Starting phenix.real_space_refine on Thu Mar 5 01:54:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u9g_20698/03_2026/6u9g_20698.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u9g_20698/03_2026/6u9g_20698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u9g_20698/03_2026/6u9g_20698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u9g_20698/03_2026/6u9g_20698.map" model { file = "/net/cci-nas-00/data/ceres_data/6u9g_20698/03_2026/6u9g_20698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u9g_20698/03_2026/6u9g_20698.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 11511 2.51 5 N 3078 2.21 5 O 3594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18219 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5079 Classifications: {'peptide': 652} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'CIS': 6, 'PTRANS': 17, 'TRANS': 628} Chain breaks: 7 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 352 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'TYR:plan': 6, 'ARG:plan': 5, 'PHE:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 6, 'GLU:plan': 2, 'GLN:plan1': 3, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 153 Chain: "B" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 994 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'TRANS': 131} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Restraints were copied for chains: C, E, D, F Time building chain proxies: 4.87, per 1000 atoms: 0.27 Number of scatterers: 18219 At special positions: 0 Unit cell: (103.79, 104.86, 223.63, 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 36 16.00 O 3594 8.00 N 3078 7.00 C 11511 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: 1.50 Conformation dependent library (CDL) restraints added in 860.0 milliseconds 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4596 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 28 sheets defined 15.2% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.576A pdb=" N ILE A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 106 through 115 removed outlier: 3.571A pdb=" N LYS A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.555A pdb=" N ILE A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.525A pdb=" N LEU A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.513A pdb=" N SER A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 249 through 254 removed outlier: 4.000A pdb=" N LEU A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 335 Processing helix chain 'A' and resid 347 through 353 removed outlier: 3.648A pdb=" N LYS A 353 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.795A pdb=" N PHE A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 removed outlier: 3.784A pdb=" N GLN A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.747A pdb=" N LYS A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 578 " --> pdb=" O CYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 772 through 776 removed outlier: 4.222A pdb=" N ASN A 776 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 92 removed outlier: 3.575A pdb=" N ILE C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 106 through 115 removed outlier: 3.501A pdb=" N ILE C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 113 " --> pdb=" O LYS C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 removed outlier: 3.555A pdb=" N ILE C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.524A pdb=" N LEU C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 171 removed outlier: 3.513A pdb=" N SER C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'C' and resid 249 through 254 removed outlier: 4.000A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 335 Processing helix chain 'C' and resid 347 through 353 removed outlier: 3.647A pdb=" N LYS C 353 " --> pdb=" O ASP C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 398 removed outlier: 3.796A pdb=" N PHE C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 396 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 428 removed outlier: 3.784A pdb=" N GLN C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 581 removed outlier: 3.747A pdb=" N LYS C 576 " --> pdb=" O LYS C 572 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 577 " --> pdb=" O TYR C 573 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 578 " --> pdb=" O CYS C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 623 No H-bonds generated for 'chain 'C' and resid 621 through 623' Processing helix chain 'C' and resid 772 through 776 removed outlier: 4.221A pdb=" N ASN C 776 " --> pdb=" O SER C 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 92 removed outlier: 3.575A pdb=" N ILE E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 106 through 115 removed outlier: 3.572A pdb=" N LYS E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 124 removed outlier: 3.557A pdb=" N ILE E 124 " --> pdb=" O SER E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.525A pdb=" N LEU E 139 " --> pdb=" O ILE E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 171 removed outlier: 3.513A pdb=" N SER E 165 " --> pdb=" O ASN E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 248 No H-bonds generated for 'chain 'E' and resid 246 through 248' Processing helix chain 'E' and resid 249 through 254 removed outlier: 4.000A pdb=" N LEU E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 335 Processing helix chain 'E' and resid 347 through 353 removed outlier: 3.647A pdb=" N LYS E 353 " --> pdb=" O ASP E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 398 removed outlier: 3.796A pdb=" N PHE E 391 " --> pdb=" O ASN E 387 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU E 396 " --> pdb=" O PHE E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 428 removed outlier: 3.784A pdb=" N GLN E 427 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 581 removed outlier: 3.746A pdb=" N LYS E 576 " --> pdb=" O LYS E 572 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN E 577 " --> pdb=" O TYR E 573 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU E 578 " --> pdb=" O CYS E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 623 No H-bonds generated for 'chain 'E' and resid 621 through 623' Processing helix chain 'E' and resid 772 through 776 removed outlier: 4.221A pdb=" N ASN E 776 " --> pdb=" O SER E 773 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 188 removed outlier: 3.770A pdb=" N LYS A 179 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 284 " --> pdb=" O ASP A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 234 removed outlier: 6.740A pdb=" N THR A 238 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU A 224 " --> pdb=" O TRP A 236 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP A 236 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 239 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 234 removed outlier: 6.359A pdb=" N LYS A 616 " --> pdb=" O SER A 562 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ARG A 564 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR A 614 " --> pdb=" O ARG A 564 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 615 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 344 Processing sheet with id=AA5, first strand: chain 'A' and resid 363 through 365 Processing sheet with id=AA6, first strand: chain 'A' and resid 479 through 481 removed outlier: 9.270A pdb=" N TYR A 462 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N LYS A 497 " --> pdb=" O TYR A 462 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LYS A 464 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASN A 499 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS A 466 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 710 through 714 removed outlier: 7.328A pdb=" N ILE A 734 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU A 750 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 736 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS A 744 " --> pdb=" O GLN A 740 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 683 through 684 removed outlier: 3.784A pdb=" N ILE A 683 " --> pdb=" O ASN C 753 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 752 through 753 removed outlier: 3.828A pdb=" N ILE E 683 " --> pdb=" O ASN A 753 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 778 through 783 removed outlier: 4.202A pdb=" N ARG A 814 " --> pdb=" O SER A 802 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP B 18 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 15 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE B 36 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLN D 51 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N SER F 46 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE D 53 " --> pdb=" O SER F 46 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D 68 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER D 75 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASN B 108 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N SER D 104 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE B 107 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 179 through 188 removed outlier: 3.770A pdb=" N LYS C 179 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 284 " --> pdb=" O ASP C 268 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 233 through 234 removed outlier: 6.740A pdb=" N THR C 238 " --> pdb=" O GLU C 222 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU C 224 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP C 236 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 233 through 234 removed outlier: 6.358A pdb=" N LYS C 616 " --> pdb=" O SER C 562 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ARG C 564 " --> pdb=" O THR C 614 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR C 614 " --> pdb=" O ARG C 564 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR C 615 " --> pdb=" O LEU C 525 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 342 through 344 Processing sheet with id=AB6, first strand: chain 'C' and resid 363 through 365 Processing sheet with id=AB7, first strand: chain 'C' and resid 479 through 481 removed outlier: 9.271A pdb=" N TYR C 462 " --> pdb=" O ILE C 495 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N LYS C 497 " --> pdb=" O TYR C 462 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LYS C 464 " --> pdb=" O LYS C 497 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASN C 499 " --> pdb=" O LYS C 464 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS C 466 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 710 through 714 removed outlier: 7.327A pdb=" N ILE C 734 " --> pdb=" O LEU C 750 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU C 750 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU C 736 " --> pdb=" O ILE C 748 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS C 744 " --> pdb=" O GLN C 740 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 683 through 684 removed outlier: 3.841A pdb=" N ILE C 683 " --> pdb=" O ASN E 753 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 778 through 783 removed outlier: 4.203A pdb=" N ARG C 814 " --> pdb=" O SER C 802 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP D 18 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 15 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 179 through 188 removed outlier: 3.770A pdb=" N LYS E 179 " --> pdb=" O SER E 269 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG E 284 " --> pdb=" O ASP E 268 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 233 through 234 removed outlier: 6.740A pdb=" N THR E 238 " --> pdb=" O GLU E 222 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU E 224 " --> pdb=" O TRP E 236 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP E 236 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE E 239 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 233 through 234 removed outlier: 6.359A pdb=" N LYS E 616 " --> pdb=" O SER E 562 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ARG E 564 " --> pdb=" O THR E 614 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR E 614 " --> pdb=" O ARG E 564 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR E 615 " --> pdb=" O LEU E 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 342 through 344 Processing sheet with id=AC6, first strand: chain 'E' and resid 363 through 365 Processing sheet with id=AC7, first strand: chain 'E' and resid 479 through 481 removed outlier: 9.271A pdb=" N TYR E 462 " --> pdb=" O ILE E 495 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N LYS E 497 " --> pdb=" O TYR E 462 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LYS E 464 " --> pdb=" O LYS E 497 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASN E 499 " --> pdb=" O LYS E 464 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS E 466 " --> pdb=" O ASN E 499 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 710 through 714 removed outlier: 7.328A pdb=" N ILE E 734 " --> pdb=" O LEU E 750 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU E 750 " --> pdb=" O ILE E 734 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU E 736 " --> pdb=" O ILE E 748 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS E 744 " --> pdb=" O GLN E 740 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 778 through 783 removed outlier: 4.203A pdb=" N ARG E 814 " --> pdb=" O SER E 802 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP F 18 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU F 15 " --> pdb=" O LEU F 30 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLN B 51 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N SER D 46 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE B 53 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B 