start: 0.6782 (mtm) cc_final: 0.6392 (mtp) REVERT: N 111 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7747 (mtt) REVERT: N 201 SER cc_start: 0.8089 (t) cc_final: 0.7842 (m) REVERT: N 267 MET cc_start: 0.6175 (tmm) cc_final: 0.5730 (mmp) REVERT: N 321 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7529 (mmtp) REVERT: N 327 LYS cc_start: 0.8860 (tppt) cc_final: 0.8562 (tttm) REVERT: N 461 GLU cc_start: 0.7867 (pm20) cc_final: 0.7617 (pm20) REVERT: N 494 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8004 (pp) REVERT: N 514 MET cc_start: 0.8473 (ttm) cc_final: 0.8238 (mtp) REVERT: B 193 MET cc_start: 0.7124 (tpt) cc_final: 0.6856 (ttm) REVERT: B 267 MET cc_start: 0.6813 (tmm) cc_final: 0.5475 (mmp) REVERT: B 321 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7622 (mmtp) REVERT: B 367 GLU cc_start: 0.7703 (pp20) cc_final: 0.7325 (pp20) REVERT: B 461 GLU cc_start: 0.7894 (pm20) cc_final: 0.7669 (pm20) REVERT: B 494 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7473 (pp) REVERT: H 267 MET cc_start: 0.6540 (tmm) cc_final: 0.5221 (mmm) REVERT: H 321 LYS cc_start: 0.8357 (ttpt) cc_final: 0.7870 (mmtp) REVERT: H 461 GLU cc_start: 0.7721 (pm20) cc_final: 0.7475 (pm20) REVERT: H 494 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7805 (pp) REVERT: C 102 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6643 (mt-10) REVERT: C 262 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6521 (tm) REVERT: C 267 MET cc_start: 0.6951 (tmm) cc_final: 0.6006 (mmp) REVERT: C 321 LYS cc_start: 0.8338 (ttpt) cc_final: 0.7927 (mmtt) REVERT: C 367 GLU cc_start: 0.7662 (pp20) cc_final: 0.7317 (pp20) REVERT: C 461 GLU cc_start: 0.7834 (pm20) cc_final: 0.7447 (pm20) REVERT: C 514 MET cc_start: 0.8727 (mtp) cc_final: 0.8445 (mtm) REVERT: I 193 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6932 (ttm) REVERT: I 267 MET cc_start: 0.6477 (tmm) cc_final: 0.5573 (mmp) REVERT: I 321 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7526 (mmtt) REVERT: I 461 GLU cc_start: 0.7754 (pm20) cc_final: 0.7522 (pm20) REVERT: I 494 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7589 (pp) REVERT: D 193 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7158 (ttm) REVERT: D 232 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6603 (pm20) REVERT: D 262 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6248 (tm) REVERT: D 267 MET cc_start: 0.6940 (tmm) cc_final: 0.5941 (mmm) REVERT: D 321 LYS cc_start: 0.8253 (ttpt) cc_final: 0.7582 (mmmt) REVERT: D 367 GLU cc_start: 0.7955 (pp20) cc_final: 0.7653 (pp20) REVERT: J 16 MET cc_start: 0.8117 (mtp) cc_final: 0.7826 (mtm) REVERT: J 267 MET cc_start: 0.5894 (tmm) cc_final: 0.4984 (mmm) REVERT: J 321 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7597 (mmtp) REVERT: J 351 GLN cc_start: 0.8390 (tp40) cc_final: 0.8104 (tp40) REVERT: J 397 GLU cc_start: 0.7795 (tp30) cc_final: 0.7497 (tt0) REVERT: J 461 GLU cc_start: 0.7538 (pm20) cc_final: 0.7173 (pm20) REVERT: E 102 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6688 (mp0) REVERT: E 111 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7922 (mtt) REVERT: E 267 MET cc_start: 0.6561 (tmm) cc_final: 0.5853 (mmp) REVERT: E 321 LYS cc_start: 0.8408 (ttpt) cc_final: 0.7815 (mmtp) REVERT: E 351 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8061 (mm110) REVERT: E 367 GLU cc_start: 0.7854 (pp20) cc_final: 0.7554 (pp20) REVERT: E 447 MET cc_start: 0.8264 (mtm) cc_final: 0.8024 (mtp) REVERT: E 461 GLU cc_start: 0.7628 (pm20) cc_final: 0.7384 (pm20) REVERT: E 473 ASP cc_start: 0.8152 (t70) cc_final: 0.7852 (t0) REVERT: E 494 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7976 (pp) REVERT: E 520 MET cc_start: 0.8614 (mtt) cc_final: 0.8399 (mtt) REVERT: K 69 MET cc_start: 0.6790 (mtp) cc_final: 0.6492 (mtp) REVERT: K 267 MET cc_start: 0.6509 (tmm) cc_final: 0.5496 (mmp) REVERT: K 321 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7740 (mmtp) REVERT: K 397 GLU cc_start: 0.7589 (tp30) cc_final: 0.7314 (tt0) REVERT: K 461 GLU cc_start: 0.8247 (pm20) cc_final: 0.7848 (pm20) REVERT: F 61 GLU cc_start: 0.7361 (pt0) cc_final: 0.7030 (pt0) REVERT: F 102 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6767 (mt-10) REVERT: F 111 MET cc_start: 0.8750 (mtp) cc_final: 0.8325 (mtt) REVERT: F 160 LYS cc_start: 0.7832 (mtpp) cc_final: 0.7549 (ptmm) REVERT: F 321 LYS cc_start: 0.8290 (ttpt) cc_final: 0.7746 (mmtt) REVERT: F 367 GLU cc_start: 0.7698 (pp20) cc_final: 0.7393 (pp20) REVERT: F 389 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.6392 (tmm) REVERT: F 520 MET cc_start: 0.8698 (mtp) cc_final: 0.8486 (mtt) REVERT: L 69 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6737 (mtp) REVERT: L 76 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7700 (tm-30) REVERT: L 267 MET cc_start: 0.6116 (tmm) cc_final: 0.5192 (mmm) REVERT: L 321 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7680 (mmtp) REVERT: L 351 GLN cc_start: 0.8423 (tp40) cc_final: 0.8111 (tp40) REVERT: L 389 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.5956 (tmm) REVERT: L 461 GLU cc_start: 0.7452 (pm20) cc_final: 0.7119 (pm20) REVERT: G 61 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7163 (pt0) REVERT: G 76 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7821 (tm-30) REVERT: G 160 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7619 (ptmm) REVERT: G 166 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.6299 (mtt) REVERT: G 262 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6388 (tm) REVERT: G 267 MET cc_start: 0.6529 (tmm) cc_final: 0.5502 (mmp) REVERT: G 321 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7777 (mmmt) REVERT: G 367 GLU cc_start: 0.7663 (pp20) cc_final: 0.7349 (pp20) REVERT: G 461 GLU cc_start: 0.7725 (pm20) cc_final: 0.7439 (pm20) REVERT: M 13 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.6179 (mpt-90) REVERT: M 142 LYS cc_start: 0.8295 (tppt) cc_final: 0.8043 (ttpp) REVERT: M 267 MET cc_start: 0.6719 (tmm) cc_final: 0.5732 (mmm) REVERT: M 307 MET cc_start: 0.7586 (mtm) cc_final: 0.7227 (ptp) REVERT: M 321 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7562 (mmtt) REVERT: M 461 GLU cc_start: 0.7402 (pm20) cc_final: 0.7109 (pm20) outliers start: 161 outliers final: 106 residues processed: 637 average time/residue: 0.5896 time to fit residues: 652.1129 Evaluate side-chains 611 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 484 time to evaluate : 6.037 ------------------------------------------------------------------------------- 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 307 MET 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 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 