Starting phenix.real_space_refine on Fri Feb 6 04:24:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmz_48408/02_2026/9mmz_48408_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmz_48408/02_2026/9mmz_48408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mmz_48408/02_2026/9mmz_48408_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmz_48408/02_2026/9mmz_48408_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mmz_48408/02_2026/9mmz_48408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmz_48408/02_2026/9mmz_48408.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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 119 5.16 5 C 13923 2.51 5 N 3871 2.21 5 O 4445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22358 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3194 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 11, 'TRANS': 425} Chain breaks: 5 Restraints were copied for chains: B, C, D, E, F, H Time building chain proxies: 3.27, per 1000 atoms: 0.15 Number of scatterers: 22358 At special positions: 0 Unit cell: (157.046, 157.046, 79.05, 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 119 16.00 O 4445 8.00 N 3871 7.00 C 13923 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: 1.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5516 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 42 sheets defined 59.5% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.539A pdb=" N ARG A 13 " --> pdb=" O GLY A 9 " (cutoff:3.500A) 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: 3.623A pdb=" N VAL A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 86 removed outlier: 3.900A pdb=" N LYS A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 109 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 removed outlier: 3.654A pdb=" N ILE A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 297 removed outlier: 3.642A pdb=" N LYS A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 375 removed outlier: 3.617A pdb=" N ARG A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 4.179A 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 425 Processing helix chain 'A' and resid 433 through 444 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 497 through 516 Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.539A pdb=" N ARG B 13 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.624A pdb=" N VAL B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 86 removed outlier: 3.900A pdb=" N LYS B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 109 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 removed outlier: 3.654A pdb=" N ILE B 205 " --> pdb=" O PRO B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 297 removed outlier: 3.642A pdb=" N LYS B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 375 removed outlier: 3.618A pdb=" N ARG B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 4.180A 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 425 Processing helix chain 'B' and resid 433 through 444 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 461 through 471 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.539A pdb=" N ARG C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.624A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 86 removed outlier: 3.900A pdb=" N LYS C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 109 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 removed outlier: 3.654A pdb=" N ILE C 205 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 297 removed outlier: 3.642A pdb=" N LYS C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 375 removed outlier: 3.618A pdb=" N ARG C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 4.179A 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 425 Processing helix chain 'C' and resid 433 through 444 Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 497 through 516 Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.539A pdb=" N ARG D 13 " --> pdb=" O GLY D 9 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.623A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.901A pdb=" N LYS D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA D 81 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 109 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 removed outlier: 3.654A pdb=" N ILE D 205 " --> pdb=" O PRO D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 297 removed outlier: 3.642A pdb=" N LYS D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 375 removed outlier: 3.618A pdb=" N ARG D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 4.179A 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 425 Processing helix chain 'D' and resid 433 through 444 Processing helix chain 'D' and resid 445 through 447 No H-bonds generated for 'chain 'D' and resid 445 through 447' Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 488 through 492 Processing helix chain 'D' and resid 497 through 516 Processing helix chain 'E' and resid 9 through 29 removed outlier: 3.538A pdb=" N ARG E 13 " --> pdb=" O GLY E 9 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 60 removed outlier: 3.623A pdb=" N VAL E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 86 removed outlier: 3.901A pdb=" N LYS E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA E 81 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 109 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 removed outlier: 3.654A pdb=" N ILE E 205 " --> pdb=" O PRO E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 297 removed outlier: 3.642A pdb=" N LYS E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 375 removed outlier: 3.618A pdb=" N ARG E 368 " --> pdb=" O LYS E 364 " (cutoff:3.500A) removed outlier: 4.179A 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 425 Processing helix chain 'E' and resid 433 through 444 Processing helix chain 'E' and resid 445 through 447 No H-bonds generated for 'chain 'E' and resid 445 through 447' Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 461 through 471 Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 497 through 516 Processing helix chain 'F' and resid 9 through 29 removed