Starting phenix.real_space_refine on Mon May 19 08:16:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u9g_20698/05_2025/6u9g_20698.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u9g_20698/05_2025/6u9g_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_20698/05_2025/6u9g_20698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u9g_20698/05_2025/6u9g_20698.map" model { file = "/net/cci-nas-00/data/ceres_data/6u9g_20698/05_2025/6u9g_20698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u9g_20698/05_2025/6u9g_20698.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 7, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} 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: {'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 9 Restraints were copied for chains: D, F, C, E Time building chain proxies: 11.21, per 1000 atoms: 0.62 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: 3.64 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.35 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: 5.70 Time building geometry restraints manager: 4.35 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: 0.11 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } 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: 2.150 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: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 38.710 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.680 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.002 TRP E 334 HIS 0.010 0.002 HIS D 6 PHE 0.024 0.003 PHE E 636 TYR 0.027 0.003 TYR C 692 ARG 0.006 0.001 ARG C 730 Details of bonding type rmsd hydrogen bonds : bond 0.30588 ( 491) hydrogen bonds : angle 10.77433 ( 1404) covalent geometry : bond 0.00541 (18465) covalent geometry : angle 1.00071 (24909) *********************** 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 : 2.024 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: 0.3326 time to fit residues: 254.9374 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 : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 4.9990 chunk 177 optimal weight: 0.2980 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 212 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 C 378 GLN C 718 ASN E 378 GLN E 764 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108244 restraints weight = 30162.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110414 restraints weight = 18202.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111889 restraints weight = 12617.794| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18465 Z= 0.129 Angle : 0.706 11.739 24909 Z= 0.371 Chirality : 0.051 0.199 2907 Planarity : 0.003 0.024 3210 Dihedral : 7.272 35.255 2439 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % Rotamer: Outliers : 2.28 % Allowed : 10.25 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.15), residues: 2301 helix: -2.99 (0.20), residues: 303 sheet: -1.48 (0.20), residues: 609 loop : -3.43 (0.14), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 236 HIS 0.005 0.001 HIS F 6 PHE 0.021 0.002 PHE E 250 TYR 0.022 0.002 TYR C 389 ARG 0.005 0.001 ARG E 287 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 491) hydrogen bonds : angle 6.12463 ( 1404) covalent geometry : bond 0.00279 (18465) covalent geometry : angle 0.70551 (24909) *********************** 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 354 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 309 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ASP cc_start: 0.7920 (p0) cc_final: 0.7667 (p0) REVERT: A 498 ASP cc_start: 0.8520 (m-30) cc_final: 0.8200 (m-30) REVERT: A 522 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6413 (mt-10) REVERT: A 703 ASP cc_start: 0.7751 (m-30) cc_final: 0.7493 (t70) REVERT: A 721 SER cc_start: 0.8340 (p) cc_final: 0.8018 (p) REVERT: A 775 GLU cc_start: 0.7594 (pp20) cc_final: 0.6985 (pp20) REVERT: C 323 LYS cc_start: 0.7949 (mttt) cc_final: 0.7629 (mttm) REVERT: C 458 LYS cc_start: 0.8714 (ttpt) cc_final: 0.8200 (ttmt) REVERT: C 703 ASP cc_start: 0.7675 (m-30) cc_final: 0.7250 (t70) REVERT: C 721 SER cc_start: 0.8065 (p) cc_final: 0.7798 (p) REVERT: E 300 ILE cc_start: 0.9524 (mt) cc_final: 0.9190 (mt) REVERT: E 323 LYS cc_start: 0.8200 (mttt) cc_final: 0.7689 (mttt) REVERT: E 438 LYS cc_start: 0.8323 (mttt) cc_final: 0.7975 (mttt) REVERT: E 498 ASP cc_start: 0.8432 (m-30) cc_final: 0.8084 (m-30) REVERT: E 650 ASN cc_start: 0.7323 (m-40) cc_final: 0.7076 (m110) REVERT: E 703 ASP cc_start: 0.7870 (m-30) cc_final: 0.7575 (t70) REVERT: E 721 SER cc_start: 0.8445 (p) cc_final: 0.8232 (p) REVERT: E 764 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7822 (mm110) REVERT: B 10 LEU cc_start: 0.9290 (mt) cc_final: 0.8998 (mp) REVERT: B 20 LYS cc_start: 0.8396 (mttt) cc_final: 0.8109 (mttm) REVERT: B 49 ASP cc_start: 0.7454 (m-30) cc_final: 0.6997 (t0) REVERT: B 69 LEU cc_start: 0.8315 (mm) cc_final: 0.8049 (mp) REVERT: B 126 LYS cc_start: 0.7893 (mttm) cc_final: 0.7619 (mtpt) REVERT: F 12 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7228 (tt0) REVERT: F 126 LYS cc_start: 0.8032 (mttm) cc_final: 0.7786 (mtpt) outliers start: 45 outliers final: 26 residues processed: 344 average time/residue: 0.2884 time to fit residues: 150.6818 Evaluate side-chains 242 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 CYS 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 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 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 86 optimal weight: 0.5980 chunk 135 optimal weight: 8.9990 chunk 227 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 226 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 529 ASN E 529 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107588 restraints weight = 30477.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.108822 restraints weight = 20326.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110578 restraints weight = 13901.392| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18465 Z= 0.141 Angle : 0.664 10.212 24909 Z= 0.353 Chirality : 0.050 0.192 2907 Planarity : 0.003 0.054 3210 Dihedral : 6.797 36.183 2439 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 2.94 % Allowed : 13.09 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.15), residues: 2301 helix: -1.99 (0.25), residues: 285 sheet: -1.44 (0.20), residues: 612 loop : -3.29 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 236 HIS 0.004 0.001 HIS B 6 PHE 0.021 0.002 PHE C 293 TYR 0.019 0.002 TYR A 692 ARG 0.006 0.001 ARG C 287 Details of bonding type rmsd hydrogen bonds : bond 0.02946 ( 491) hydrogen bonds : angle 5.43461 ( 1404) covalent geometry : bond 0.00315 (18465) covalent geometry : angle 0.66363 (24909) *********************** 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 273 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 215 time to evaluate : 2.338 Fit side-chains revert: symmetry clash REVERT: A 498 ASP cc_start: 0.8449 (m-30) cc_final: 0.8102 (m-30) REVERT: A 522 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6436 (mt-10) REVERT: A 685 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7384 (t0) REVERT: A 689 ASP cc_start: 0.7561 (m-30) cc_final: 0.7358 (t0) REVERT: A 703 ASP cc_start: 0.7854 (m-30) cc_final: 0.7544 (t70) REVERT: A 721 SER cc_start: 0.8094 (p) cc_final: 0.7851 (p) REVERT: C 458 LYS cc_start: 0.8881 (ttpt) cc_final: 0.8160 (ttmt) REVERT: C 474 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7059 (tt) REVERT: C 498 ASP cc_start: 0.8295 (m-30) cc_final: 0.8043 (m-30) REVERT: C 685 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7499 (t0) REVERT: C 700 MET cc_start: 0.8796 (mtp) cc_final: 0.8582 (tpp) REVERT: C 703 ASP cc_start: 0.7704 (m-30) cc_final: 0.7232 (t70) REVERT: E 300 ILE cc_start: 0.9504 (mt) cc_final: 0.9244 (mt) REVERT: E 436 ASP cc_start: 0.6735 (t0) cc_final: 0.6495 (t0) REVERT: E 498 ASP cc_start: 0.8374 (m-30) cc_final: 0.8056 (m-30) REVERT: E 522 GLU cc_start: 0.6563 (mt-10) cc_final: 0.5856 (mt-10) REVERT: E 703 ASP cc_start: 0.7893 (m-30) cc_final: 0.7568 (t70) REVERT: B 49 ASP cc_start: 0.7504 (m-30) cc_final: 0.7037 (t0) REVERT: D 126 LYS cc_start: 0.8235 (mttm) cc_final: 0.7966 (tttt) REVERT: F 12 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7363 (tt0) REVERT: F 60 LYS cc_start: 0.7963 (mttt) cc_final: 0.7739 (mttp) REVERT: F 126 LYS cc_start: 0.8119 (mttm) cc_final: 0.7428 (tmtt) outliers start: 58 outliers final: 31 residues processed: 260 average time/residue: 0.2911 time to fit residues: 118.0770 Evaluate side-chains 209 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 2.023 ------------------------------------------------------------------------------- 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 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 685 ASN 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 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 545 ASN Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 685 ASN 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 530 THR 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 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 114 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 141 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 54 optimal weight: 0.2980 chunk 233 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 764 GLN D 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.103993 restraints weight = 31111.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.105851 restraints weight = 20237.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107507 restraints weight = 13455.876| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18465 Z= 0.186 Angle : 0.693 8.872 24909 Z= 0.367 Chirality : 0.050 0.199 2907 Planarity : 0.003 0.055 3210 Dihedral : 6.851 35.762 2439 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.08 % Favored : 86.92 % Rotamer: Outliers : 3.60 % Allowed : 13.95 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.16), residues: 2301 helix: -1.34 (0.27), residues: 303 sheet: -1.38 (0.20), residues: 636 loop : -3.29 (0.14), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 236 HIS 0.004 0.001 HIS A 337 PHE 0.019 0.002 PHE C 293 TYR 0.019 0.002 TYR C 692 ARG 0.006 0.001 ARG E 287 Details of bonding type rmsd hydrogen bonds : bond 0.02918 ( 491) hydrogen bonds : angle 5.22563 ( 1404) covalent geometry : bond 0.00424 (18465) covalent geometry : angle 0.69316 (24909) *********************** 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 276 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 205 time to evaluate : 2.123 Fit side-chains revert: symmetry clash REVERT: A 458 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8291 (ptmt) REVERT: A 498 ASP cc_start: 0.8501 (m-30) cc_final: 0.8144 (m-30) REVERT: A 522 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6665 (mt-10) REVERT: A 612 SER cc_start: 0.8660 (m) cc_final: 0.8433 (t) REVERT: A 685 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7675 (t0) REVERT: A 703 ASP cc_start: 0.7873 (m-30) cc_final: 0.7477 (t70) REVERT: C 240 ASP cc_start: 0.8140 (m-30) cc_final: 0.7812 (m-30) REVERT: C 436 ASP cc_start: 0.6481 (t0) cc_final: 0.6225 (t0) REVERT: C 458 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8100 (ttmt) REVERT: C 474 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6952 (tt) REVERT: C 498 ASP cc_start: 0.8394 (m-30) cc_final: 0.8031 (m-30) REVERT: C 612 SER cc_start: 0.8842 (m) cc_final: 0.8605 (t) REVERT: C 703 ASP cc_start: 0.7798 (m-30) cc_final: 0.7194 (t70) REVERT: E 225 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7760 (tt0) REVERT: E 300 ILE cc_start: 0.9476 (mt) cc_final: 0.9259 (mt) REVERT: E 436 ASP cc_start: 0.6616 (t0) cc_final: 0.6247 (t0) REVERT: E 438 LYS cc_start: 0.8180 (mttt) cc_final: 0.7906 (mmtp) REVERT: E 498 ASP cc_start: 0.8400 (m-30) cc_final: 0.8194 (m-30) REVERT: E 700 MET cc_start: 0.8772 (tpp) cc_final: 0.8458 (tpp) REVERT: E 703 ASP cc_start: 0.7871 (m-30) cc_final: 0.7595 (t70) REVERT: B 49 ASP cc_start: 0.7592 (m-30) cc_final: 0.7169 (t0) REVERT: B 60 LYS cc_start: 0.8244 (mttt) cc_final: 0.7911 (mttp) REVERT: B 126 LYS cc_start: 0.8457 (mttm) cc_final: 0.8184 (mtpt) REVERT: D 39 ASN cc_start: 0.8734 (m-40) cc_final: 0.8141 (t0) REVERT: D 60 LYS cc_start: 0.8081 (mttt) cc_final: 0.7794 (mttp) REVERT: F 12 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7345 (tt0) REVERT: F 39 ASN cc_start: 0.8637 (m-40) cc_final: 0.8198 (t0) REVERT: F 60 LYS cc_start: 0.8041 (mttt) cc_final: 0.7825 (mttp) REVERT: F 126 LYS cc_start: 0.8280 (mttm) cc_final: 0.7765 (tmtt) outliers start: 71 outliers final: 42 residues processed: 266 average time/residue: 0.2784 time to fit residues: 114.1770 Evaluate side-chains 221 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 2.064 ------------------------------------------------------------------------------- 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 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 522 GLU 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 685 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 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 545 ASN 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 C residue 690 ILE Chi-restraints excluded: chain C residue 732 ASP Chi-restraints excluded: chain E residue 227 CYS 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 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 789 THR Chi-restraints excluded: chain B residue 18 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 54 optimal weight: 0.7980 chunk 203 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 152 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.104949 restraints weight = 31020.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.107184 restraints weight = 20841.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.107931 restraints weight = 13611.027| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18465 Z= 0.140 Angle : 0.635 8.316 24909 Z= 0.338 Chirality : 0.049 0.217 2907 Planarity : 0.003 0.056 3210 Dihedral : 6.454 35.146 2439 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Rotamer: Outliers : 3.04 % Allowed : 15.83 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.16), residues: 2301 helix: -0.92 (0.29), residues: 303 sheet: -1.29 (0.20), residues: 636 loop : -3.25 (0.14), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 236 HIS 0.003 0.001 HIS C 220 PHE 0.016 0.001 PHE E 326 TYR 0.017 0.001 TYR C 692 ARG 0.004 0.001 ARG A 570 Details of bonding type rmsd hydrogen bonds : bond 0.02554 ( 491) hydrogen bonds : angle 4.99349 ( 1404) covalent geometry : bond 0.00316 (18465) covalent geometry : angle 0.63470 (24909) *********************** 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 259 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 2.009 Fit side-chains revert: symmetry clash REVERT: A 458 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8339 (ptmt) REVERT: A 498 ASP cc_start: 0.8388 (m-30) cc_final: 0.8025 (m-30) REVERT: A 612 SER cc_start: 0.8717 (m) cc_final: 0.8494 (t) REVERT: A 703 ASP cc_start: 0.7853 (m-30) cc_final: 0.7479 (t70) REVERT: C 240 ASP cc_start: 0.8078 (m-30) cc_final: 0.7703 (m-30) REVERT: C 287 ARG cc_start: 0.8120 (ttt180) cc_final: 0.7864 (ttt90) REVERT: C 436 ASP cc_start: 0.6499 (t0) cc_final: 0.6249 (t0) REVERT: C 438 LYS cc_start: 0.8022 (mttt) cc_final: 0.7761 (mmtp) REVERT: C 458 LYS cc_start: 0.8844 (ttpt) cc_final: 0.8115 (ttmt) REVERT: C 474 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7010 (tt) REVERT: C 498 ASP cc_start: 0.8337 (m-30) cc_final: 0.8011 (m-30) REVERT: C 612 SER cc_start: 0.8828 (m) cc_final: 0.8606 (t) REVERT: C 703 ASP cc_start: 0.7797 (m-30) cc_final: 0.7166 (t70) REVERT: E 328 ASP cc_start: 0.8497 (p0) cc_final: 0.8191 (p0) REVERT: E 436 ASP cc_start: 0.6659 (t0) cc_final: 0.6159 (t0) REVERT: E 438 LYS cc_start: 0.8159 (mttt) cc_final: 0.7909 (mmtp) REVERT: E 498 ASP cc_start: 0.8496 (m-30) cc_final: 0.8189 (m-30) REVERT: E 700 MET cc_start: 0.8874 (tpp) cc_final: 0.8475 (tpp) REVERT: E 703 ASP cc_start: 0.7937 (m-30) cc_final: 0.7629 (t70) REVERT: B 49 ASP cc_start: 0.7422 (m-30) cc_final: 0.7135 (t0) REVERT: B 60 LYS cc_start: 0.8112 (mttt) cc_final: 0.7801 (mttp) REVERT: B 126 LYS cc_start: 0.8463 (mttm) cc_final: 0.8204 (tttt) REVERT: D 39 ASN cc_start: 0.8606 (m-40) cc_final: 0.8025 (t0) REVERT: D 60 LYS cc_start: 0.7954 (mttt) cc_final: 0.7730 (mttp) REVERT: F 12 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7304 (tt0) REVERT: F 39 ASN cc_start: 0.8568 (m-40) cc_final: 0.8089 (t0) REVERT: F 60 LYS cc_start: 0.8011 (mttt) cc_final: 0.7783 (mttp) REVERT: F 126 LYS cc_start: 0.8261 (mttm) cc_final: 0.7645 (tmtt) outliers start: 60 outliers final: 48 residues processed: 248 average time/residue: 0.2695 time to fit residues: 105.3939 Evaluate side-chains 229 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 2.020 ------------------------------------------------------------------------------- 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 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 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 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 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 474 LEU Chi-restraints excluded: chain E residue 485 SER 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 721 SER 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 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 81 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 chunk 39 optimal weight: 0.6980 chunk 218 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 139 optimal weight: 0.0000 overall best weight: 0.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.107339 restraints weight = 30457.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109428 restraints weight = 20365.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110278 restraints weight = 13245.515| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18465 Z= 0.108 Angle : 0.603 7.645 24909 Z= 0.321 Chirality : 0.048 0.196 2907 Planarity : 0.003 0.056 3210 Dihedral : 6.038 34.382 2439 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer: Outliers : 2.94 % Allowed : 16.69 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.16), residues: 2301 helix: -0.52 (0.30), residues: 303 sheet: -1.21 (0.20), residues: 651 loop : -3.18 (0.15), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 236 HIS 0.003 0.001 HIS E 337 PHE 0.015 0.001 PHE E 326 TYR 0.017 0.001 TYR C 692 ARG 0.004 0.001 ARG A 570 Details of bonding type rmsd hydrogen bonds : bond 0.02308 ( 491) hydrogen bonds : angle 4.78852 ( 1404) covalent geometry : bond 0.00238 (18465) covalent geometry : angle 0.60254 (24909) *********************** 