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 160 LYS 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 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 240 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 494 LEU 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 213 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 LEU 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 348 GLN 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 D residue 48 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain J residue 43 SER 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 388 GLU 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 351 GLN 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 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 351 GLN Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 389 MET 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 389 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 213 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 307 MET 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 442 VAL Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 489 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 10.0000 chunk 633 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 413 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 704 optimal weight: 0.9980 chunk 584 optimal weight: 3.9990 chunk 326 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 369 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN C 319 GLN M 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 54362 Z= 0.237 Angle : 0.503 9.704 73402 Z= 0.266 Chirality : 0.042 0.151 8932 Planarity : 0.003 0.032 9618 Dihedral : 4.067 31.803 7734 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.27 % Allowed : 15.15 % Favored : 81.58 % 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: 1.66 (0.10), residues: 7308 helix: 2.18 (0.08), residues: 4046 sheet: 0.48 (0.17), residues: 938 loop : -0.56 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS N 401 PHE 0.008 0.001 PHE L 8 TYR 0.011 0.001 TYR A 476 ARG 0.004 0.000 ARG I 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 685 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 500 time to evaluate : 5.877 Fit side-chains revert: symmetry clash REVERT: A 267 MET cc_start: 0.5761 (mmm) cc_final: 0.5077 (mmm) REVERT: A 321 LYS cc_start: 0.8354 (ttpt) cc_final: 0.7861 (mmtp) REVERT: A 367 GLU cc_start: 0.7722 (pp20) cc_final: 0.7409 (pp20) REVERT: A 461 GLU cc_start: 0.7729 (pm20) cc_final: 0.7347 (pm20) REVERT: N 16 MET cc_start: 0.7871 (mmm) cc_final: 0.7602 (mtt) REVERT: N 61 GLU cc_start: 0.6921 (tt0) cc_final: 0.6688 (tt0) REVERT: N 69 MET cc_start: 0.6764 (mtm) cc_final: 0.6488 (mtp) REVERT: N 111 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7747 (mtt) REVERT: N 142 LYS cc_start: 0.8103 (tppt) cc_final: 0.7809 (ttpp) REVERT: N 201 SER cc_start: 0.8073 (t) cc_final: 0.7842 (m) REVERT: N 267 MET cc_start: 0.6709 (tmm) cc_final: 0.5756 (mmp) REVERT: N 321 LYS cc_start: 0.8101 (ttpt) cc_final: 0.7532 (mmtp) REVERT: N 327 LYS cc_start: 0.8856 (tppt) cc_final: 0.8554 (tttm) REVERT: N 461 GLU cc_start: 0.7783 (pm20) cc_final: 0.7533 (pm20) REVERT: N 494 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7961 (pp) REVERT: N 514 MET cc_start: 0.8465 (ttm) cc_final: 0.8232 (mtp) REVERT: B 193 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6854 (ttm) REVERT: B 204 PHE cc_start: 0.7861 (m-80) cc_final: 0.7561 (m-80) REVERT: B 267 MET cc_start: 0.6808 (tmm) cc_final: 0.5543 (mmp) REVERT: B 321 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7671 (mmtp) REVERT: B 367 GLU cc_start: 0.7672 (pp20) cc_final: 0.7275 (pp20) REVERT: B 461 GLU cc_start: 0.7898 (pm20) cc_final: 0.7660 (pm20) REVERT: B 494 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7448 (pp) REVERT: H 267 MET cc_start: 0.6510 (tmm) cc_final: 0.5265 (mmp) REVERT: H 321 LYS cc_start: 0.8368 (ttpt) cc_final: 0.7869 (mmtp) REVERT: H 461 GLU cc_start: 0.7797 (pm20) cc_final: 0.7484 (pm20) REVERT: H 494 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7802 (pp) REVERT: C 102 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6605 (mt-10) REVERT: C 262 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6541 (tm) REVERT: C 267 MET cc_start: 0.6913 (tmm) cc_final: 0.5906 (mmp) REVERT: C 321 LYS cc_start: 0.8323 (ttpt) cc_final: 0.7983 (mmtt) REVERT: C 322 ARG cc_start: 0.8349 (mtp-110) cc_final: 0.7921 (ttm110) REVERT: C 367 GLU cc_start: 0.7653 (pp20) cc_final: 0.7289 (pp20) REVERT: C 461 GLU cc_start: 0.7731 (pm20) cc_final: 0.7377 (pm20) REVERT: C 488 MET cc_start: 0.7634 (tpt) cc_final: 0.7368 (mmt) REVERT: I 193 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.7014 (ttm) REVERT: I 267 MET cc_start: 0.6556 (tmm) cc_final: 0.5609 (mmp) REVERT: I 321 LYS cc_start: 0.7998 (ttpt) cc_final: 0.7533 (mmtt) REVERT: I 461 GLU cc_start: 0.7716 (pm20) cc_final: 0.7485 (pm20) REVERT: I 494 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7585 (pp) REVERT: D 193 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7131 (ttm) REVERT: D 262 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6094 (tm) REVERT: D 267 MET cc_start: 0.6984 (tmm) cc_final: 0.5889 (mmm) REVERT: D 321 LYS cc_start: 0.8256 (ttpt) cc_final: 0.7593 (mmmt) REVERT: D 367 GLU cc_start: 0.7940 (pp20) cc_final: 0.7626 (pp20) REVERT: J 16 MET cc_start: 0.8121 (mtp) cc_final: 0.7794 (mtm) REVERT: J 204 PHE cc_start: 0.7581 (m-80) cc_final: 0.7314 (m-80) REVERT: J 267 MET cc_start: 0.5840 (tmm) cc_final: 0.4981 (mmm) REVERT: J 321 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7600 (mmtp) REVERT: J 351 GLN cc_start: 0.8456 (tp40) cc_final: 0.8158 (tp40) REVERT: J 397 GLU cc_start: 0.7811 (tp30) cc_final: 0.7521 (tt0) REVERT: J 461 GLU cc_start: 0.7331 (pm20) cc_final: 0.6934 (pm20) REVERT: E 102 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6666 (mp0) REVERT: E 111 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7918 (mtt) REVERT: E 262 LEU cc_start: 0.5368 (OUTLIER) cc_final: 0.4899 (pp) REVERT: E 267 MET cc_start: 0.6850 (tmm) cc_final: 0.5859 (mmp) REVERT: E 321 LYS cc_start: 0.8412 (ttpt) cc_final: 0.7821 (mmtp) REVERT: E 351 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8086 (mm110) REVERT: E 367 GLU cc_start: 0.7847 (pp20) cc_final: 0.7524 (pp20) REVERT: E 447 MET cc_start: 0.8184 (mtm) cc_final: 0.7923 (mtp) REVERT: E 461 GLU cc_start: 0.7613 (pm20) cc_final: 0.7369 (pm20) REVERT: E 473 ASP cc_start: 0.8036 (t70) cc_final: 0.7835 (t0) REVERT: E 494 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7965 (pp) REVERT: E 520 MET cc_start: 0.8562 (mtt) cc_final: 0.8361 (mtt) REVERT: K 267 MET cc_start: 0.6471 (tmm) cc_final: 0.5504 (mmp) REVERT: K 321 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7751 (mmtp) REVERT: K 397 GLU cc_start: 0.7587 (tp30) cc_final: 0.7316 (tt0) REVERT: K 461 GLU cc_start: 0.8212 (pm20) cc_final: 0.7791 (pm20) REVERT: F 61 GLU cc_start: 0.7372 (pt0) cc_final: 0.7045 (pt0) REVERT: F 111 MET cc_start: 0.8738 (mtp) cc_final: 0.8303 (mtt) REVERT: F 160 LYS cc_start: 0.7829 (mtpp) cc_final: 0.7545 (ptmm) REVERT: F 321 LYS cc_start: 0.8323 (ttpt) cc_final: 0.7783 (mmtt) REVERT: F 367 GLU cc_start: 0.7693 (pp20) cc_final: 0.7376 (pp20) REVERT: F 389 MET cc_start: 0.6611 (OUTLIER) cc_final: 0.6405 (tmm) REVERT: F 520 MET cc_start: 0.8649 (mtp) cc_final: 0.8383 (mtt) REVERT: L 69 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6574 (mtp) REVERT: L 76 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7663 (tm-30) REVERT: L 262 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6033 (tp) REVERT: L 267 MET cc_start: 0.5967 (tmm) cc_final: 0.5035 (mmm) REVERT: L 321 LYS cc_start: 0.8058 (ttpt) cc_final: 0.7638 (mmtp) REVERT: L 351 GLN cc_start: 0.8401 (tp40) cc_final: 0.8083 (tp40) REVERT: L 389 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.6184 (tmm) REVERT: L 461 GLU cc_start: 0.7424 (pm20) cc_final: 0.7216 (pm20) REVERT: G 61 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7166 (pt0) REVERT: G 160 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7631 (ptmm) REVERT: G 166 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6294 (mtt) REVERT: G 262 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6384 (tm) REVERT: G 267 MET cc_start: 0.6594 (tmm) cc_final: 0.5734 (mmp) REVERT: G 321 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7852 (mmpt) REVERT: G 322 ARG cc_start: 0.7979 (mtp-110) cc_final: 0.7670 (ttm110) REVERT: G 367 GLU cc_start: 0.7658 (pp20) cc_final: 0.7336 (pp20) REVERT: G 461 GLU cc_start: 0.7713 (pm20) cc_final: 0.7233 (pm20) REVERT: M 13 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6267 (mpt-90) REVERT: M 142 LYS cc_start: 0.8290 (tppt) cc_final: 0.8042 (ttpp) REVERT: M 267 MET cc_start: 0.6625 (tmm) cc_final: 0.5813 (mmm) REVERT: M 307 MET cc_start: 0.7570 (mtm) cc_final: 0.7215 (ptp) REVERT: M 321 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7556 (mmtt) REVERT: M 461 GLU cc_start: 0.7295 (pm20) cc_final: 0.7039 (pm20) outliers start: 185 outliers final: 134 residues processed: 651 average time/residue: 0.5931 time to fit residues: 671.8389 Evaluate side-chains 638 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 481 time to evaluate : 6.144 ------------------------------------------------------------------------------- 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 213 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 MET 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 234 LEU Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 240 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 124 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 193 MET 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 499 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 187 LEU 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 494 LEU 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 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 261 THR Chi-restraints excluded: chain C residue 262 LEU 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 517 THR Chi-restraints excluded: chain I residue 11 ASP 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 213 VAL 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 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 61 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 300 VAL 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 43 SER 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 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 262 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 307 MET Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 124 VAL 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 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 389 MET 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 389 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 124 VAL 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 213 VAL Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 262 LEU 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 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 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 499 VAL 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 679 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 401 optimal weight: 3.9990 chunk 514 optimal weight: 0.9990 chunk 398 optimal weight: 0.8980 chunk 592 optimal weight: 6.9990 chunk 393 optimal weight: 5.9990 chunk 701 optimal weight: 8.9990 chunk 439 optimal weight: 4.9990 chunk 427 optimal weight: 1.9990 chunk 323 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2285 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= 0.167 Angle : 0.478 9.060 73402 Z= 0.252 Chirality : 0.040 0.147 8932 Planarity : 0.003 0.030 9618 Dihedral : 3.941 29.763 7733 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.49 % Allowed : 16.07 % Favored : 81.44 % 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: 1.82 (0.10), residues: 7308 helix: 2.33 (0.08), residues: 4046 sheet: 0.54 (0.17), residues: 938 loop : -0.53 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.007 0.001 PHE N 195 TYR 0.011 0.001 TYR A 476 ARG 0.003 0.000 ARG L 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 662 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 521 time to evaluate : 5.987 Fit side-chains revert: symmetry clash REVERT: A 267 MET cc_start: 0.5936 (mmm) cc_final: 0.5211 (mmm) REVERT: A 307 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.6774 (ptp) REVERT: A 321 LYS cc_start: 0.8383 (ttpt) cc_final: 0.7876 (mmtp) REVERT: A 367 GLU cc_start: 0.7737 (pp20) cc_final: 0.7431 (pp20) REVERT: A 461 GLU cc_start: 0.7697 (pm20) cc_final: 0.7320 (pm20) REVERT: N 16 MET cc_start: 0.7914 (mmm) cc_final: 0.7623 (mtt) REVERT: N 61 GLU cc_start: 0.6897 (tt0) cc_final: 0.6667 (tt0) REVERT: N 111 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7719 (mtt) REVERT: N 201 SER cc_start: 0.8077 (t) cc_final: 0.7843 (m) REVERT: N 267 MET cc_start: 0.6665 (tmm) cc_final: 0.5718 (mmp) REVERT: N 321 LYS cc_start: 0.8102 (ttpt) cc_final: 0.7502 (mmtp) REVERT: N 327 LYS cc_start: 0.8850 (tppt) cc_final: 0.8503 (tttm) REVERT: N 397 GLU cc_start: 0.7702 (tp30) cc_final: 0.7416 (tt0) REVERT: N 461 GLU cc_start: 0.7656 (pm20) cc_final: 0.7403 (pm20) REVERT: N 494 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8004 (pp) REVERT: N 514 MET cc_start: 