68 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE F 109 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.776A pdb=" N ILE F 68 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER F 75 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ASN D 108 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N SER F 104 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 109 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP F 124 " --> pdb=" O ILE B 115 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1404 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: 3.76 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5071 1.33 - 1.45: 2702 1.45 - 1.57: 10647 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 18465 Sorted by residual: bond pdb=" CG1 ILE E 739 " pdb=" CD1 ILE E 739 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.86e+00 bond pdb=" CG1 ILE A 739 " pdb=" CD1 ILE A 739 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.83e+00 bond pdb=" CG1 ILE C 739 " pdb=" CD1 ILE C 739 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.82e+00 bond pdb=" N SER E 686 " pdb=" CA SER E 686 " ideal model delta sigma weight residual 1.461 1.479 -0.018 1.38e-02 5.25e+03 1.78e+00 bond pdb=" CG1 ILE E 393 " pdb=" CD1 ILE E 393 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.68e+00 ... (remaining 18460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 23773 2.10 - 4.21: 973 4.21 - 6.31: 110 6.31 - 8.41: 35 8.41 - 10.52: 18 Bond angle restraints: 24909 Sorted by residual: angle pdb=" N ILE C 455 " pdb=" CA ILE C 455 " pdb=" C ILE C 455 " ideal model delta sigma weight residual 109.34 99.59 9.75 2.08e+00 2.31e-01 2.20e+01 angle pdb=" N ILE E 455 " pdb=" CA ILE E 455 " pdb=" C ILE E 455 " ideal model delta sigma weight residual 109.34 99.66 9.68 2.08e+00 2.31e-01 2.16e+01 angle pdb=" N ILE A 455 " pdb=" CA ILE A 455 " pdb=" C ILE A 455 " ideal model delta sigma weight residual 109.34 99.67 9.67 2.08e+00 2.31e-01 2.16e+01 angle pdb=" C SER A 773 " pdb=" N LYS A 774 " pdb=" CA LYS A 774 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C SER C 773 " pdb=" N LYS C 774 " pdb=" CA LYS C 774 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 ... (remaining 24904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.27: 10878 15.27 - 30.54: 471 30.54 - 45.81: 48 45.81 - 61.08: 0 61.08 - 76.35: 6 Dihedral angle restraints: 11403 sinusoidal: 4410 harmonic: 6993 Sorted by residual: dihedral pdb=" CA ASN E 218 " pdb=" C ASN E 218 " pdb=" N PRO E 219 " pdb=" CA PRO E 219 " ideal model delta harmonic sigma weight residual -180.00 -138.28 -41.72 0 5.00e+00 4.00e-02 6.96e+01 dihedral pdb=" CA ASN C 218 " pdb=" C ASN C 218 " pdb=" N PRO C 219 " pdb=" CA PRO C 219 " ideal model delta harmonic sigma weight residual -180.00 -138.30 -41.70 0 5.00e+00 4.00e-02 6.96e+01 dihedral pdb=" CA ASN A 218 " pdb=" C ASN A 218 " pdb=" N PRO A 219 " pdb=" CA PRO A 219 " ideal model delta harmonic sigma weight residual -180.00 -138.34 -41.66 0 5.00e+00 4.00e-02 6.94e+01 ... (remaining 11400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2070 0.056 - 0.112: 597 0.112 - 0.169: 199 0.169 - 0.225: 32 0.225 - 0.281: 9 Chirality restraints: 2907 Sorted by residual: chirality pdb=" CB ILE A 735 " pdb=" CA ILE A 735 " pdb=" CG1 ILE A 735 " pdb=" CG2 ILE A 735 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE C 735 " pdb=" CA ILE C 735 " pdb=" CG1 ILE C 735 " pdb=" CG2 ILE C 735 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB ILE E 735 " pdb=" CA ILE E 735 " pdb=" CG1 ILE E 735 " pdb=" CG2 ILE E 735 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 2904 not shown) Planarity restraints: 3210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 217 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C LYS C 217 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS C 217 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN C 218 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 217 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C LYS E 217 " -0.041 2.00e-02 2.50e+03 pdb=" O LYS E 217 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN E 218 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 217 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C LYS A 217 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS A 217 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 218 " 0.014 2.00e-02 2.50e+03 ... (remaining 3207 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2725 2.76 - 3.30: 15196 3.30 - 3.83: 26746 3.83 - 4.37: 31682 4.37 - 4.90: 54609 Nonbonded interactions: 130958 Sorted by model distance: nonbonded pdb=" O TYR C 505 " pdb=" OG SER C 686 " model vdw 2.228 3.040 nonbonded pdb=" O TYR A 505 " pdb=" OG SER A 686 " model vdw 2.228 3.040 nonbonded pdb=" O TYR E 505 " pdb=" OG SER E 686 " model vdw 2.229 3.040 nonbonded pdb=" OD1 ASN B 39 " pdb=" OG SER F 47 " model vdw 2.246 3.040 nonbonded pdb=" O PRO C 339 " pdb=" OG1 THR C 383 " model vdw 2.259 3.040 ... (remaining 130953 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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 group one per residue 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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.320 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 : 0.005 0.053 18465 Z= 0.248 Angle : 1.001 10.517 24909 Z= 0.549 Chirality : 0.062 0.281 2907 Planarity : 0.004 0.038 3210 Dihedral : 9.071 76.351 6807 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.79 % 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: -4.65 (0.14), residues: 2301 helix: -4.36 (0.13), residues: 288 sheet: -2.00 (0.19), residues: 630 loop : -3.50 (0.14), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 730 TYR 0.027 0.003 TYR C 692 PHE 0.024 0.003 PHE E 636 TRP 0.017 0.002 TRP E 334 HIS 0.010 0.002 HIS D 6 Details of bonding type rmsd covalent geometry : bond 0.00541 (18465) covalent geometry : angle 1.00071 (24909) hydrogen bonds : bond 0.30588 ( 491) hydrogen bonds : angle 10.77433 ( 1404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 0.766 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: A 419 VAL cc_start: 0.8719 (t) cc_final: 0.8499 (t) REVERT: A 498 ASP cc_start: 0.8762 (m-30) cc_final: 0.8383 (m-30) REVERT: A 650 ASN cc_start: 0.8011 (m-40) cc_final: 0.7602 (m110) REVERT: A 703 ASP cc_start: 0.7817 (m-30) cc_final: 0.7450 (t70) REVERT: A 721 SER cc_start: 0.8504 (p) cc_final: 0.8226 (p) REVERT: A 723 ASN cc_start: 0.7243 (m110) cc_final: 0.6544 (t0) REVERT: C 287 ARG cc_start: 0.7980 (ttt180) cc_final: 0.7764 (ttt90) REVERT: C 458 LYS cc_start: 0.8727 (ttpt) cc_final: 0.7993 (ttmt) REVERT: C 498 ASP cc_start: 0.8589 (m-30) cc_final: 0.8292 (m-30) REVERT: C 703 ASP cc_start: 0.7796 (m-30) cc_final: 0.7291 (t70) REVERT: C 721 SER cc_start: 0.8246 (p) cc_final: 0.8019 (p) REVERT: C 733 ASP cc_start: 0.8079 (m-30) cc_final: 0.7713 (m-30) REVERT: E 498 ASP cc_start: 0.8619 (m-30) cc_final: 0.8209 (m-30) REVERT: E 612 SER cc_start: 0.8645 (p) cc_final: 0.8436 (p) REVERT: E 703 ASP cc_start: 0.7888 (m-30) cc_final: 0.7509 (t70) REVERT: E 721 SER cc_start: 0.8647 (p) cc_final: 0.8417 (p) REVERT: B 12 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7319 (tt0) REVERT: B 60 LYS cc_start: 0.8062 (mttt) cc_final: 0.7841 (mptt) REVERT: D 12 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7176 (tt0) REVERT: D 60 LYS cc_start: 0.8079 (mttt) cc_final: 0.7686 (mttp) REVERT: F 12 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7273 (tt0) REVERT: F 52 ILE cc_start: 0.9225 (mt) cc_final: 0.9013 (mm) REVERT: F 60 LYS cc_start: 0.8325 (mttt) cc_final: 0.7904 (mttp) REVERT: F 126 LYS cc_start: 0.8075 (mttm) cc_final: 0.7780 (mtpt) outliers start: 0 outliers final: 0 residues processed: 531 average time/residue: 0.1593 time to fit residues: 122.5042 Evaluate side-chains 254 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0170 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN A 395 GLN A 718 ASN A 764 GLN C 378 GLN C 718 ASN E 294 ASN E 378 GLN E 764 GLN D 9 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106977 restraints weight = 30470.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109017 restraints weight = 18816.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.110394 restraints weight = 13166.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111395 restraints weight = 10104.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.112037 restraints weight = 8222.498| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18465 Z= 0.148 Angle : 0.726 11.791 24909 Z= 0.382 Chirality : 0.051 0.205 2907 Planarity : 0.003 0.025 3210 Dihedral : 7.482 35.586 2439 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 2.49 % Allowed : 10.25 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % 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: -4.13 (0.15), residues: 2301 helix: -2.99 (0.20), residues: 300 sheet: -1.53 (0.20), residues: 609 loop : -3.44 (0.14), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 287 TYR 0.021 0.002 TYR E 692 PHE 0.023 0.002 PHE E 250 TRP 0.007 0.001 TRP E 236 HIS 0.005 0.001 HIS D 6 Details of bonding type rmsd covalent geometry : bond 0.00327 (18465) covalent geometry : angle 0.72580 (24909) hydrogen bonds : bond 0.03635 ( 491) hydrogen bonds : angle 6.18866 ( 1404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 291 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ASP cc_start: 0.7902 (p0) cc_final: 0.7645 (p0) REVERT: A 498 ASP cc_start: 0.8494 (m-30) cc_final: 0.8181 (m-30) REVERT: A 522 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6433 (mt-10) REVERT: A 650 ASN cc_start: 0.7438 (m-40) cc_final: 0.7216 (m110) REVERT: A 703 ASP cc_start: 0.7843 (m-30) cc_final: 0.7599 (t70) REVERT: A 721 SER cc_start: 0.8412 (p) cc_final: 0.8098 (p) REVERT: A 775 GLU cc_start: 0.7597 (pp20) cc_final: 0.6973 (pp20) REVERT: C 253 LEU cc_start: 0.9255 (mt) cc_final: 0.8836 (mt) REVERT: C 323 LYS cc_start: 0.7966 (mttt) cc_final: 0.7632 (mttm) REVERT: C 458 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8202 (ttmt) REVERT: C 703 ASP cc_start: 0.7700 (m-30) cc_final: 0.7295 (t70) REVERT: C 721 SER cc_start: 0.8121 (p) cc_final: 0.7885 (p) REVERT: E 300 ILE cc_start: 0.9540 (mt) cc_final: 0.9205 (mt) REVERT: E 438 LYS cc_start: 0.8369 (mttt) cc_final: 0.8032 (mttt) REVERT: E 498 ASP cc_start: 0.8463 (m-30) cc_final: 0.8132 (m-30) REVERT: E 516 ILE cc_start: 0.9045 (mp) cc_final: 0.8671 (mp) REVERT: E 650 ASN cc_start: 0.7379 (m-40) cc_final: 0.7107 (m110) REVERT: E 703 ASP cc_start: 0.7878 (m-30) cc_final: 0.7587 (t70) REVERT: E 721 SER cc_start: 0.8483 (p) cc_final: 0.8256 (p) REVERT: E 764 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7847 (mm110) REVERT: B 12 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7388 (tt0) REVERT: B 18 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.8034 (p0) REVERT: B 20 LYS cc_start: 0.8459 (mttt) cc_final: 0.8200 (mttm) REVERT: B 49 ASP cc_start: 0.7485 (m-30) cc_final: 0.7110 (t0) REVERT: B 60 LYS cc_start: 0.8092 (mttt) cc_final: 0.7745 (mttp) REVERT: F 12 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7356 (tt0) REVERT: F 60 LYS cc_start: 0.8136 (mttt) cc_final: 0.7751 (mttp) REVERT: F 126 LYS cc_start: 0.8092 (mttm) cc_final: 0.7862 (mtpt) outliers start: 49 outliers final: 28 residues processed: 330 average time/residue: 0.1334 time to fit residues: 67.6484 Evaluate side-chains 244 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 634 SER Chi-restraints excluded: chain E residue 667 SER Chi-restraints excluded: chain E residue 671 GLU Chi-restraints excluded: chain E residue 764 GLN Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain F residue 97 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 101 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 529 ASN C 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.105411 restraints weight = 31029.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107420 restraints weight = 19562.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.108982 restraints weight = 13577.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109325 restraints weight = 9592.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109576 restraints weight = 8691.120| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18465 Z= 0.153 Angle : 0.684 10.004 24909 Z= 0.363 Chirality : 0.050 0.222 2907 Planarity : 0.003 0.055 3210 Dihedral : 6.982 36.324 2439 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % Rotamer: Outliers : 2.94 % Allowed : 12.99 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % 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: -3.76 (0.15), residues: 2301 helix: -2.08 (0.25), residues: 285 sheet: -1.41 (0.20), residues: 621 loop : -3.29 (0.14), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 287 TYR 0.019 0.002 TYR A 692 PHE 0.015 0.002 PHE C 449 TRP 0.011 0.002 TRP A 236 HIS 0.004 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00349 (18465) covalent geometry : angle 0.68365 (24909) hydrogen bonds : bond 0.03025 ( 491) hydrogen bonds : angle 5.49783 ( 1404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ASP cc_start: 0.7979 (p0) cc_final: 0.7535 (p0) REVERT: A 498 ASP cc_start: 0.8479 (m-30) cc_final: 0.8142 (m-30) REVERT: A 522 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6552 (mt-10) REVERT: A 650 ASN cc_start: 0.7403 (m-40) cc_final: 0.7162 (m110) REVERT: A 703 ASP cc_start: 0.7760 (m-30) cc_final: 0.7514 (t70) REVERT: A 721 SER cc_start: 0.8172 (p) cc_final: 0.7921 (p) REVERT: C 458 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8150 (ttmt) REVERT: C 498 ASP cc_start: 0.8310 (m-30) cc_final: 0.8029 (m-30) REVERT: C 522 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6583 (mt-10) REVERT: C 