outlier: 3.539A pdb=" N ARG F 13 " --> pdb=" O GLY F 9 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.623A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 86 removed outlier: 3.900A pdb=" N LYS F 80 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA F 81 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 109 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 removed outlier: 3.654A pdb=" N ILE F 205 " --> pdb=" O PRO F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 297 removed outlier: 3.642A pdb=" N LYS F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 375 removed outlier: 3.617A pdb=" N ARG F 368 " --> pdb=" O LYS F 364 " (cutoff:3.500A) removed outlier: 4.179A 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 425 Processing helix chain 'F' and resid 433 through 444 Processing helix chain 'F' and resid 445 through 447 No H-bonds generated for 'chain 'F' and resid 445 through 447' Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 461 through 471 Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 497 through 516 Processing helix chain 'H' and resid 9 through 29 removed outlier: 3.539A pdb=" N ARG H 13 " --> pdb=" O GLY H 9 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 60 removed outlier: 3.624A pdb=" N VAL H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 86 removed outlier: 3.900A pdb=" N LYS H 80 " --> pdb=" O GLU H 76 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 109 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 Processing helix chain 'H' and resid 201 through 205 removed outlier: 3.654A pdb=" N ILE H 205 " --> pdb=" O PRO H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 297 removed outlier: 3.642A pdb=" N LYS H 286 " --> pdb=" O GLY H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 375 removed outlier: 3.617A pdb=" N ARG H 368 " --> pdb=" O LYS H 364 " (cutoff:3.500A) removed outlier: 4.179A 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 425 Processing helix chain 'H' and resid 433 through 444 Processing helix chain 'H' and resid 445 through 447 No H-bonds generated for 'chain 'H' and resid 445 through 447' Processing helix chain 'H' and resid 448 through 458 Processing helix chain 'H' and resid 461 through 471 Processing helix chain 'H' and resid 488 through 492 Processing helix chain 'H' and resid 497 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 5.381A pdb=" N ASN B 37 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS A 519 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS B 42 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 50 removed outlier: 4.964A pdb=" N ALA A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS A 42 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN A 37 " --> pdb=" O CYS H 519 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL H 521 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 39 " --> pdb=" O VAL H 521 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.861A pdb=" N VAL A 174 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE A 379 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR A 176 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL A 381 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLU A 178 " --> pdb=" O VAL A 381 " (cutoff:3.500A) 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 275 through 277 removed outlier: 5.861A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 8 removed outlier: 5.381A pdb=" N ASN C 37 " --> pdb=" O THR B 517 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS B 519 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS C 42 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.860A pdb=" N VAL B 174 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE B 379 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU B 178 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AB2, first strand: chain 'B' and resid 275 through 277 removed outlier: 5.861A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AB4, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 8 removed outlier: 5.381A pdb=" N ASN D 37 " --> pdb=" O THR C 517 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS C 519 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS D 42 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 174 through 179 removed outlier: 6.861A pdb=" N VAL C 174 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE C 379 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR C 176 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 381 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLU C 178 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 195 Processing sheet with id=AB8, first strand: chain 'C' and resid 275 through 277 removed outlier: 5.861A pdb=" N ILE C 249 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC1, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AC2, first strand: chain 'D' and resid 5 through 8 removed outlier: 5.381A pdb=" N ASN E 37 " --> pdb=" O THR D 517 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS D 519 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS E 42 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ALA E 46 " --> pdb=" O LYS E 42 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 174 through 179 removed outlier: 6.861A pdb=" N VAL D 174 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE D 379 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR D 176 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL D 381 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU D 178 " --> pdb=" O VAL D 381 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 193 through 195 Processing sheet with id=AC5, first strand: chain 'D' and resid 275 through 277 removed outlier: 5.861A pdb=" N ILE D 249 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AC7, first strand: chain 'D' and resid 476 through 479 Processing sheet with id=AC8, first strand: chain 'E' and resid 5 through 8 removed outlier: 5.381A pdb=" N ASN F 37 " --> pdb=" O THR E 517 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS E 519 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS F 42 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ALA