0.8449 (ttm) cc_final: 0.8239 (mtp) REVERT: B 193 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6773 (ttm) REVERT: B 204 PHE cc_start: 0.7899 (m-80) cc_final: 0.7635 (m-80) REVERT: B 267 MET cc_start: 0.6821 (tmm) cc_final: 0.5597 (mmp) REVERT: B 321 LYS cc_start: 0.8209 (ttpt) cc_final: 0.7695 (mmtp) REVERT: B 367 GLU cc_start: 0.7647 (pp20) cc_final: 0.7287 (pp20) REVERT: B 461 GLU cc_start: 0.7817 (pm20) cc_final: 0.7597 (pm20) REVERT: B 494 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7402 (pp) REVERT: H 267 MET cc_start: 0.6533 (tmm) cc_final: 0.5373 (mmp) REVERT: H 321 LYS cc_start: 0.8393 (ttpt) cc_final: 0.7891 (mmtp) REVERT: H 461 GLU cc_start: 0.7760 (pm20) cc_final: 0.7242 (pm20) REVERT: H 494 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7899 (pp) REVERT: C 102 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6518 (mt-10) REVERT: C 262 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6534 (tm) REVERT: C 267 MET cc_start: 0.7102 (tmm) cc_final: 0.6116 (mmp) REVERT: C 321 LYS cc_start: 0.8316 (ttpt) cc_final: 0.8004 (mmtt) REVERT: C 322 ARG cc_start: 0.8372 (mtp-110) cc_final: 0.7943 (ttm110) REVERT: C 367 GLU cc_start: 0.7627 (pp20) cc_final: 0.7259 (pp20) REVERT: C 461 GLU cc_start: 0.7725 (pm20) cc_final: 0.7350 (pm20) REVERT: I 193 MET cc_start: 0.7287 (tpt) cc_final: 0.6987 (ttm) REVERT: I 267 MET cc_start: 0.6496 (tmm) cc_final: 0.5608 (mmp) REVERT: I 321 LYS cc_start: 0.8007 (ttpt) cc_final: 0.7566 (mmtp) REVERT: I 461 GLU cc_start: 0.7656 (pm20) cc_final: 0.7430 (pm20) REVERT: I 494 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7552 (pp) REVERT: D 262 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6357 (tm) REVERT: D 267 MET cc_start: 0.6920 (tmm) cc_final: 0.5865 (mmp) REVERT: D 321 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7586 (mmmt) REVERT: D 367 GLU cc_start: 0.7882 (pp20) cc_final: 0.7554 (pp20) REVERT: D 461 GLU cc_start: 0.7650 (pm20) cc_final: 0.7266 (pm20) REVERT: D 491 MET cc_start: 0.7409 (ptp) cc_final: 0.7181 (ptm) REVERT: J 16 MET cc_start: 0.8140 (mtp) cc_final: 0.7829 (mtm) REVERT: J 204 PHE cc_start: 0.7645 (m-80) cc_final: 0.7392 (m-80) REVERT: J 267 MET cc_start: 0.5937 (tmm) cc_final: 0.5080 (mmm) REVERT: J 321 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7668 (mmtp) REVERT: J 397 GLU cc_start: 0.7794 (tp30) cc_final: 0.7519 (tt0) REVERT: J 461 GLU cc_start: 0.7317 (pm20) cc_final: 0.6891 (pm20) REVERT: E 61 GLU cc_start: 0.7758 (pp20) cc_final: 0.7426 (pp20) REVERT: E 102 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6703 (mp0) REVERT: E 267 MET cc_start: 0.6683 (tmm) cc_final: 0.5785 (mmp) REVERT: E 321 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7823 (mmtp) REVERT: E 367 GLU cc_start: 0.7846 (pp20) cc_final: 0.7516 (pp20) REVERT: E 447 MET cc_start: 0.8081 (mtm) cc_final: 0.7847 (mtp) REVERT: E 461 GLU cc_start: 0.7576 (pm20) cc_final: 0.7206 (pm20) REVERT: E 473 ASP cc_start: 0.8035 (t70) cc_final: 0.7829 (t0) REVERT: E 494 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7904 (pp) REVERT: K 267 MET cc_start: 0.6325 (tmm) cc_final: 0.5420 (mmp) REVERT: K 321 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7736 (mmtp) REVERT: K 397 GLU cc_start: 0.7567 (tp30) cc_final: 0.7309 (tt0) REVERT: K 461 GLU cc_start: 0.8098 (pm20) cc_final: 0.7634 (pm20) REVERT: F 111 MET cc_start: 0.8767 (mtp) cc_final: 0.8292 (mtt) REVERT: F 160 LYS cc_start: 0.7906 (mtpp) cc_final: 0.7627 (ptmm) REVERT: F 321 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7783 (mmtt) REVERT: F 367 GLU cc_start: 0.7657 (pp20) cc_final: 0.7352 (pp20) REVERT: F 461 GLU cc_start: 0.7617 (pm20) cc_final: 0.7215 (pm20) REVERT: F 520 MET cc_start: 0.8644 (mtp) cc_final: 0.8342 (mtt) REVERT: L 69 MET cc_start: 0.6918 (mtm) cc_final: 0.6425 (mtp) REVERT: L 76 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7601 (tm-30) REVERT: L 262 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6198 (tp) REVERT: L 267 MET cc_start: 0.5894 (tmm) cc_final: 0.5188 (mmm) REVERT: L 321 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7645 (mmtp) REVERT: L 351 GLN cc_start: 0.8423 (tp40) cc_final: 0.8112 (tp40) REVERT: L 389 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.5944 (tmm) REVERT: L 461 GLU cc_start: 0.7283 (pm20) cc_final: 0.7076 (pm20) REVERT: G 61 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7168 (pt0) REVERT: G 76 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7858 (tm-30) REVERT: G 262 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6332 (tm) REVERT: G 267 MET cc_start: 0.6579 (tmm) cc_final: 0.5747 (mmp) REVERT: G 321 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7826 (mmpt) REVERT: G 322 ARG cc_start: 0.8120 (mtp-110) cc_final: 0.7853 (ttm110) REVERT: G 367 GLU cc_start: 0.7655 (pp20) cc_final: 0.7327 (pp20) REVERT: G 461 GLU cc_start: 0.7666 (pm20) cc_final: 0.7203 (pm20) REVERT: M 13 ARG cc_start: 0.6517 (OUTLIER) cc_final: 0.6114 (mpt-90) REVERT: M 142 LYS cc_start: 0.8273 (tppt) cc_final: 0.8028 (ttpp) REVERT: M 267 MET cc_start: 0.6501 (tmm) cc_final: 0.5691 (mmm) REVERT: M 307 MET cc_start: 0.7560 (mtm) cc_final: 0.7175 (ptp) REVERT: M 321 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7597 (mmtp) REVERT: M 461 GLU cc_start: 0.7322 (pm20) cc_final: 0.7060 (pm20) outliers start: 141 outliers final: 108 residues processed: 641 average time/residue: 0.5773 time to fit residues: 645.0904 Evaluate side-chains 605 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 482 time to evaluate : 6.017 ------------------------------------------------------------------------------- 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 270 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 MET 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 237 LEU Chi-restraints excluded: chain N residue 240 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 160 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 213 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 463 SER Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 499 VAL 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 228 SER 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 494 LEU 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 262 LEU 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 348 GLN 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 213 VAL 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 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 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 262 LEU Chi-restraints excluded: chain D residue 300 VAL 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 232 GLU 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 