703 ASP cc_start: 0.7702 (m-30) cc_final: 0.7278 (t70) REVERT: C 721 SER cc_start: 0.8048 (p) cc_final: 0.7842 (p) REVERT: E 299 ASP cc_start: 0.7977 (t0) cc_final: 0.7746 (t0) REVERT: E 300 ILE cc_start: 0.9520 (mt) cc_final: 0.9308 (mt) REVERT: E 436 ASP cc_start: 0.6742 (t0) cc_final: 0.6518 (t0) REVERT: E 498 ASP cc_start: 0.8417 (m-30) cc_final: 0.8052 (m-30) REVERT: E 703 ASP cc_start: 0.7880 (m-30) cc_final: 0.7635 (t70) REVERT: B 12 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7407 (tt0) REVERT: B 49 ASP cc_start: 0.7581 (m-30) cc_final: 0.7138 (t0) REVERT: B 60 LYS cc_start: 0.8163 (mttt) cc_final: 0.7859 (mttp) REVERT: D 39 ASN cc_start: 0.8636 (m-40) cc_final: 0.8009 (t0) REVERT: D 60 LYS cc_start: 0.8110 (mttt) cc_final: 0.7743 (mttp) REVERT: D 126 LYS cc_start: 0.8236 (mttm) cc_final: 0.7975 (tttt) REVERT: F 12 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7345 (tt0) REVERT: F 39 ASN cc_start: 0.8578 (m-40) cc_final: 0.8115 (t0) REVERT: F 60 LYS cc_start: 0.8075 (mttt) cc_final: 0.7830 (mttp) REVERT: F 126 LYS cc_start: 0.8189 (mttm) cc_final: 0.7504 (tmtt) outliers start: 58 outliers final: 34 residues processed: 274 average time/residue: 0.1327 time to fit residues: 56.1306 Evaluate side-chains 228 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 732 ASP Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 634 SER Chi-restraints excluded: chain E residue 671 GLU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 97 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 217 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 174 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 0.0470 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 overall best weight: 1.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 685 ASN E 529 ASN E 764 GLN D 114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103500 restraints weight = 31344.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.105832 restraints weight = 18823.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.106309 restraints weight = 13686.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106901 restraints weight = 10598.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.108174 restraints weight = 9372.179| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18465 Z= 0.177 Angle : 0.688 9.081 24909 Z= 0.364 Chirality : 0.050 0.200 2907 Planarity : 0.003 0.054 3210 Dihedral : 6.865 35.622 2439 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.21 % Favored : 86.79 % Rotamer: Outliers : 3.45 % Allowed : 13.55 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % 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: -3.60 (0.16), residues: 2301 helix: -1.39 (0.27), residues: 303 sheet: -1.39 (0.20), residues: 636 loop : -3.31 (0.14), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 287 TYR 0.019 0.002 TYR A 692 PHE 0.016 0.002 PHE C 356 TRP 0.022 0.002 TRP A 236 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00404 (18465) covalent geometry : angle 0.68804 (24909) hydrogen bonds : bond 0.02853 ( 491) hydrogen bonds : angle 5.20729 ( 1404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 214 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ASP cc_start: 0.8458 (m-30) cc_final: 0.8153 (m-30) REVERT: A 522 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6649 (mt-10) REVERT: A 612 SER cc_start: 0.8675 (m) cc_final: 0.8406 (t) REVERT: A 703 ASP cc_start: 0.7838 (m-30) cc_final: 0.7523 (t70) REVERT: C 240 ASP cc_start: 0.8158 (m-30) cc_final: 0.7839 (m-30) REVERT: C 436 ASP cc_start: 0.6611 (t0) cc_final: 0.6401 (t0) REVERT: C 458 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8092 (ttmt) REVERT: C 612 SER cc_start: 0.8831 (m) cc_final: 0.8583 (t) REVERT: C 703 ASP cc_start: 0.7699 (m-30) cc_final: 0.7190 (t70) REVERT: E 299 ASP cc_start: 0.8057 (t0) cc_final: 0.7828 (t0) REVERT: E 436 ASP cc_start: 0.6635 (t0) cc_final: 0.6253 (t0) REVERT: E 438 LYS cc_start: 0.8145 (mttt) cc_final: 0.7881 (mmtp) REVERT: E 498 ASP cc_start: 0.8353 (m-30) cc_final: 0.8048 (m-30) REVERT: E 700 MET cc_start: 0.8756 (tpp) cc_final: 0.8471 (tpp) REVERT: B 12 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7479 (tt0) REVERT: B 18 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8269 (p0) REVERT: B 49 ASP cc_start: 0.7607 (m-30) cc_final: 0.7244 (t0) REVERT: B 60 LYS cc_start: 0.8241 (mttt) cc_final: 0.7901 (mttp) REVERT: D 39 ASN cc_start: 0.8667 (m-40) cc_final: 0.8143 (t0) REVERT: D 60 LYS cc_start: 0.8090 (mttt) cc_final: 0.7775 (mttp) REVERT: F 12 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7284 (tt0) REVERT: F 39 ASN cc_start: 0.8648 (m-40) cc_final: 0.8177 (t0) REVERT: F 60 LYS cc_start: 0.8123 (mttt) cc_final: 0.7884 (mttp) outliers start: 68 outliers final: 42 residues processed: 268 average time/residue: 0.1266 time to fit residues: 53.4529 Evaluate side-chains 223 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 634 SER Chi-restraints excluded: chain E residue 667 SER Chi-restraints excluded: chain E residue 671 GLU Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 789 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 97 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 224 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 209 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 181 optimal weight: 0.0040 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 ASN B 114 ASN F 114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103102 restraints weight = 31284.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103366 restraints weight = 26092.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.105076 restraints weight = 17625.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.105921 restraints weight = 12262.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106631 restraints weight = 11262.327| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18465 Z= 0.176 Angle : 0.670 8.623 24909 Z= 0.357 Chirality : 0.050 0.196 2907 Planarity : 0.003 0.055 3210 Dihedral : 6.728 35.699 2439 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 3.30 % Allowed : 15.88 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % 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: -3.53 (0.16), residues: 2301 helix: -1.01 (0.29), residues: 303 sheet: -1.38 (0.20), residues: 636 loop : -3.32 (0.14), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 570 TYR 0.017 0.002 TYR A 692 PHE 0.019 0.002 PHE C 356 TRP 0.025 0.003 TRP E 236 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00400 (18465) covalent geometry : angle 0.67026 (24909) hydrogen bonds : bond 0.02717 ( 491) hydrogen bonds : angle 5.12092 ( 1404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 195 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ASP cc_start: 0.8445 (m-30) cc_final: 0.8129 (m-30) REVERT: A 612 SER cc_start: 0.8738 (m) cc_final: 0.8490 (t) REVERT: A 703 ASP cc_start: 0.7825 (m-30) cc_final: 0.7491 (t70) REVERT: C 240 ASP cc_start: 0.8121 (m-30) cc_final: 0.7781 (m-30) REVERT: C 436 ASP cc_start: 0.6456 (t0) cc_final: 0.6185 (t0) REVERT: C 438 LYS cc_start: 0.8088 (mttt) cc_final: 0.7819 (mmtp) REVERT: C 458 LYS cc_start: 0.8859 (ttpt) cc_final: 0.8148 (ttmt) REVERT: C 612 SER cc_start: 0.8826 (m) cc_final: 0.8603 (t) REVERT: C 700 MET cc_start: 0.9112 (tpp) cc_final: 0.8885 (mmm) REVERT: C 703 ASP cc_start: 0.7769 (m-30) cc_final: 0.7213 (t70) REVERT: E 328 ASP cc_start: 0.8440 (p0) cc_final: 0.8088 (p0) REVERT: E 330 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9190 (mt) REVERT: E 427 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.7047 (mt0) REVERT: E 436 ASP cc_start: 0.6530 (t0) cc_final: 0.6014 (t0) REVERT: E 438 LYS cc_start: 0.8200 (mttt) cc_final: 0.7957 (mmtp) REVERT: E 498 ASP cc_start: 0.8367 (m-30) cc_final: 0.8100 (m-30) REVERT: E 700 MET cc_start: 0.8906 (tpp) cc_final: 0.8484 (tpp) REVERT: B 12 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7519 (tt0) REVERT: B 60 LYS cc_start: 0.8241 (mttt) cc_final: 0.7899 (mttp) REVERT: D 39 ASN cc_start: 0.8692 (m-40) cc_final: 0.8201 (t0) REVERT: D 60 LYS cc_start: 0.8079 (mttt) cc_final: 0.7829 (mttp) REVERT: F 12 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7296 (tt0) REVERT: F 39 ASN cc_start: 0.8676 (m-40) cc_final: 0.8234 (t0) REVERT: F 60 LYS cc_start: 0.8185 (mttt) cc_final: 0.7924 (mttp) REVERT: F 126 LYS cc_start: 0.8311 (mttm) cc_final: 0.7660 (tmtt) outliers start: 65 outliers final: 52 residues processed: 245 average time/residue: 0.1181 time to fit residues: 46.4289 Evaluate side-chains 229 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 175 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 544 ASP Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 404 LYS Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 634 SER Chi-restraints excluded: chain E residue 667 SER Chi-restraints excluded: chain E residue 671 GLU Chi-restraints excluded: chain E residue 690 ILE Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 735 ILE Chi-restraints excluded: chain E residue 789 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain F residue 97 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 106 optimal weight: 0.0770 chunk 221 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 164 optimal weight: 0.0060 chunk 117 optimal weight: 0.4980 chunk 177 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.4554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 806 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105967 restraints weight = 30387.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.107966 restraints weight = 18823.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109410 restraints weight = 13365.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110408 restraints weight = 10246.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.111098 restraints weight = 8363.057| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18465 Z= 0.107 Angle : 0.608 7.797 24909 Z= 0.325 Chirality : 0.048 0.184 2907 Planarity : 0.003 0.056 3210 Dihedral : 6.094 34.225 2439 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 2.74 % Allowed : 16.95 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.04 % 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: -3.25 (0.16), residues: 2301 helix: -0.59 (0.29), residues: 303 sheet: -1.16 (0.20), residues: 636 loop : -3.21 (0.14), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 570 TYR 0.016 0.001 TYR A 692 PHE 0.021 0.001 PHE A 250 TRP 0.026 0.003 TRP E 236 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00234 (18465) covalent geometry : angle 0.60789 (24909) hydrogen bonds : bond 0.02355 ( 491) hydrogen bonds : angle 4.87352 ( 1404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ASP cc_start: 0.8354 (m-30) cc_final: 0.8040 (m-30) REVERT: A 612 SER cc_start: 0.8736 (m) cc_final: 0.8482 (t) REVERT: A 703 ASP cc_start: 0.7784 (m-30) cc_final: 0.7471 (t70) REVERT: A 775 GLU cc_start: 0.7532 (pp20) cc_final: 0.7130 (pp20) REVERT: C 240 ASP cc_start: 0.8003 (m-30) cc_final: 0.7696 (m-30) REVERT: C 436 ASP cc_start: 0.6411 (t0) cc_final: 0.6120 (t0) REVERT: C 438 LYS cc_start: 0.8019 (mttt) cc_final: 0.7761 (mmtp) REVERT: C 458 LYS cc_start: 0.8825 (ttpt) cc_final: 0.8095 (ttmt) REVERT: C 612 SER cc_start: 0.8753 (m) cc_final: 0.8500 (t) REVERT: C 703 ASP cc_start: 0.7589 (m-30) cc_final: 0.7137 (t70) REVERT: E 328 ASP cc_start: 0.8359 (p0) cc_final: 0.8153 (p0) REVERT: E 436 ASP cc_start: 0.6490 (t0) cc_final: 0.6023 (t0) REVERT: E 498 ASP cc_start: 0.8216 (m-30) cc_final: 0.7883 (m-30) REVERT: E 523 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8550 (tt) REVERT: E 700 MET cc_start: 0.8851 (tpp) cc_final: 0.8401 (tpp) REVERT: B 12 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7383 (tt0) REVERT: F 12 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7299 (tt0) REVERT: F 39 ASN cc_start: 0.8463 (m-40) cc_final: 0.7968 (t0) REVERT: F 126 LYS cc_start: 0.8187 (mttm) cc_final: 0.7539 (tmtt) outliers start: 54 outliers final: 41 residues processed: 244 average time/residue: 0.1193 time to fit residues: 46.4196 Evaluate side-chains 211 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 404 LYS Chi-restraints excluded: chain E residue 472 VAL Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 634 SER Chi-restraints excluded: chain E residue 667 SER Chi-restraints excluded: chain E residue 671 GLU Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 735 ILE Chi-restraints excluded: chain E residue 751 ILE Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 97 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 193 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 93 optimal weight: 0.2980 chunk 167 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 226 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.121341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105576 restraints weight = 30834.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.107993 restraints weight = 20369.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.108959 restraints weight = 13970.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.109807 restraints weight = 10197.