F 46 " --> pdb=" O LYS F 42 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 174 through 179 removed outlier: 6.862A pdb=" N VAL E 174 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE E 379 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR E 176 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL E 381 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLU E 178 " --> pdb=" O VAL E 381 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 193 through 195 Processing sheet with id=AD2, first strand: chain 'E' and resid 275 through 277 removed outlier: 5.861A pdb=" N ILE E 249 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AD4, first strand: chain 'E' and resid 476 through 479 Processing sheet with id=AD5, first strand: chain 'F' and resid 5 through 8 removed outlier: 5.381A pdb=" N ASN H 37 " --> pdb=" O THR F 517 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS F 519 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS H 42 " --> pdb=" O ALA H 46 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ALA H 46 " --> pdb=" O LYS H 42 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 174 through 179 removed outlier: 6.862A pdb=" N VAL F 174 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE F 379 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR F 176 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL F 381 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLU F 178 " --> pdb=" O VAL F 381 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 193 through 195 Processing sheet with id=AD8, first strand: chain 'F' and resid 275 through 277 removed outlier: 5.861A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AE1, first strand: chain 'F' and resid 476 through 479 Processing sheet with id=AE2, first strand: chain 'H' and resid 174 through 179 removed outlier: 6.861A pdb=" N VAL H 174 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE H 379 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR H 176 " --> pdb=" O ILE H 379 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL H 381 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLU H 178 " --> pdb=" O VAL H 381 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 193 through 195 Processing sheet with id=AE4, first strand: chain 'H' and resid 275 through 277 removed outlier: 5.861A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AE6, first strand: chain 'H' and resid 476 through 479 1502 hydrogen bonds defined for protein. 4317 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.14 Time building geometry restraints manager: 2.51 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: 7679 1.34 - 1.46: 2202 1.46 - 1.57: 12393 1.57 - 1.69: 0 1.69 - 1.81: 217 Bond restraints: 22491 Sorted by residual: bond pdb=" CA SER B 217 " pdb=" C SER B 217 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.68e+00 bond pdb=" CA SER F 217 " pdb=" C SER F 217 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.65e+00 bond pdb=" CA SER C 217 " pdb=" C SER C 217 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.60e+00 bond pdb=" CA SER A 217 " pdb=" C SER A 217 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.58e+00 bond pdb=" CA SER D 217 " pdb=" C SER D 217 " ideal model delta sigma weight residual 1.524 1.539 -0.016 1.26e-02 6.30e+03 1.54e+00 ... (remaining 22486 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 28918 0.95 - 1.91: 1122 1.91 - 2.86: 192 2.86 - 3.82: 57 3.82 - 4.77: 14 Bond angle restraints: 30303 Sorted by residual: angle pdb=" N LYS D 65 " pdb=" CA LYS D 65 " pdb=" C LYS D 65 " ideal model delta sigma weight residual 111.36 113.73 -2.37 1.09e+00 8.42e-01 4.74e+00 angle pdb=" N LYS H 65 " pdb=" CA LYS H 65 " pdb=" C LYS H 65 " ideal model delta sigma weight residual 111.36 113.73 -2.37 1.09e+00 8.42e-01 4.73e+00 angle pdb=" N LYS C 65 " pdb=" CA LYS C 65 " pdb=" C LYS C 65 " ideal model delta sigma weight residual 111.36 113.73 -2.37 1.09e+00 8.42e-01 4.72e+00 angle pdb=" N LYS F 65 " pdb=" CA LYS F 65 " pdb=" C LYS F 65 " ideal model delta sigma weight residual 111.36 113.72 -2.36 1.09e+00 8.42e-01 4.68e+00 angle pdb=" N LYS E 65 " pdb=" CA LYS E 65 " pdb=" C LYS E 65 " ideal model delta sigma weight residual 111.36 113.72 -2.36 1.09e+00 8.42e-01 4.67e+00 ... (remaining 30298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.76: 12796 13.76 - 27.51: 832 27.51 - 41.27: 211 41.27 - 55.03: 42 55.03 - 68.78: 21 Dihedral angle restraints: 13902 sinusoidal: 5327 harmonic: 8575 Sorted by residual: dihedral pdb=" CA ASP E 398 " pdb=" CB ASP E 398 " pdb=" CG ASP E 398 " pdb=" OD1 ASP E 398 " ideal model delta sinusoidal sigma weight residual -30.00 -83.98 53.98 1 2.00e+01 2.50e-03 9.88e+00 dihedral pdb=" CA ASP C 398 " pdb=" CB ASP C 398 " pdb=" CG ASP C 398 " pdb=" OD1 ASP C 398 " ideal model delta sinusoidal sigma weight residual -30.00 -83.97 53.97 1 2.00e+01 2.50e-03 9.88e+00 dihedral pdb=" CA ASP H 398 " pdb=" CB ASP H 398 " pdb=" CG ASP H 398 " pdb=" OD1 ASP H 398 " ideal model delta sinusoidal sigma weight residual -30.00 -83.96 53.96 1 2.00e+01 2.50e-03 9.88e+00 ... (remaining 13899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2444 0.028 - 0.056: 775 0.056 - 0.084: 264 0.084 - 0.112: 178 0.112 - 0.140: 42 Chirality restraints: 3703 Sorted by residual: chirality pdb=" CB VAL F 412 " pdb=" CA VAL F 412 " pdb=" CG1 VAL F 412 " pdb=" CG2 VAL F 412 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CB VAL E 412 " pdb=" CA VAL E 412 " pdb=" CG1 VAL E 412 " pdb=" CG2 VAL E 412 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CB VAL A 412 " pdb=" CA VAL A 412 " pdb=" CG1 VAL A 412 " pdb=" CG2 VAL A 412 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 3700 not shown) Planarity restraints: 3934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 278 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 279 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 279 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 279 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 278 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO B 279 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 279 