288 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 499 VAL 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 463 SER Chi-restraints excluded: chain K residue 517 THR 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 213 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 270 ILE 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 146 GLN Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 389 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 213 VAL Chi-restraints excluded: chain G residue 262 LEU 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 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 234 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 499 VAL Chi-restraints excluded: chain M residue 517 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 7.9990 chunk 280 optimal weight: 9.9990 chunk 419 optimal weight: 5.9990 chunk 211 optimal weight: 0.0470 chunk 137 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 446 optimal weight: 7.9990 chunk 478 optimal weight: 2.9990 chunk 346 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 551 optimal weight: 6.9990 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 351 GLN G 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 54362 Z= 0.407 Angle : 0.581 11.174 73402 Z= 0.307 Chirality : 0.045 0.161 8932 Planarity : 0.003 0.034 9618 Dihedral : 4.135 34.206 7731 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.47 % Allowed : 15.49 % Favored : 81.05 % 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: 1.51 (0.10), residues: 7308 helix: 2.03 (0.08), residues: 4046 sheet: 0.25 (0.15), residues: 1148 loop : -0.54 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 401 PHE 0.011 0.001 PHE L 8 TYR 0.013 0.002 TYR A 478 ARG 0.011 0.001 ARG C 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 690 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 494 time to evaluate : 5.887 Fit side-chains revert: symmetry clash REVERT: A 267 MET cc_start: 0.5655 (mmm) cc_final: 0.4947 (mmm) REVERT: A 307 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7094 (ptp) REVERT: A 321 LYS cc_start: 0.8321 (ttpt) cc_final: 0.7831 (mmtp) REVERT: A 367 GLU cc_start: 0.7750 (pp20) cc_final: 0.7446 (pp20) REVERT: A 461 GLU cc_start: 0.7763 (pm20) cc_final: 0.7370 (pm20) REVERT: N 16 MET cc_start: 0.7906 (mmm) cc_final: 0.7626 (mtt) REVERT: N 61 GLU cc_start: 0.6884 (tt0) cc_final: 0.6634 (tt0) REVERT: N 111 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7837 (mtt) REVERT: N 142 LYS cc_start: 0.8206 (tppt) cc_final: 0.7898 (ttpp) REVERT: N 201 SER cc_start: 0.7977 (t) cc_final: 0.7763 (m) REVERT: N 262 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6392 (tp) REVERT: N 267 MET cc_start: 0.6690 (tmm) cc_final: 0.5788 (mmp) REVERT: N 321 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7514 (mmtp) REVERT: N 327 LYS cc_start: 0.8780 (tppt) cc_final: 0.8487 (tttp) REVERT: N 461 GLU cc_start: 0.7820 (pm20) cc_final: 0.7566 (pm20) REVERT: N 494 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8004 (pp) REVERT: N 520 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7679 (mtp) REVERT: B 111 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7817 (mtt) REVERT: B 204 PHE cc_start: 0.7908 (m-80) cc_final: 0.7610 (m-80) REVERT: B 267 MET cc_start: 0.6854 (tmm) cc_final: 0.5555 (mmp) REVERT: B 321 LYS cc_start: 0.8230 (ttpt) cc_final: 0.7732 (mmtp) REVERT: B 367 GLU cc_start: 0.7662 (pp20) cc_final: 0.7295 (pp20) REVERT: B 461 GLU cc_start: 0.7809 (pm20) cc_final: 0.7557 (pm20) REVERT: B 494 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7442 (pp) REVERT: H 184 GLN cc_start: 0.8473 (mp10) cc_final: 0.8246 (mm-40) REVERT: H 267 MET cc_start: 0.6674 (tmm) cc_final: 0.5452 (mmm) REVERT: H 321 LYS cc_start: 0.8385 (ttpt) cc_final: 0.7899 (mmpt) REVERT: H 389 MET cc_start: 0.6435 (tmm) cc_final: 0.6145 (tmm) REVERT: H 461 GLU cc_start: 0.7763 (pm20) cc_final: 0.7434 (pm20) REVERT: H 494 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7824 (pp) REVERT: C 102 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6687 (mt-10) REVERT: C 232 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6537 (pm20) REVERT: C 262 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6521 (tm) REVERT: C 267 MET cc_start: 0.7178 (tmm) cc_final: 0.6297 (mmp) REVERT: C 321 LYS cc_start: 0.8361 (ttpt) cc_final: 0.8010 (mmtt) REVERT: C 367 GLU cc_start: 0.7603 (pp20) cc_final: 0.7234 (pp20) REVERT: C 461 GLU cc_start: 0.7747 (pm20) cc_final: 0.7425 (pm20) REVERT: I 142 LYS cc_start: 0.8115 (tppt) cc_final: 0.7791 (ttpp) REVERT: I 193 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.7047 (ttm) REVERT: I 267 MET cc_start: 0.6527 (tmm) cc_final: 0.5667 (mmp) REVERT: I 321 LYS cc_start: 0.7990 (ttpt) cc_final: 0.7526 (mmtt) REVERT: I 461 GLU cc_start: 0.7643 (pm20) cc_final: 0.7398 (pm20) REVERT: I 494 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7641 (pp) REVERT: D 262 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6375 (tm) REVERT: D 267 MET cc_start: 0.7042 (tmm) cc_final: 0.6023 (mmp) REVERT: D 321 LYS cc_start: 0.8234 (ttpt) cc_final: 0.7610 (mmmt) REVERT: D 367 GLU cc_start: 0.7871 (pp20) cc_final: 0.7537 (pp20) REVERT: J 16 MET cc_start: 0.8170 (mtp) cc_final: 0.7919 (mtm) REVERT: J 204 PHE cc_start: 0.7648 (m-80) cc_final: 0.7341 (m-80) REVERT: J 267 MET cc_start: 0.5891 (tmm) cc_final: 0.5109 (mmm) REVERT: J 321 LYS cc_start: 0.8070 (ttpt) cc_final: 0.7643 (mmtp) REVERT: J 397 GLU cc_start: 0.7839 (tp30) cc_final: 0.7540 (tt0) REVERT: J 461 GLU cc_start: 0.7352 (pm20) cc_final: 0.6901 (pm20) REVERT: E 102 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6651 (mp0) REVERT: E 267 MET cc_start: 0.6689 (tmm) cc_final: 0.5846 (mmp) REVERT: E 321 LYS cc_start: 0.8313 (ttpt) cc_final: 0.7705 (mmtt) REVERT: E 351 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8097 (mm110) REVERT: E 367 GLU cc_start: 0.7856 (pp20) cc_final: 0.7569 (pp20) REVERT: E 447 MET cc_start: 0.8245 (mtm) cc_final: 0.8005 (mtp) REVERT: E 461 GLU cc_start: 0.7637 (pm20) cc_final: 0.7380 (pm20) REVERT: E 494 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7932 (pp) REVERT: K 142 LYS cc_start: 0.8011 (tppt) cc_final: 0.7710 (ttpp) REVERT: K 267 MET cc_start: 0.6360 (tmm) cc_final: 0.5435 (mmm) REVERT: K 321 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7770 (mmtp) REVERT: K 397 GLU cc_start: 0.7599 (tp30) cc_final: 0.7319 (tt0) REVERT: K 461 GLU cc_start: 0.8207 (pm20) cc_final: 0.7768 (pm20) REVERT: F 61 GLU cc_start: 0.7332 (pt0) cc_final: 0.6990 (pt0) REVERT: F 111 MET cc_start: 0.8733 (mtp) cc_final: 0.8314 (mtt) REVERT: F 160 LYS cc_start: 0.7843 (mtpp) cc_final: 0.7547 (ptmm) REVERT: F 321 LYS cc_start: 0.8328 (ttpt) cc_final: 0.7770 (mmtt) REVERT: F 367 GLU cc_start: 0.7630 (pp20) cc_final: 0.7358 (pp20) REVERT: F 461 GLU cc_start: 0.7742 (pm20) cc_final: 0.7474 (pm20) REVERT: F 520 MET cc_start: 0.8742 (mtp) cc_final: 0.8435 (mtt) REVERT: L 69 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6832 (mtp) REVERT: L 76 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7669 (tm-30) REVERT: L 262 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.5884 (tp) REVERT: L 267 MET cc_start: 0.5997 (tmm) cc_final: 0.5155 (mmm) REVERT: L 321 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7708 (mmtp) REVERT: L 351 GLN cc_start: 0.8340 (tp40) cc_final: 0.7983 (tp40) REVERT: L 389 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.5915 (tmm) REVERT: L 461 GLU cc_start: 0.7393 (pm20) cc_final: 0.7178 (pm20) REVERT: G 61 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7121 (pt0) REVERT: G 160 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7606 (ptmm) REVERT: G 166 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6298 (mtt) REVERT: G 262 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6587 (tt) REVERT: G 267 MET cc_start: 0.6707 (tmm) cc_final: 0.6070 (mmp) REVERT: G 321 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7769 (mmpt) REVERT: G 322 ARG cc_start: 0.7948 (mtp-110) cc_final: 0.7746 (ttm110) REVERT: G 367 GLU cc_start: 0.7687 (pp20) cc_final: 0.7358 (pp20) REVERT: G 461 GLU cc_start: 0.7684 (pm20) cc_final: 0.7431 (pm20) REVERT: M 142 LYS cc_start: 0.8315 (tppt) cc_final: 0.8099 (ttpp) REVERT: M 267 MET cc_start: 0.6682 (tmm) cc_final: 0.5864 (mmm) REVERT: M 307 MET cc_start: 0.7507 (mtm) cc_final: 0.7152 (ptp) REVERT: M 321 LYS cc_start: 0.8026 (ttpt) cc_final: 0.7542 (mmtt) REVERT: M 461 GLU cc_start: 0.7315 (pm20) cc_final: 0.7053 (pm20) outliers start: 196 outliers final: 149 residues processed: 655 average time/residue: 0.5802 time to fit residues: 663.3301 Evaluate side-chains 650 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 479 time to evaluate : 6.385 ------------------------------------------------------------------------------- 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 270 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 510 VAL 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 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 420 ILE 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 111 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 213 VAL 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 463 SER Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 499 VAL 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 240 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 494 LEU 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 232 GLU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 LEU 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 11 ASP 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 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 240 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 124 VAL 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 517 THR 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 213 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 307 MET 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 499 VAL 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 124 VAL 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 499 VAL 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 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 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 389 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 124 VAL 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 213 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 348 GLN 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 234 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 499 VAL 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 638 optimal weight: 0.9980 chunk 672 optimal weight: 2.9990 chunk 613 optimal weight: 0.8980 chunk 653 optimal weight: 6.9990 chunk 393 optimal weight: 6.9990 chunk 284 optimal weight: 0.0270 chunk 513 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 590 optimal weight: 0.8980 chunk 618 optimal weight: 0.0870 chunk 651 optimal weight: 5.9990 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 GLN J 184 GLN E 146 GLN M 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 54362 Z= 0.141 Angle : 0.486 10.028 73402 Z= 0.256 Chirality : 0.040 0.156 8932 Planarity : 0.003 0.030 9618 Dihedral : 3.923 30.064 7731 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.86 % Allowed : 17.20 % Favored : 80.94 % 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: 2.34 (0.08), residues: 4046 sheet: 0.30 (0.17), residues: 966 loop : -0.47 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS J 401 PHE 0.008 0.001 PHE I 195 TYR 0.011 0.001 TYR C 476 ARG 0.010 0.000 ARG G 350 *********************** 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 619 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 514 time to evaluate : 6.573 Fit side-chains REVERT: A 76 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7813 (tm-30) REVERT: A 267 MET cc_start: 0.5708 (mmm) cc_final: 0.4979 (mmm) REVERT: A 307 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6904 (ptp) REVERT: A 321 LYS cc_start: 0.8344 (ttpt) cc_final: 0.7864 (mmtp) REVERT: A 367 GLU cc_start: 0.7697 (pp20) cc_final: 0.7381 (pp20) REVERT: A 461 GLU cc_start: 0.7686 (pm20) cc_final: 0.7347 (pm20) REVERT: N 201 SER cc_start: 0.8007 (t) cc_final: 0.7795 (m) REVERT: N 267 MET cc_start: 0.6611 (tmm) cc_final: 0.5747 (mmp) REVERT: N 321 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7511 (mmtp) REVERT: N 327 LYS cc_start: 0.8822 (tppt) cc_final: 0.8488 (tttp) REVERT: N 336 VAL cc_start: 0.7550 (OUTLIER) cc_final: 0.7206 (m) REVERT: N 397 GLU cc_start: 0.7682 (tp30) cc_final: 0.7403 (tt0) REVERT: N 461 GLU cc_start: 0.7645 (pm20) cc_final: 0.7397 (pm20) REVERT: N 494 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8001 (pp) REVERT: N 520 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7825 (mmt) REVERT: B 204 PHE cc_start: 0.7790 (m-80) cc_final: 0.7531 (m-80) REVERT: B 267 MET cc_start: 0.6880 (tmm) cc_final: 0.5722 (mmp) REVERT: B 321 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7734 (mmtp) REVERT: B 367 GLU cc_start: 0.7624 (pp20) cc_final: 0.7275 (pp20) REVERT: B 461 GLU cc_start: 0.7777 (pm20) cc_final: 0.7552 (pm20) REVERT: B 494 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7390 (pp) REVERT: H 267 MET cc_start: 0.6370 (tmm) cc_final: 0.5230 (mmp) REVERT: H 321 LYS cc_start: 0.8331 (ttpt) cc_final: 0.7868 (mmtp) REVERT: H 