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.109903 restraints weight = 9114.183| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18465 Z= 0.117 Angle : 0.610 7.592 24909 Z= 0.325 Chirality : 0.048 0.184 2907 Planarity : 0.003 0.057 3210 Dihedral : 6.022 35.217 2439 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 2.99 % Allowed : 17.00 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.04 % 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: -3.13 (0.16), residues: 2301 helix: -0.25 (0.30), residues: 303 sheet: -1.08 (0.21), residues: 621 loop : -3.17 (0.14), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 570 TYR 0.016 0.001 TYR A 692 PHE 0.015 0.001 PHE C 326 TRP 0.029 0.003 TRP E 236 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00262 (18465) covalent geometry : angle 0.61004 (24909) hydrogen bonds : bond 0.02352 ( 491) hydrogen bonds : angle 4.76024 ( 1404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 191 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ASP cc_start: 0.8307 (m-30) cc_final: 0.7991 (m-30) REVERT: A 523 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8537 (tt) REVERT: A 612 SER cc_start: 0.8738 (m) cc_final: 0.8503 (t) REVERT: A 703 ASP cc_start: 0.7804 (m-30) cc_final: 0.7432 (t70) REVERT: A 775 GLU cc_start: 0.7514 (pp20) cc_final: 0.7091 (pp20) REVERT: C 240 ASP cc_start: 0.7990 (m-30) cc_final: 0.7740 (m-30) REVERT: C 436 ASP cc_start: 0.6431 (t0) cc_final: 0.6133 (t0) REVERT: C 438 LYS cc_start: 0.8031 (mttt) cc_final: 0.7725 (mmtp) REVERT: C 458 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8109 (ttmt) REVERT: C 612 SER cc_start: 0.8710 (m) cc_final: 0.8491 (t) REVERT: C 703 ASP cc_start: 0.7650 (m-30) cc_final: 0.7184 (t70) REVERT: E 498 ASP cc_start: 0.8150 (m-30) cc_final: 0.7816 (m-30) REVERT: E 523 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8577 (tt) REVERT: B 12 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7330 (tt0) REVERT: D 39 ASN cc_start: 0.8559 (m-40) cc_final: 0.7968 (t0) REVERT: F 12 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7280 (tt0) REVERT: F 39 ASN cc_start: 0.8575 (m-40) cc_final: 0.8024 (t0) REVERT: F 126 LYS cc_start: 0.8255 (mttm) cc_final: 0.7718 (tmtt) outliers start: 59 outliers final: 48 residues processed: 240 average time/residue: 0.1211 time to fit residues: 46.9618 Evaluate side-chains 225 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 404 LYS Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 634 SER Chi-restraints excluded: chain E residue 667 SER Chi-restraints excluded: chain E residue 671 GLU Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 735 ILE Chi-restraints excluded: chain E residue 751 ILE Chi-restraints excluded: chain E residue 789 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 97 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 136 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 129 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 159 optimal weight: 0.2980 chunk 65 optimal weight: 10.0000 chunk 121 optimal weight: 0.5980 chunk 170 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.120952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.105710 restraints weight = 30575.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.107706 restraints weight = 20584.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108585 restraints weight = 14923.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109378 restraints weight = 11059.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109484 restraints weight = 9812.913| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18465 Z= 0.126 Angle : 0.622 10.681 24909 Z= 0.329 Chirality : 0.048 0.194 2907 Planarity : 0.003 0.059 3210 Dihedral : 6.004 34.437 2439 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer: Outliers : 2.99 % Allowed : 17.71 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.04 % 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: -3.07 (0.16), residues: 2301 helix: -0.07 (0.31), residues: 303 sheet: -1.04 (0.21), residues: 624 loop : -3.17 (0.14), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 570 TYR 0.015 0.001 TYR A 692 PHE 0.021 0.001 PHE C 250 TRP 0.034 0.003 TRP A 236 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00286 (18465) covalent geometry : angle 0.62158 (24909) hydrogen bonds : bond 0.02378 ( 491) hydrogen bonds : angle 4.74913 ( 1404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ASP cc_start: 0.8255 (m-30) cc_final: 0.7944 (m-30) REVERT: A 612 SER cc_start: 0.8791 (m) cc_final: 0.8545 (t) REVERT: A 703 ASP cc_start: 0.7765 (m-30) cc_final: 0.7379 (t70) REVERT: A 775 GLU cc_start: 0.7532 (pp20) cc_final: 0.7094 (pp20) REVERT: C 240 ASP cc_start: 0.8031 (m-30) cc_final: 0.7729 (m-30) REVERT: C 436 ASP cc_start: 0.6442 (t0) cc_final: 0.6125 (t0) REVERT: C 438 LYS cc_start: 0.8051 (mttt) cc_final: 0.7677 (mmtp) REVERT: C 458 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8159 (ttmt) REVERT: C 612 SER cc_start: 0.8725 (m) cc_final: 0.8501 (t) REVERT: C 703 ASP cc_start: 0.7727 (m-30) cc_final: 0.7253 (t70) REVERT: E 436 ASP cc_start: 0.6336 (t0) cc_final: 0.5823 (t0) REVERT: E 498 ASP cc_start: 0.8145 (m-30) cc_final: 0.7823 (m-30) REVERT: E 523 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8511 (tt) REVERT: B 12 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7347 (tt0) REVERT: D 39 ASN cc_start: 0.8594 (m-40) cc_final: 0.8000 (t0) REVERT: F 12 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7292 (tt0) REVERT: F 39 ASN cc_start: 0.8603 (m-40) cc_final: 0.8072 (t0) REVERT: F 126 LYS cc_start: 0.8262 (mttm) cc_final: 0.7766 (tmtt) outliers start: 59 outliers final: 50 residues processed: 233 average time/residue: 0.1105 time to fit residues: 42.1789 Evaluate side-chains 223 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 404 LYS Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 634 SER Chi-restraints excluded: chain E residue 671 GLU Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 735 ILE Chi-restraints excluded: chain E residue 751 ILE Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 789 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 97 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 0.4980 chunk 48 optimal weight: 0.3980 chunk 138 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 218 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.121549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106185 restraints weight = 30645.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.108334 restraints weight = 19171.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109344 restraints weight = 13637.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.110093 restraints weight = 9872.