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 263 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 424 ASN cc_start: 0.7204 (m-40) cc_final: 0.7003 (p0) REVERT: A 498 ASP cc_start: 0.8334 (m-30) cc_final: 0.8023 (m-30) REVERT: A 612 SER cc_start: 0.8738 (m) cc_final: 0.8507 (t) REVERT: A 703 ASP cc_start: 0.7851 (m-30) cc_final: 0.7528 (t70) REVERT: C 240 ASP cc_start: 0.7945 (m-30) cc_final: 0.7610 (m-30) REVERT: C 436 ASP cc_start: 0.6394 (t0) cc_final: 0.6168 (t0) REVERT: C 438 LYS cc_start: 0.8046 (mttt) cc_final: 0.7776 (mmtp) REVERT: C 458 LYS cc_start: 0.8831 (ttpt) cc_final: 0.8167 (ttmt) REVERT: C 498 ASP cc_start: 0.8302 (m-30) cc_final: 0.7983 (m-30) REVERT: C 612 SER cc_start: 0.8774 (m) cc_final: 0.8525 (t) REVERT: C 703 ASP cc_start: 0.7779 (m-30) cc_final: 0.7142 (t70) REVERT: E 328 ASP cc_start: 0.8401 (p0) cc_final: 0.8109 (p0) REVERT: E 436 ASP cc_start: 0.6519 (t0) cc_final: 0.5970 (t0) REVERT: E 438 LYS cc_start: 0.8212 (mttt) cc_final: 0.7939 (mmtp) REVERT: E 700 MET cc_start: 0.8900 (tpp) cc_final: 0.8445 (tpp) REVERT: E 703 ASP cc_start: 0.7913 (m-30) cc_final: 0.7606 (t70) REVERT: B 126 LYS cc_start: 0.8423 (mttm) cc_final: 0.8158 (tttt) REVERT: F 12 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7322 (tt0) REVERT: F 126 LYS cc_start: 0.8156 (mttm) cc_final: 0.7432 (tmtt) outliers start: 58 outliers final: 43 residues processed: 253 average time/residue: 0.2617 time to fit residues: 105.2977 Evaluate side-chains 213 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 2.000 ------------------------------------------------------------------------------- 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 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 485 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 634 SER 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 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 721 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 9 optimal weight: 0.0020 chunk 89 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 159 optimal weight: 0.2980 chunk 5 optimal weight: 0.1980 chunk 150 optimal weight: 1.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.122832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107333 restraints weight = 30362.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109371 restraints weight = 18712.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.110777 restraints weight = 13174.930| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18465 Z= 0.106 Angle : 0.598 8.668 24909 Z= 0.318 Chirality : 0.048 0.190 2907 Planarity : 0.003 0.056 3210 Dihedral : 5.845 34.678 2439 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 2.59 % Allowed : 17.55 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.16), residues: 2301 helix: -0.16 (0.31), residues: 303 sheet: -1.11 (0.20), residues: 651 loop : -3.11 (0.15), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 236 HIS 0.003 0.001 HIS E 337 PHE 0.015 0.001 PHE C 357 TYR 0.016 0.001 TYR C 692 ARG 0.005 0.001 ARG A 570 Details of bonding type rmsd hydrogen bonds : bond 0.02327 ( 491) hydrogen bonds : angle 4.67049 ( 1404) covalent geometry : bond 0.00236 (18465) covalent geometry : angle 0.59759 (24909) *********************** 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 247 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 2.131 Fit side-chains revert: symmetry clash REVERT: A 498 ASP cc_start: 0.8270 (m-30) cc_final: 0.7916 (m-30) REVERT: A 612 SER cc_start: 0.8718 (m) cc_final: 0.8505 (t) REVERT: A 703 ASP cc_start: 0.7786 (m-30) cc_final: 0.7402 (t70) REVERT: A 775 GLU cc_start: 0.7592 (pp20) cc_final: 0.7160 (pp20) REVERT: C 240 ASP cc_start: 0.7914 (m-30) cc_final: 0.7644 (m-30) REVERT: C 436 ASP cc_start: 0.6397 (t0) cc_final: 0.6175 (t0) REVERT: C 438 LYS cc_start: 0.7992 (mttt) cc_final: 0.7731 (mmtp) REVERT: C 458 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8175 (ttmt) REVERT: C 498 ASP cc_start: 0.8253 (m-30) cc_final: 0.7927 (m-30) REVERT: C 612 SER cc_start: 0.8761 (m) cc_final: 0.8526 (t) REVERT: C 703 ASP cc_start: 0.7732 (m-30) cc_final: 0.7237 (t70) REVERT: E 328 ASP cc_start: 0.8402 (p0) cc_final: 0.8126 (p0) REVERT: E 436 ASP cc_start: 0.6409 (t0) cc_final: 0.5837 (t0) REVERT: E 438 LYS cc_start: 0.8093 (mttt) cc_final: 0.7860 (mmtp) REVERT: E 703 ASP cc_start: 0.7810 (m-30) cc_final: 0.7543 (t70) REVERT: B 126 LYS cc_start: 0.8424 (mttm) cc_final: 0.8193 (tttt) REVERT: F 12 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7275 (tt0) REVERT: F 126 LYS cc_start: 0.8192 (mttm) cc_final: 0.7551 (tmtt) outliers start: 51 outliers final: 44 residues processed: 235 average time/residue: 0.2855 time to fit residues: 104.3775 Evaluate side-chains 211 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 1.961 ------------------------------------------------------------------------------- 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 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 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 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 683 ILE Chi-restraints excluded: chain C residue 751 ILE 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 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 721 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.3766 > 50: distance: 21 - 107: 7.817 distance: 56 - 73: 7.722 distance: 59 - 70: 10.765 distance: 65 - 70: 10.687 distance: 70 - 71: 7.751 distance: 71 - 72: 24.100 distance: 71 - 74: 21.060 distance: 72 - 73: 12.889 distance: 72 - 78: 21.043 distance: 74 - 75: 17.285 distance: 75 - 76: 17.517 distance: 75 - 77: 12.290 distance: 78 - 79: 18.073 distance: 79 - 80: 18.468 distance: 80 - 81: 16.133 distance: 80 - 82: 11.317 distance: 82 - 83: 5.032 distance: 83 - 84: 4.816 distance: 83 - 86: 13.839 distance: 84 - 85: 23.661 distance: 84 - 96: 4.407 distance: 86 - 87: 21.488 distance: 87 - 88: 12.077 distance: 87 - 89: 6.341 distance: 88 - 90: 6.356 distance: 89 - 92: 9.268 distance: 90 - 91: 8.126 distance: 91 - 93: 7.904 distance: 92 - 94: 6.885 distance: 93 - 95: 7.447 distance: 96 - 97: 5.671 distance: 96 - 211: 7.769 distance: 97 - 98: 6.905 distance: 98 - 99: 7.476 distance: 98 - 104: 3.755 distance: 99 - 208: 6.800 distance: 100 - 101: 3.910 distance: 101 - 102: 9.546 distance: 101 - 103: 12.103 distance: 104 - 105: 12.845 distance: 105 - 106: 6.588 distance: 105 - 108: 8.792 distance: 106 - 107: 8.596 distance: 106 - 111: 8.223 distance: 108 - 109: 4.461 distance: 108 - 110: 16.489 distance: 111 - 112: 6.634 distance: 111 - 192: 5.001 distance: 112 - 115: 6.223 distance: 113 - 114: 4.986 distance: 114 - 189: 4.029 distance: 116 - 117: 4.730 distance: 117 - 119: 7.538 distance: 118 - 120: 6.029 distance: 119 - 121: 3.080 distance: 120 - 121: 4.049 distance: 122 - 123: 14.581 distance: 123 - 124: 4.551 distance: 123 - 126: 17.201 distance: 124 - 125: 12.091 distance: 124 - 130: 20.625 distance: 126 - 127: 15.193 distance: 127 - 128: 8.154 distance: 127 - 129: 24.276 distance: 130 - 131: 4.239 distance: 130 - 175: 7.610 distance: 131 - 132: 6.723 distance: 131 - 134: 15.267 distance: 132 - 133: 5.979 distance: 132 - 138: 25.096 distance: 133 - 172: 11.419 distance: 134 - 135: 15.008 distance: 135 - 136: 17.500 distance: 135 - 137: 24.847 distance: 138 - 139: 23.757 distance: 139 - 140: 33.044 distance: 139 - 142: 34.734 distance: 140 - 141: 22.682 distance: 140 - 143: 19.190 distance: 143 - 144: 6.124 distance: 144 - 145: 25.811 distance: 144 - 147: 8.140 distance: 145 - 146: 15.846