461 GLU cc_start: 0.7630 (pm20) cc_final: 0.7155 (pm20) REVERT: C 102 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6516 (mt-10) REVERT: C 262 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6542 (tm) REVERT: C 267 MET cc_start: 0.7088 (tmm) cc_final: 0.6293 (mmp) REVERT: C 321 LYS cc_start: 0.8315 (ttpt) cc_final: 0.8007 (mmtt) REVERT: C 322 ARG cc_start: 0.8417 (mtp-110) cc_final: 0.7987 (ttm110) REVERT: C 367 GLU cc_start: 0.7598 (pp20) cc_final: 0.7225 (pp20) REVERT: C 461 GLU cc_start: 0.7721 (pm20) cc_final: 0.7200 (pm20) REVERT: I 193 MET cc_start: 0.7263 (tpt) cc_final: 0.6935 (ttm) REVERT: I 267 MET cc_start: 0.6409 (tmm) cc_final: 0.5624 (mmp) REVERT: I 288 MET cc_start: 0.6550 (mmp) cc_final: 0.6287 (mmp) REVERT: I 321 LYS cc_start: 0.7999 (ttpt) cc_final: 0.7532 (mmtt) REVERT: I 461 GLU cc_start: 0.7646 (pm20) cc_final: 0.7422 (pm20) REVERT: I 494 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7495 (pp) REVERT: D 50 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8146 (p) REVERT: D 267 MET cc_start: 0.6855 (tmm) cc_final: 0.5641 (mmp) REVERT: D 321 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7590 (mmmt) REVERT: D 367 GLU cc_start: 0.7860 (pp20) cc_final: 0.7595 (pp20) REVERT: D 461 GLU cc_start: 0.7627 (pm20) cc_final: 0.7276 (pm20) REVERT: D 491 MET cc_start: 0.7272 (ptp) cc_final: 0.7033 (ptm) REVERT: J 267 MET cc_start: 0.5858 (tmm) cc_final: 0.5157 (mmm) REVERT: J 321 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7631 (mmtp) REVERT: J 461 GLU cc_start: 0.7264 (pm20) cc_final: 0.6863 (pm20) REVERT: E 102 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6873 (mt-10) REVERT: E 262 LEU cc_start: 0.5120 (OUTLIER) cc_final: 0.4754 (pp) REVERT: E 267 MET cc_start: 0.6625 (tmm) cc_final: 0.5880 (mmp) REVERT: E 321 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7711 (mmtp) REVERT: E 351 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8106 (mm110) REVERT: E 367 GLU cc_start: 0.7833 (pp20) cc_final: 0.7546 (pp20) REVERT: E 447 MET cc_start: 0.8037 (mtm) cc_final: 0.7779 (mtp) REVERT: E 461 GLU cc_start: 0.7573 (pm20) cc_final: 0.7157 (pm20) REVERT: E 494 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7978 (pp) REVERT: K 204 PHE cc_start: 0.7370 (m-80) cc_final: 0.7167 (m-80) REVERT: K 267 MET cc_start: 0.6284 (tmm) cc_final: 0.5526 (mmp) REVERT: K 321 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7724 (mmtp) REVERT: K 397 GLU cc_start: 0.7544 (tp30) cc_final: 0.7304 (tt0) REVERT: K 461 GLU cc_start: 0.8151 (pm20) cc_final: 0.7692 (pm20) REVERT: F 61 GLU cc_start: 0.7421 (pt0) cc_final: 0.7083 (pt0) REVERT: F 111 MET cc_start: 0.8766 (mtp) cc_final: 0.8269 (mtt) REVERT: F 160 LYS cc_start: 0.7892 (mtpp) cc_final: 0.7611 (ptmm) REVERT: F 277 LYS cc_start: 0.7911 (mttt) cc_final: 0.7556 (mmmm) REVERT: F 321 LYS cc_start: 0.8319 (ttpt) cc_final: 0.7751 (mmtt) REVERT: F 367 GLU cc_start: 0.7643 (pp20) cc_final: 0.7417 (pp20) REVERT: F 461 GLU cc_start: 0.7589 (pm20) cc_final: 0.7197 (pm20) REVERT: F 520 MET cc_start: 0.8615 (mtp) cc_final: 0.8365 (mtt) REVERT: L 69 MET cc_start: 0.6783 (mtm) cc_final: 0.6306 (mtp) REVERT: L 76 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7540 (tm-30) REVERT: L 267 MET cc_start: 0.5865 (tmm) cc_final: 0.5151 (mmm) REVERT: L 321 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7641 (mmtp) REVERT: L 351 GLN cc_start: 0.8357 (tp40) cc_final: 0.8041 (tp40) REVERT: L 389 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.6006 (tmm) REVERT: G 61 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6971 (pt0) REVERT: G 76 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7925 (tm-30) REVERT: G 166 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6226 (mtt) REVERT: G 267 MET cc_start: 0.6989 (tmm) cc_final: 0.6054 (mmp) REVERT: G 321 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7747 (mmpt) REVERT: G 322 ARG cc_start: 0.8085 (mtp-110) cc_final: 0.7610 (ttm110) REVERT: G 367 GLU cc_start: 0.7648 (pp20) cc_final: 0.7370 (pp20) REVERT: G 461 GLU cc_start: 0.7672 (pm20) cc_final: 0.7199 (pm20) REVERT: M 142 LYS cc_start: 0.8259 (tppt) cc_final: 0.8016 (ttpp) REVERT: M 267 MET cc_start: 0.6623 (tmm) cc_final: 0.5787 (mmm) REVERT: M 307 MET cc_start: 0.7528 (mtm) cc_final: 0.7121 (ptp) REVERT: M 321 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7550 (mmtt) REVERT: M 461 GLU cc_start: 0.7284 (pm20) cc_final: 0.7063 (pm20) outliers start: 105 outliers final: 84 residues processed: 598 average time/residue: 0.5859 time to fit residues: 611.2715 Evaluate side-chains 587 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 489 time to evaluate : 6.283 ------------------------------------------------------------------------------- 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 270 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 494 LEU Chi-restraints excluded: chain N residue 520 MET Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 213 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 348 GLN 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 331 THR 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 174 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 262 LEU 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 I residue 61 GLU 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 D residue 43 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 300 VAL 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 124 VAL Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 262 LEU 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 K residue 213 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 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 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 L residue 146 GLN Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 389 MET 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 213 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 442 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 2.9990 chunk 691 optimal weight: 5.9990 chunk 422 optimal weight: 0.9980 chunk 328 optimal weight: 5.9990 chunk 480 optimal weight: 4.9990 chunk 725 optimal weight: 0.0020 chunk 667 optimal weight: 3.9990 chunk 577 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 446 optimal weight: 8.9990 chunk 354 optimal weight: 0.8980 overall best weight: 1.5792 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2449 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= 0.187 Angle : 0.496 9.833 73402 Z= 0.259 Chirality : 0.041 0.161 8932 Planarity : 0.003 0.030 9618 Dihedral : 3.867 29.235 7729 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.12 % Allowed : 17.01 % Favored : 80.87 % 