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.110211 restraints weight = 8932.264| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18465 Z= 0.120 Angle : 0.612 9.754 24909 Z= 0.324 Chirality : 0.048 0.193 2907 Planarity : 0.003 0.060 3210 Dihedral : 5.894 34.605 2439 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 2.74 % Allowed : 18.16 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % 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: -3.00 (0.16), residues: 2301 helix: 0.03 (0.31), residues: 303 sheet: -0.95 (0.21), residues: 627 loop : -3.18 (0.14), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 570 TYR 0.015 0.001 TYR A 692 PHE 0.023 0.001 PHE C 250 TRP 0.036 0.003 TRP E 236 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00272 (18465) covalent geometry : angle 0.61156 (24909) hydrogen bonds : bond 0.02314 ( 491) hydrogen bonds : angle 4.70760 ( 1404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 180 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ASP cc_start: 0.8271 (m-30) cc_final: 0.7974 (m-30) REVERT: A 612 SER cc_start: 0.8791 (m) cc_final: 0.8539 (t) REVERT: A 703 ASP cc_start: 0.7768 (m-30) cc_final: 0.7500 (t70) REVERT: A 775 GLU cc_start: 0.7589 (pp20) cc_final: 0.7193 (pp20) REVERT: C 240 ASP cc_start: 0.8050 (m-30) cc_final: 0.7758 (m-30) REVERT: C 436 ASP cc_start: 0.6452 (t0) cc_final: 0.6120 (t0) REVERT: C 438 LYS cc_start: 0.8017 (mttt) cc_final: 0.7626 (mmtp) REVERT: C 458 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8171 (ttmt) REVERT: C 612 SER cc_start: 0.8719 (m) cc_final: 0.8501 (t) REVERT: C 703 ASP cc_start: 0.7720 (m-30) cc_final: 0.7281 (t70) REVERT: E 498 ASP cc_start: 0.8157 (m-30) cc_final: 0.7811 (m-30) REVERT: E 523 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8544 (tt) REVERT: B 12 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7318 (tt0) REVERT: D 39 ASN cc_start: 0.8562 (m-40) cc_final: 0.7965 (t0) REVERT: F 12 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7293 (tt0) REVERT: F 39 ASN cc_start: 0.8585 (m-40) cc_final: 0.8011 (t0) outliers start: 54 outliers final: 51 residues processed: 225 average time/residue: 0.1167 time to fit residues: 42.3956 Evaluate side-chains 221 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 472 VAL Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 634 SER Chi-restraints excluded: chain E residue 667 SER Chi-restraints excluded: chain E residue 671 GLU Chi-restraints excluded: chain E residue 735 ILE Chi-restraints excluded: chain E residue 751 ILE Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 789 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 97 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 181 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 144 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 230 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.121933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106155 restraints weight = 30589.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.108662 restraints weight = 20087.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109625 restraints weight = 13676.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110433 restraints weight = 9905.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110575 restraints weight = 8902.395| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18465 Z= 0.117 Angle : 0.608 9.685 24909 Z= 0.322 Chirality : 0.048 0.192 2907 Planarity : 0.003 0.061 3210 Dihedral : 5.840 34.220 2439 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 2.69 % Allowed : 18.26 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.09 % 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: -2.94 (0.16), residues: 2301 helix: 0.15 (0.31), residues: 303 sheet: -0.88 (0.21), residues: 627 loop : -3.16 (0.14), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 570 TYR 0.015 0.001 TYR A 692 PHE 0.028 0.001 PHE C 326 TRP 0.035 0.003 TRP E 236 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00265 (18465) covalent geometry : angle 0.60784 (24909) hydrogen bonds : bond 0.02288 ( 491) hydrogen bonds : angle 4.67695 ( 1404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 185 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 ASP cc_start: 0.8222 (m-30) cc_final: 0.7910 (m-30) REVERT: A 612 SER cc_start: 0.8743 (m) cc_final: 0.8466 (t) REVERT: A 703 ASP cc_start: 0.7778 (m-30) cc_final: 0.7486 (t70) REVERT: A 775 GLU cc_start: 0.7593 (pp20) cc_final: 0.7203 (pp20) REVERT: C 240 ASP cc_start: 0.8038 (m-30) cc_final: 0.7763 (m-30) REVERT: C 436 ASP cc_start: 0.6466 (t0) cc_final: 0.6144 (t0) REVERT: C 438 LYS cc_start: 0.7991 (mttt) cc_final: 0.7592 (mmtp) REVERT: C 458 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8173 (ttmt) REVERT: C 612 SER cc_start: 0.8735 (m) cc_final: 0.8501 (t) REVERT: C 703 ASP cc_start: 0.7736 (m-30) cc_final: 0.7268 (t70) REVERT: E 436 ASP cc_start: 0.6381 (t0) cc_final: 0.5602 (t0) REVERT: E 523 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8577 (tt) REVERT: B 12 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7320 (tt0) REVERT: D 39 ASN cc_start: 0.8562 (m-40) cc_final: 0.7952 (t0) REVERT: F 12 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7284 (tt0) REVERT: F 39 ASN cc_start: 0.8575 (m-40) cc_final: 0.8008 (t0) outliers start: 53 outliers final: 51 residues processed: 229 average time/residue: 0.1092 time to fit residues: 41.4301 Evaluate side-chains 225 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 173 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 617 ILE Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 472 VAL Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 634 SER Chi-restraints excluded: chain E residue 667 SER Chi-restraints excluded: chain E residue 671 GLU Chi-restraints excluded: chain E residue 735 ILE Chi-restraints excluded: chain E residue 751 ILE Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 789 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 97 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 199 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 233 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 187 optimal weight: 0.0020 chunk 70 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102711 restraints weight = 31075.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104984 restraints weight = 20380.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.105935 restraints weight = 14289.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.106816 restraints weight = 10498.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106946 restraints weight = 9270.857| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18465 Z= 0.172 Angle : 0.656 9.877 24909 Z= 0.348 Chirality : 0.049 0.189 2907 Planarity : 0.003 0.059 3210 Dihedral : 6.263 35.171 2439 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.43 % Favored : 86.57 % Rotamer: Outliers : 2.69 % Allowed : 18.52 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % 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: -3.07 (0.16), residues: 2301 helix: 0.00 (0.31), residues: 303 sheet: -1.19 (0.20), residues: 675 loop : -3.17 (0.15), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 570 TYR 0.016 0.001 TYR E 692 PHE 0.027 0.002 PHE C 250 TRP 0.036 0.004 TRP E 236 HIS 0.004 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00395 (18465) covalent geometry : angle 0.65631 (24909) hydrogen bonds : bond 0.02584 ( 491) hydrogen bonds : angle 4.83010 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2511.85 seconds wall clock time: 44 minutes 41.69 seconds (2681.69 seconds total)