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 279 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 278 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO H 279 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO H 279 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 279 " -0.020 5.00e-02 4.00e+02 ... (remaining 3931 not shown) Histogram of nonbonded interaction distances: 0.24 - 1.17: 21 1.17 - 2.11: 56 2.11 - 3.04: 14228 3.04 - 3.97: 58097 3.97 - 4.90: 105116 Warning: very small nonbonded interaction distances. Nonbonded interactions: 177518 Sorted by model distance: nonbonded pdb=" SD MET A 69 " pdb=" CG ASP B 41 " model vdw 0.243 3.630 nonbonded pdb=" SD MET D 69 " pdb=" CG ASP E 41 " model vdw 0.244 3.630 nonbonded pdb=" CG ASP A 41 " pdb=" SD MET H 69 " model vdw 0.244 3.630 nonbonded pdb=" SD MET C 69 " pdb=" CG ASP D 41 " model vdw 0.244 3.630 nonbonded pdb=" SD MET B 69 " pdb=" CG ASP C 41 " model vdw 0.244 3.630 ... (remaining 177513 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: 0.08 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 'H' } 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: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.770 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 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 : 0.002 0.020 22491 Z= 0.118 Angle : 0.467 4.773 30303 Z= 0.269 Chirality : 0.038 0.140 3703 Planarity : 0.003 0.036 3934 Dihedral : 10.672 68.783 8386 Min Nonbonded Distance : 0.243 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.15), residues: 2975 helix: 2.23 (0.13), residues: 1743 sheet: 0.53 (0.23), residues: 434 loop : -0.10 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 501 TYR 0.008 0.001 TYR D 478 PHE 0.008 0.001 PHE F 281 HIS 0.001 0.000 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00217 (22491) covalent geometry : angle 0.46738 (30303) hydrogen bonds : bond 0.13084 ( 1502) hydrogen bonds : angle 5.41683 ( 4317) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 595 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.7593 (tppt) cc_final: 0.6808 (pttm) REVERT: D 364 LYS cc_start: 0.7633 (tppt) cc_final: 0.6947 (pttm) REVERT: E 364 LYS cc_start: 0.7479 (tppt) cc_final: 0.6935 (pttm) REVERT: F 199 TYR cc_start: 0.8031 (p90) cc_final: 0.7669 (p90) REVERT: F 364 LYS cc_start: 0.7752 (tppt) cc_final: 0.7117 (pttm) REVERT: H 50 THR cc_start: 0.8806 (p) cc_final: 0.8583 (p) REVERT: H 364 LYS cc_start: 0.7719 (tppt) cc_final: 0.6974 (pttm) outliers start: 0 outliers final: 0 residues processed: 595 average time/residue: 0.1679 time to fit residues: 152.2856 Evaluate side-chains 317 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN B 505 GLN C 505 GLN D 505 GLN E 505 GLN F 505 GLN H 505 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.219696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.183910 restraints weight = 28630.675| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.61 r_work: 0.3936 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22491 Z= 0.148 Angle : 0.551 8.216 30303 Z= 0.290 Chirality : 0.042 0.142 3703 Planarity : 0.004 0.053 3934 Dihedral : 3.715 18.154 3178 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.16 % Allowed : 13.98 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.15), residues: 2975 helix: 2.18 (0.12), residues: 1771 sheet: 1.13 (0.24), residues: 420 loop : -0.13 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 13 TYR 0.017 0.002 TYR C 485 PHE 0.017 0.002 PHE A 8 HIS 0.000 0.000 HIS C 401 Details of bonding type rmsd covalent geometry : bond 0.00334 (22491) covalent geometry : angle 0.55085 (30303) hydrogen bonds : bond 0.04246 ( 1502) hydrogen bonds : angle 4.41877 ( 4317) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 370 time to evaluate : 0.877 Fit side-chains REVERT: A 193 MET cc_start: 0.7880 (ttp) cc_final: 0.7546 (ttp) REVERT: A 364 LYS cc_start: 0.7771 (tppt) cc_final: 0.7024 (tptt) REVERT: C 364 LYS cc_start: 0.8367 (tppt) cc_final: 0.7825 (mmtp) REVERT: C 389 MET cc_start: 0.7672 (tmm) cc_final: 0.7466 (tmm) REVERT: D 364 LYS cc_start: 0.7881 (tppt) cc_final: 0.7354 (tptt) REVERT: D 488 MET cc_start: 0.7540 (mmm) cc_final: 0.7172 (mmm) REVERT: E 186 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7684 (mt-10) REVERT: E 364 LYS cc_start: 0.7747 (tppt) cc_final: 0.7138 (tptt) REVERT: F 364 LYS cc_start: 0.7851 (tppt) cc_final: 0.7276 (tptt) outliers start: 50 outliers final: 32 residues processed: 408 average time/residue: 0.1421 time to fit residues: 94.7180 Evaluate side-chains 342 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 310 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 509 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 225 optimal weight: 0.9980 chunk 299 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 122 optimal weight: 0.0270 chunk 144 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN B 72 GLN C 72 GLN D 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.214907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.177811 restraints weight = 28830.341| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.63 r_work: 0.3844 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22491 Z= 0.142 Angle : 0.530 8.129 30303 Z= 0.276 Chirality : 0.041 0.138 3703 Planarity : 0.003 0.036 3934 Dihedral : 3.733 18.695 3178 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.01 % Allowed : 12.99 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.15), residues: 2975 helix: 2.07 (0.12), residues: 1764 sheet: 0.79 (0.25), residues: 434 loop : -0.04 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 501 TYR 0.012 0.002 TYR A 478 PHE 0.008 0.001 PHE B 195 HIS 0.000 0.000 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00329 (22491) covalent geometry : angle 0.52976 (30303) hydrogen bonds : bond 0.04002 ( 1502) hydrogen bonds : angle 4.12063 ( 4317) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 337 time to evaluate : 0.861 Fit side-chains REVERT: A 73 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7298 (ptm) REVERT: A 364 LYS cc_start: 0.7733 (tppt) cc_final: 0.6951 (tptt) REVERT: B 62 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8884 (mm) REVERT: B 222 LEU cc_start: 0.5498 (OUTLIER) cc_final: 0.5057 (mt) REVERT: C 364 LYS cc_start: 0.8144 (tppt) cc_final: 0.6763 (tptt) REVERT: D 62 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8766 (mm) REVERT: D 364 LYS cc_start: 0.8036 (tppt) cc_final: 0.7261 (tptt) REVERT: D 488 MET cc_start: 0.7736 (mmm) cc_final: 0.7100 (mmm) REVERT: E 186 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7745 (mt-10) REVERT: E 364 LYS cc_start: 0.7840 (tppt) cc_final: 0.7028 (tptt) REVERT: E 366 GLN cc_start: 0.7053 (tm-30) cc_final: 0.6851 (tm-30) REVERT: E 447 MET cc_start: 0.7995 (mpp) cc_final: 0.7536 (mtt) REVERT: F 364 LYS cc_start: 0.7830 (tppt) cc_final: 0.7072 (tptt) REVERT: F 438 VAL cc_start: 0.8269 (t) cc_final: 0.8054 (t) REVERT: H 490 ASP cc_start: 0.7754 (t0) cc_final: 0.7489 (t0) outliers start: 93 outliers final: 58 residues processed: 421 average time/residue: 0.1296 time to fit residues: 91.6403 Evaluate side-chains 354 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 292 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 494 LEU Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 519 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 205 optimal weight: 0.0170 chunk 195 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 291 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.211025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.174905 restraints weight = 28759.759| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.65 r_work: 0.3803 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22491 Z= 0.151 Angle : 0.539 8.579 30303 Z= 0.280 Chirality : 0.041 0.139 3703 Planarity : 0.003 0.030 3934 Dihedral : 3.778 19.745 3178 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.84 % Allowed : 14.33 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.15), residues: 2975 helix: 1.95 (0.12), residues: 1764 sheet: 0.68 (0.25), residues: 448 loop : -0.03 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 501 TYR 0.012 0.002 TYR A 478 PHE 0.008 0.001 PHE D 8 HIS 0.000 0.000 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00356 (22491) covalent geometry : angle 0.53934 (30303) hydrogen bonds : bond 0.04160 ( 1502) hydrogen bonds : angle 4.12153 ( 4317) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 316 time to evaluate : 0.930 Fit side-chains REVERT: A 364 LYS cc_start: 0.7846 (tppt) cc_final: 0.6975 (tptt) REVERT: A 380 LYS cc_start: 0.8492 (mttt) cc_final: 0.8292 (mmtp) REVERT: A 447 MET cc_start: 0.8148 (mtt) cc_final: 0.7485 (mtt) REVERT: B 111 MET cc_start: 0.7929 (tpp) cc_final: 0.7656 (mmt) REVERT: B 121 ASP cc_start: 0.6965 (t0) cc_final: 0.6717 (t0) REVERT: C 364 LYS cc_start: 0.8117 (tppt) cc_final: 0.6833 (tptt) REVERT: D 62 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8719 (mm) REVERT: D 186 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7810 (mt-10) REVERT: D 364 LYS cc_start: 0.8111 (tppt) cc_final: 0.7274 (tptt) REVERT: D 467 ASN cc_start: 0.7251 (m-40) cc_final: 0.6956 (m-40) REVERT: D 488 MET cc_start: 0.7712 (mmm) cc_final: 0.7030 (mmm) REVERT: E 178 GLU cc_start: 0.8401 (pm20) cc_final: 0.7941 (pm20) REVERT: E 186 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7793 (mt-10) REVERT: E 364 LYS cc_start: 0.7984 (tppt) cc_final: 0.7077 (tptt) REVERT: E 447 MET cc_start: 0.8047 (mpp) cc_final: 0.7805 (mtt) REVERT: F 364 LYS cc_start: 0.7879 (tppt) cc_final: 0.7064 (tptt) REVERT: H 389 MET cc_start: 0.7834 (tmm) cc_final: 0.7634 (tmm) REVERT: H 447 MET cc_start: 0.8163 (mtt) cc_final: 0.7565 (mtt) REVERT: H 490 ASP cc_start: 0.7855 (t0) cc_final: 0.7576 (t0) outliers start: 89 outliers final: 61 residues processed: 394 average time/residue: 0.1287 time to fit residues: 85.3306 Evaluate side-chains 348 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 286 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 494 LEU Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 519 CYS Chi-restraints excluded: chain H residue 524 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 52 optimal weight: 0.6980 chunk 283 optimal weight: 8.9990 chunk 192 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 260 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 266 optimal weight: 0.9990 chunk 23 optimal weight: 0.0050 chunk 278 optimal weight: 0.6980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.214393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.179300 restraints weight = 28669.072| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 1.49 r_work: 0.3857 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22491 Z= 0.107 Angle : 0.494 8.663 30303 Z= 0.256 Chirality : 0.040 0.137 3703 Planarity : 0.003 0.025 3934 Dihedral : 3.666 18.704 3178 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.50 % Allowed : 14.76 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.15), residues: 2975 helix: 2.07 (0.12), residues: 1771 sheet: 0.56 (0.26), residues: 434 loop : 0.02 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 501 TYR 0.011 0.001 TYR A 478 PHE 0.008 0.001 PHE B 8 HIS 0.000 0.000 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00234 (22491) covalent geometry : angle 0.49418 (30303) hydrogen bonds : bond 0.03701 ( 1502) hydrogen bonds : angle 3.98386 ( 4317) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 307 time to evaluate : 0.858 Fit side-chains REVERT: A 73 MET cc_start: 0.7350 (ptp) cc_final: 0.7147 (ptm) REVERT: A 364 LYS cc_start: 0.7823 (tppt) cc_final: 0.6937 (tptt) REVERT: A 380 LYS cc_start: 0.8458 (mttt) cc_final: 0.8248 (mmtp) REVERT: A 488 MET cc_start: 0.7399 (mmm) cc_final: 0.6542 (mmm) REVERT: B 62 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8868 (mm) REVERT: B 111 MET cc_start: 0.7840 (tpp) cc_final: 0.7581 (mmt) REVERT: B 193 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6373 (mtp) REVERT: B 490 ASP cc_start: 0.7690 (t0) cc_final: 0.7439 (t0) REVERT: C 364 LYS cc_start: 0.8141 (tppt) cc_final: 0.6806 (tptt) REVERT: D 186 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7709 (mt-10) REVERT: D 490 ASP cc_start: 0.7837 (t0) cc_final: 0.7494 (t0) REVERT: E 186 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7770 (mt-10) REVERT: F 364 LYS cc_start: 0.7875 (tppt) cc_final: 0.7050 (tptt) REVERT: H 156 GLU cc_start: 0.8033 (mp0) cc_final: 0.7821 (mp0) REVERT: H 193 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6220 (mtp) REVERT: H 389 MET cc_start: 0.7909 (tmm) cc_final: 0.7676 (tmm) REVERT: H 490 ASP cc_start: 0.7698 (t0) cc_final: 0.7430 (t0) outliers start: 81 outliers final: 57 residues processed: 376 average time/residue: 0.1308 time to fit residues: 83.2038 Evaluate side-chains 342 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 282 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 494 LEU Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 519 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 87 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 152 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 103 optimal weight: 0.0270 chunk 221 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.184896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.156311 restraints weight = 27106.368| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.97 r_work: 0.3768 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22491 Z= 0.129 Angle : 0.513 8.814 30303 Z= 0.264 Chirality : 0.040 0.140 3703 Planarity : 0.003 0.026 3934 Dihedral : 3.709 20.331 3178 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.37 % Allowed : 15.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.15), residues: 2975 helix: 1.97 (0.12), residues: 1771 sheet: 0.47 (0.26), residues: 413 loop : -0.04 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.010 0.001 TYR A 478 PHE 0.008 0.001 PHE B 8 HIS 0.000 0.000 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00298 (22491) covalent geometry : angle 0.51289 (30303) hydrogen bonds : bond 0.03944 ( 1502) hydrogen bonds : angle 4.01429 ( 4317) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 291 time to evaluate : 0.921 Fit side-chains REVERT: A 364 LYS cc_start: 0.7837 (tppt) cc_final: 0.6914 (tptt) REVERT: B 62 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8937 (mm) REVERT: B 111 MET cc_start: 0.7906 (tpp) cc_final: 0.7621 (mmt) REVERT: B 121 ASP cc_start: 0.7359 (t0) cc_final: 0.6847 (t0) REVERT: B 193 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.6478 (mtp) REVERT: B 490 ASP cc_start: 0.7778 (t0) cc_final: 0.7490 (t0) REVERT: C 364 LYS cc_start: 0.8149 (tppt) cc_final: 0.6776 (tptt) REVERT: D 62 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8712 (mm) REVERT: D 186 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7789 (mt-10) REVERT: D 490 ASP cc_start: 0.7935 (t0) cc_final: 0.7570 (t0) REVERT: E 186 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7880 (mt-10) REVERT: F 364 LYS cc_start: 0.7956 (tppt) cc_final: 0.7100 (tptt) REVERT: H 156 GLU cc_start: 0.8139 (mp0) cc_final: 0.7928 (mp0) REVERT: H 193 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.6444 (mtp) REVERT: H 290 GLN cc_start: 0.7052 (tm-30) cc_final: 0.6847 (tm-30) REVERT: H 328 ASP cc_start: 0.7938 (p0) cc_final: 0.7666 (p0) REVERT: H 389 MET cc_start: 0.7959 (tmm) cc_final: 0.7705 (tmm) REVERT: H 447 MET cc_start: 0.8129 (mtt) cc_final: 0.7598 (mtt) REVERT: H 490 ASP cc_start: 0.7830 (t0) cc_final: 0.7554 (t0) outliers start: 78 outliers final: 62 residues processed: 362 average time/residue: 0.1334 time to fit residues: 82.0995 Evaluate side-chains 345 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 279 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 494 LEU Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 519 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 242 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 179 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 243 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 192 optimal weight: 0.0470 chunk 202 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.185819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.157479 restraints weight = 27192.947| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.97 r_work: 0.3783 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22491 Z= 0.118 Angle : 0.510 9.103 30303 Z= 0.261 Chirality : 0.040 0.136 3703 Planarity : 0.003 0.025 3934 Dihedral : 3.699 19.577 3178 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.50 % Allowed : 15.93 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.15), residues: 2975 helix: 2.01 (0.12), residues: 1771 sheet: 0.69 (0.28), residues: 364 loop : 0.07 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 197 TYR 0.012 0.001 TYR E 199 PHE 0.008 0.001 PHE F 8 HIS 0.000 0.000 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00266 (22491) covalent geometry : angle 0.50969 (30303) hydrogen bonds : bond 0.03804 ( 1502) hydrogen bonds : angle 3.97700 ( 4317) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 290 time to evaluate : 0.925 Fit side-chains REVERT: A 41 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6901 (m-30) REVERT: A 364 LYS cc_start: 0.7844 (tppt) cc_final: 0.6909 (tptt) REVERT: A 380 LYS cc_start: 0.8517 (mttt) cc_final: 0.8244 (mmtp) REVERT: A 488 MET cc_start: 0.7447 (mmm) cc_final: 0.6523 (mmm) REVERT: B 62 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8929 (mm) REVERT: B 111 MET cc_start: 0.7955 (tpp) cc_final: 0.7668 (mmt) REVERT: B 121 ASP cc_start: 0.7302 (t0) cc_final: 0.6781 (t0) REVERT: B 193 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.6470 (mtp) REVERT: B 490 ASP cc_start: 0.7797 (t0) cc_final: 0.7527 (t0) REVERT: C 364 LYS cc_start: 0.8151 (tppt) cc_final: 0.6794 (tptt) REVERT: C 490 ASP cc_start: 0.7696 (t0) cc_final: 0.7459 (t0) REVERT: D 62 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8707 (mm) REVERT: D 111 MET cc_start: 0.8127 (mmt) cc_final: 0.7278 (mmt) REVERT: D 186 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7756 (mt-10) REVERT: D 490 ASP cc_start: 0.7921 (t0) cc_final: 0.7520 (t0) REVERT: E 186 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7868 (mt-10) REVERT: E 364 LYS cc_start: 0.8037 (tppt) cc_final: 0.7074 (tptt) REVERT: E 494 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8262 (pp) REVERT: F 364 LYS cc_start: 0.7959 (tppt) cc_final: 0.7078 (tptt) REVERT: H 41 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6752 (m-30) REVERT: H 156 GLU cc_start: 0.8096 (mp0) cc_final: 0.7865 (mp0) REVERT: H 186 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7716 (mt-10) REVERT: H 193 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.6350 (mtp) REVERT: H 389 MET cc_start: 0.7957 (tmm) cc_final: 0.7712 (tmm) REVERT: H 447 MET cc_start: 0.8068 (mtt) cc_final: 0.7483 (mtt) REVERT: H 490 ASP cc_start: 0.7848 (t0) cc_final: 0.7568 (t0) outliers start: 81 outliers final: 67 residues processed: 365 average time/residue: 0.1294 time to fit residues: 81.2360 Evaluate side-chains 351 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 277 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 494 LEU Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 519 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 230 optimal weight: 4.9990 chunk 149 optimal weight: 0.1980 chunk 197 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 246 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.183377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.154793 restraints weight = 27077.479| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.98 r_work: 0.3776 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22491 Z= 0.142 Angle : 0.540 9.485 30303 Z= 0.274 Chirality : 0.041 0.138 3703 Planarity : 0.003 0.026 3934 Dihedral : 3.779 24.111 3178 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.54 % Allowed : 15.88 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.15), residues: 2975 helix: 1.88 (0.12), residues: 1771 sheet: 0.63 (0.28), residues: 364 loop : -0.04 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 197 TYR 0.011 0.001 TYR A 478 PHE 0.009 0.001 PHE F 8 HIS 0.000 0.000 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00334 (22491) covalent geometry : angle 0.53988 (30303) hydrogen bonds : bond 0.04078 ( 1502) hydrogen bonds : angle 4.04931 ( 4317) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 298 time to evaluate : 0.904 Fit side-chains REVERT: A 41 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6874 (m-30) REVERT: A 364 LYS cc_start: 0.7876 (tppt) cc_final: 0.6920 (tptt) REVERT: A 488 MET cc_start: 0.7502 (mmm) cc_final: 0.6622 (mmm) REVERT: A 491 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7495 (mtt) REVERT: B 62 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8938 (mm) REVERT: B 111 MET cc_start: 0.7949 (tpp) cc_final: 0.7669 (mmt) REVERT: B 193 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.6520 (mtp) REVERT: B 326 ASN cc_start: 0.7496 (p0) cc_final: 0.7209 (p0) REVERT: B 445 ARG cc_start: 0.7897 (tpt170) cc_final: 0.7651 (tpt170) REVERT: B 490 ASP cc_start: 0.7813 (t0) cc_final: 0.7542 (t0) REVERT: C 290 GLN cc_start: 0.6714 (tm-30) cc_final: 0.6457 (pp30) REVERT: C 364 LYS cc_start: 0.8191 (tppt) cc_final: 0.6859 (tptt) REVERT: D 62 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8755 (mm) REVERT: D 111 MET cc_start: 0.8100 (mmt) cc_final: 0.7171 (mmt) REVERT: D 186 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7709 (mt-10) REVERT: D 490 ASP cc_start: 0.7815 (t0) cc_final: 0.7440 (t0) REVERT: E 186 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7840 (mt-10) REVERT: E 364 LYS cc_start: 0.8083 (tppt) cc_final: 0.7117 (tptt) REVERT: E 494 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8122 (pp) REVERT: F 111 MET cc_start: 0.7738 (mtt) cc_final: 0.7281 (ttm) REVERT: H 41 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6681 (m-30) REVERT: H 186 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7735 (mt-10) REVERT: H 193 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.6470 (mtp) REVERT: H 290 GLN cc_start: 0.7018 (tm-30) cc_final: 0.6738 (tm-30) REVERT: H 364 LYS cc_start: 0.8247 (tppt) cc_final: 0.7287 (tptt) REVERT: H 447 MET cc_start: 0.8235 (mtt) cc_final: 0.7740 (mtt) REVERT: H 490 ASP cc_start: 0.7890 (t0) cc_final: 0.7617 (t0) outliers start: 82 outliers final: 70 residues processed: 369 average time/residue: 0.1262 time to fit residues: 79.2382 Evaluate side-chains 361 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 283 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 494 LEU Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 524 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 80 optimal weight: 2.9990 chunk 20 optimal weight: 0.0020 chunk 258 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 296 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 255 optimal weight: 3.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.185423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157235 restraints weight = 27349.789| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.99 r_work: 0.3805 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22491 Z= 0.118 Angle : 0.534 11.588 30303 Z= 0.267 Chirality : 0.040 0.147 3703 Planarity : 0.003 0.025 3934 Dihedral : 3.755 24.558 3178 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.58 % Allowed : 16.53 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.15), residues: 2975 helix: 1.90 (0.12), residues: 1778 sheet: 0.66 (0.28), residues: 364 loop : 0.03 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 197 TYR 0.010 0.001 TYR A 478 PHE 0.007 0.001 PHE F 8 HIS 0.000 0.000 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00265 (22491) covalent geometry : angle 0.53382 (30303) hydrogen bonds : bond 0.03823 ( 1502) hydrogen bonds : angle 4.00077 ( 4317) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 283 time to evaluate : 0.897 Fit side-chains REVERT: A 41 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7038 (m-30) REVERT: A 364 LYS cc_start: 0.7860 (tppt) cc_final: 0.6889 (tptt) REVERT: A 380 LYS cc_start: 0.8553 (mttt) cc_final: 0.8265 (mmtp) REVERT: A 488 MET cc_start: 0.7464 (mmm) cc_final: 0.6606 (mmm) REVERT: B 62 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8934 (mm) REVERT: B 111 MET cc_start: 0.7897 (tpp) cc_final: 0.7609 (mmt) REVERT: B 121 ASP cc_start: 0.7285 (t0) cc_final: 0.6728 (t0) REVERT: B 453 GLN cc_start: 0.8694 (tp40) cc_final: 0.8275 (tp40) REVERT: B 490 ASP cc_start: 0.7741 (t0) cc_final: 0.7519 (t0) REVERT: C 290 GLN cc_start: 0.6610 (tm-30) cc_final: 0.6401 (pp30) REVERT: C 364 LYS cc_start: 0.8177 (tppt) cc_final: 0.6802 (tptt) REVERT: D 62 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8707 (mm) REVERT: D 111 MET cc_start: 0.8122 (mmt) cc_final: 0.7247 (mmt) REVERT: D 186 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7831 (mt-10) REVERT: D 490 ASP cc_start: 0.7722 (t0) cc_final: 0.7346 (t0) REVERT: E 186 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7881 (mt-10) REVERT: E 364 LYS cc_start: 0.8070 (tppt) cc_final: 0.7108 (tptt) REVERT: E 494 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8121 (pp) REVERT: F 111 MET cc_start: 0.7688 (mtt) cc_final: 0.7231 (ttm) REVERT: H 41 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6773 (m-30) REVERT: H 186 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7749 (mt-10) REVERT: H 193 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.6460 (mtp) REVERT: H 290 GLN cc_start: 0.6957 (tm-30) cc_final: 0.6684 (tm-30) REVERT: H 364 LYS cc_start: 0.8237 (tppt) cc_final: 0.7262 (tptt) REVERT: H 447 MET cc_start: 0.8142 (mtt) cc_final: 0.7622 (mtt) REVERT: H 490 ASP cc_start: 0.7826 (t0) cc_final: 0.7554 (t0) outliers start: 83 outliers final: 70 residues processed: 354 average time/residue: 0.1271 time to fit residues: 77.0340 Evaluate side-chains 354 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 278 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 494 LEU Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 519 CYS Chi-restraints excluded: chain H residue 524 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 83 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 96 optimal weight: 0.0370 chunk 233 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.185839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.157769 restraints weight = 27470.871| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.98 r_work: 0.3812 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22491 Z= 0.117 Angle : 0.542 13.552 30303 Z= 0.271 Chirality : 0.040 0.155 3703 Planarity : 0.003 0.025 3934 Dihedral : 3.764 24.273 3178 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.54 % Allowed : 16.44 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.15), residues: 2975 helix: 1.94 (0.12), residues: 1764 sheet: 0.67 (0.28), residues: 364 loop : 0.04 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 197 TYR 0.016 0.001 TYR E 199 PHE 0.011 0.001 PHE B 195 HIS 0.000 0.000 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00263 (22491) covalent geometry : angle 0.54183 (30303) hydrogen bonds : bond 0.03783 ( 1502) hydrogen bonds : angle 4.02054 ( 4317) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 286 time to evaluate : 0.844 Fit side-chains REVERT: A 41 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.6976 (m-30) REVERT: A 364 LYS cc_start: 0.7912 (tppt) cc_final: 0.6917 (tptt) REVERT: A 380 LYS cc_start: 0.8559 (mttt) cc_final: 0.8270 (mmtp) REVERT: B 62 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8868 (mm) REVERT: B 111 MET cc_start: 0.7916 (tpp) cc_final: 0.7632 (mmt) REVERT: B 121 ASP cc_start: 0.7263 (t0) cc_final: 0.6700 (t0) REVERT: B 326 ASN cc_start: 0.7478 (p0) cc_final: 0.7141 (p0) REVERT: C 16 MET cc_start: 0.7688 (mtp) cc_final: 0.7482 (mtp) REVERT: C 364 LYS cc_start: 0.8133 (tppt) cc_final: 0.6778 (tptt) REVERT: D 62 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8696 (mm) REVERT: D 111 MET cc_start: 0.8131 (mmt) cc_final: 0.7200 (mmt) REVERT: D 186 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7805 (mt-10) REVERT: D 490 ASP cc_start: 0.7684 (t0) cc_final: 0.7329 (t0) REVERT: E 364 LYS cc_start: 0.8076 (tppt) cc_final: 0.7107 (tptt) REVERT: E 494 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8130 (pp) REVERT: F 111 MET cc_start: 0.7661 (mtt) cc_final: 0.7411 (ttm) REVERT: F 326 ASN cc_start: 0.7271 (p0) cc_final: 0.6516 (m-40) REVERT: F 364 LYS cc_start: 0.8058 (tppt) cc_final: 0.7144 (tptt) REVERT: H 41 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6675 (m-30) REVERT: H 186 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7756 (mt-10) REVERT: H 193 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.6401 (mtp) REVERT: H 290 GLN cc_start: 0.6931 (tm-30) cc_final: 0.6602 (tm-30) REVERT: H 364 LYS cc_start: 0.8238 (tppt) cc_final: 0.7254 (tptt) REVERT: H 447 MET cc_start: 0.8131 (mtt) cc_final: 0.7623 (mtt) REVERT: H 490 ASP cc_start: 0.7830 (t0) cc_final: 0.7590 (t0) REVERT: H 520 MET cc_start: 0.8605 (mtt) cc_final: 0.8239 (mtt) outliers start: 82 outliers final: 71 residues processed: 360 average time/residue: 0.1159 time to fit residues: 71.6454 Evaluate side-chains 355 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 278 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 494 LEU Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 519 CYS Chi-restraints excluded: chain H residue 524 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 76 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 267 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 250 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.185341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.157243 restraints weight = 27355.928| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.97 r_work: 0.3808 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22491 Z= 0.122 Angle : 0.547 11.833 30303 Z= 0.273 Chirality : 0.040 0.152 3703 Planarity : 0.003 0.025 3934 Dihedral : 3.768 24.940 3178 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.37 % Allowed : 17.00 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.15), residues: 2975 helix: 1.89 (0.12), residues: 1771 sheet: 0.66 (0.29), residues: 364 loop : 0.04 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 197 TYR 0.010 0.001 TYR A 478 PHE 0.008 0.001 PHE B 8 HIS 0.000 0.000 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00279 (22491) covalent geometry : angle 0.54745 (30303) hydrogen bonds : bond 0.03802 ( 1502) hydrogen bonds : angle 4.04190 ( 4317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5486.63 seconds wall clock time: 94 minutes 53.34 seconds (5693.34 seconds total)