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: 1.81 (0.10), residues: 7308 helix: 2.34 (0.08), residues: 4046 sheet: 0.32 (0.17), residues: 966 loop : -0.47 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS N 401 PHE 0.007 0.001 PHE N 8 TYR 0.011 0.001 TYR J 476 ARG 0.006 0.000 ARG B 350 ********************** 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 614 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 494 time to evaluate : 6.319 Fit side-chains REVERT: A 76 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7807 (tm-30) REVERT: A 267 MET cc_start: 0.5707 (mmm) cc_final: 0.4980 (mmm) REVERT: A 307 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.6939 (ptp) REVERT: A 321 LYS cc_start: 0.8420 (ttpt) cc_final: 0.7913 (mmtp) REVERT: A 367 GLU cc_start: 0.7719 (pp20) cc_final: 0.7403 (pp20) REVERT: A 461 GLU cc_start: 0.7691 (pm20) cc_final: 0.7319 (pm20) REVERT: N 267 MET cc_start: 0.6610 (tmm) cc_final: 0.5727 (mmp) REVERT: N 321 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7523 (mmtp) REVERT: N 327 LYS cc_start: 0.8829 (tppt) cc_final: 0.8512 (tttm) REVERT: N 336 VAL cc_start: 0.7495 (OUTLIER) cc_final: 0.7134 (m) REVERT: N 397 GLU cc_start: 0.7742 (tp30) cc_final: 0.7455 (tt0) REVERT: N 461 GLU cc_start: 0.7643 (pm20) cc_final: 0.7391 (pm20) REVERT: N 494 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8040 (pp) REVERT: N 520 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7577 (mtp) REVERT: B 204 PHE cc_start: 0.7797 (m-80) cc_final: 0.7518 (m-80) REVERT: B 267 MET cc_start: 0.6873 (tmm) cc_final: 0.5717 (mmp) REVERT: B 321 LYS cc_start: 0.8258 (ttpt) cc_final: 0.7754 (mmtp) REVERT: B 367 GLU cc_start: 0.7675 (pp20) cc_final: 0.7377 (pp20) REVERT: B 461 GLU cc_start: 0.7819 (pm20) cc_final: 0.7598 (pm20) REVERT: B 494 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7388 (pp) REVERT: H 267 MET cc_start: 0.6382 (tmm) cc_final: 0.5241 (mmp) REVERT: H 321 LYS cc_start: 0.8316 (ttpt) cc_final: 0.7861 (mmtp) REVERT: H 461 GLU cc_start: 0.7634 (pm20) cc_final: 0.7119 (pm20) REVERT: C 102 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6507 (mt-10) REVERT: C 262 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6466 (tm) REVERT: C 267 MET cc_start: 0.7089 (tmm) cc_final: 0.6283 (mmp) REVERT: C 321 LYS cc_start: 0.8318 (ttpt) cc_final: 0.8013 (mmtt) REVERT: C 322 ARG cc_start: 0.8425 (mtp-110) cc_final: 0.8008 (ttm110) REVERT: C 367 GLU cc_start: 0.7593 (pp20) cc_final: 0.7215 (pp20) REVERT: C 461 GLU cc_start: 0.7720 (pm20) cc_final: 0.7337 (pm20) REVERT: I 183 LEU cc_start: 0.8896 (tp) cc_final: 0.8529 (tp) REVERT: I 267 MET cc_start: 0.6397 (tmm) cc_final: 0.5623 (mmp) REVERT: I 288 MET cc_start: 0.6604 (mmp) cc_final: 0.6339 (mmp) REVERT: I 321 LYS cc_start: 0.8012 (ttpt) cc_final: 0.7540 (mmtt) REVERT: I 461 GLU cc_start: 0.7632 (pm20) cc_final: 0.7404 (pm20) REVERT: I 494 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7559 (pp) REVERT: D 50 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.8010 (p) REVERT: D 262 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6377 (tm) REVERT: D 267 MET cc_start: 0.6957 (tmm) cc_final: 0.5788 (mmp) REVERT: D 321 LYS cc_start: 0.8265 (ttpt) cc_final: 0.7618 (mmmt) REVERT: D 367 GLU cc_start: 0.7855 (pp20) cc_final: 0.7586 (pp20) REVERT: D 461 GLU cc_start: 0.7663 (pm20) cc_final: 0.7438 (pm20) REVERT: D 491 MET cc_start: 0.7247 (ptp) cc_final: 0.7022 (ptm) REVERT: J 193 MET cc_start: 0.7147 (tpt) cc_final: 0.6690 (tpt) REVERT: J 267 MET cc_start: 0.5855 (tmm) cc_final: 0.5148 (mmm) REVERT: J 321 LYS cc_start: 0.8076 (ttpt) cc_final: 0.7633 (mmtp) REVERT: J 461 GLU cc_start: 0.7271 (pm20) cc_final: 0.6805 (pm20) REVERT: E 102 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6908 (mt-10) REVERT: E 262 LEU cc_start: 0.515------------------------------------------------------------------------------- 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 270 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 494 LEU 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 160 LYS Chi-restraints excluded: chain B residue 213 VAL 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 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 300 VAL Chi-restraints excluded: chain H residue 331 THR 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 174 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 262 LEU 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 I residue 61 GLU 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 D residue 43 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 300 VAL 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 124 VAL Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 491 MET Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 61 GLU 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 262 LEU 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 213 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 K residue 517 THR 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 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 L residue 146 GLN Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 389 MET 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 213 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 442 VAL 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 458 optimal weight: 1.9990 chunk 615 optimal weight: 3.9990 chunk 176 optimal weight: 0.0980 chunk 532 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 160 optimal weight: 0.3980 chunk 578 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 593 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 106 optimal weight: 0.4980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 348 GLN G 351 GLN 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 = 0.150774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.108861 restraints weight = 68363.143| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.80 r_work: 0.3137 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2475 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= 0.173 Angle : 0.489 10.568 73402 Z= 0.255 Chirality : 0.040 0.156 8932 Planarity : 0.003 0.029 9618 Dihedral : 3.828 27.520 7729 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.09 % Allowed : 17.19 % Favored : 80.73 % 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: 1.81 (0.10), residues: 7308 helix: 2.27 (0.08), residues: 4102 sheet: 0.37 (0.15), residues: 1148 loop : -0.47 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS N 401 PHE 0.014 0.001 PHE N 204 TYR 0.011 0.001 TYR A 476 ARG 0.004 0.000 ARG C 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12760.05 seconds wall clock time: 518 minutes 48.51 seconds (31128.51 seconds total)