Starting phenix.real_space_refine on Sat Feb 17 09:26:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9g_20698/02_2024/6u9g_20698.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9g_20698/02_2024/6u9g_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9g_20698/02_2024/6u9g_20698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9g_20698/02_2024/6u9g_20698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9g_20698/02_2024/6u9g_20698.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9g_20698/02_2024/6u9g_20698.pdb" } 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 Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18219 Number of models: 1 Model: "" Number of chains: 6 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: "C" 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: "E" 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 Chain: "D" 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 Chain: "F" 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 Time building chain proxies: 9.90, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 6.28 Conformation dependent library (CDL) restraints added in 3.2 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: 2.09 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: 5.97 Time building geometry restraints manager: 6.85 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: 97.91 - 105.13: 197 105.13 - 112.34: 9404 112.34 - 119.55: 6106 119.55 - 126.76: 9058 126.76 - 133.97: 144 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 2.440 nonbonded pdb=" O TYR A 505 " pdb=" OG SER A 686 " model vdw 2.228 2.440 nonbonded pdb=" O TYR E 505 " pdb=" OG SER E 686 " model vdw 2.229 2.440 nonbonded pdb=" OD1 ASN B 39 " pdb=" OG SER F 47 " model vdw 2.246 2.440 nonbonded pdb=" O PRO C 339 " pdb=" OG1 THR C 383 " model vdw 2.259 2.440 ... (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 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: 2.830 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: 9.720 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 47.090 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.950 ------------------------------------------------------------------------------- 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= 0.353 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 531 time to evaluate : 2.435 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: 0.3358 time to fit residues: 257.0558 Evaluate side-chains 254 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.314 ------------------------------------------------------------------------------- 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: 1.9990 chunk 177 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN A 395 GLN A 718 ASN A 764 GLN C 294 ASN ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 GLN C 545 ASN C 718 ASN E 294 ASN ** E 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN E 764 GLN D 9 ASN D 114 ASN F 114 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18465 Z= 0.241 Angle : 0.724 11.577 24909 Z= 0.379 Chirality : 0.051 0.205 2907 Planarity : 0.003 0.026 3210 Dihedral : 7.538 35.831 2439 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.08 % Favored : 86.92 % Rotamer: Outliers : 2.99 % Allowed : 9.94 % Favored : 87.06 % 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: -4.14 (0.15), residues: 2301 helix: -2.95 (0.20), residues: 300 sheet: -1.56 (0.20), residues: 603 loop : -3.45 (0.14), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 236 HIS 0.005 0.001 HIS D 6 PHE 0.024 0.002 PHE E 250 TYR 0.023 0.002 TYR A 389 ARG 0.009 0.001 ARG E 287 *********************** 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 350 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 291 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ASP cc_start: 0.8071 (p0) cc_final: 0.7800 (p0) REVERT: A 498 ASP cc_start: 0.8582 (m-30) cc_final: 0.8309 (m-30) REVERT: A 522 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6488 (mt-10) REVERT: A 650 ASN cc_start: 0.7588 (m-40) cc_final: 0.7339 (m110) REVERT: A 689 ASP cc_start: 0.7501 (m-30) cc_final: 0.7300 (t0) REVERT: A 703 ASP cc_start: 0.7881 (m-30) cc_final: 0.7551 (t70) REVERT: A 721 SER cc_start: 0.8514 (p) cc_final: 0.8226 (p) REVERT: A 732 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8457 (t0) REVERT: A 775 GLU cc_start: 0.7537 (pp20) cc_final: 0.6906 (pp20) REVERT: C 253 LEU cc_start: 0.9302 (mt) cc_final: 0.8928 (mt) REVERT: C 323 LYS cc_start: 0.7973 (mttt) cc_final: 0.7625 (mttm) REVERT: C 419 VAL cc_start: 0.8873 (t) cc_final: 0.8664 (t) REVERT: C 458 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8095 (ttmt) REVERT: C 522 GLU cc_start: 0.6597 (mt-10) cc_final: 0.6206 (mt-10) REVERT: C 703 ASP cc_start: 0.7835 (m-30) cc_final: 0.7362 (t70) REVERT: C 721 SER cc_start: 0.8184 (p) cc_final: 0.7951 (p) REVERT: E 300 ILE cc_start: 0.9541 (mt) cc_final: 0.9270 (mt) REVERT: E 458 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8407 (ptmt) REVERT: E 498 ASP cc_start: 0.8520 (m-30) cc_final: 0.8191 (m-30) REVERT: E 703 ASP cc_start: 0.7855 (m-30) cc_final: 0.7461 (t70) REVERT: E 721 SER cc_start: 0.8611 (p) cc_final: 0.8240 (m) REVERT: E 732 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8332 (t0) REVERT: E 764 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7891 (mm110) REVERT: E 775 GLU cc_start: 0.7538 (pp20) cc_final: 0.7223 (pp20) REVERT: B 18 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7993 (p0) REVERT: B 20 LYS cc_start: 0.8477 (mttt) cc_final: 0.8186 (mttm) REVERT: B 49 ASP cc_start: 0.7576 (m-30) cc_final: 0.7116 (t0) REVERT: B 60 LYS cc_start: 0.8176 (mttt) cc_final: 0.7822 (mttp) REVERT: B 126 LYS cc_start: 0.8210 (mttm) cc_final: 0.7959 (mtpt) REVERT: D 12 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7181 (tt0) REVERT: D 60 LYS cc_start: 0.8127 (mttt) cc_final: 0.7741 (mttp) REVERT: F 12 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7354 (tt0) REVERT: F 39 ASN cc_start: 0.8564 (m-40) cc_final: 0.8075 (t0) REVERT: F 60 LYS cc_start: 0.8181 (mttt) cc_final: 0.7767 (mttp) REVERT: F 81 GLU cc_start: 0.6362 (tp30) cc_final: 0.6028 (tp30) REVERT: F 126 LYS cc_start: 0.8040 (mttm) cc_final: 0.7751 (mtpt) outliers start: 59 outliers final: 33 residues processed: 339 average time/residue: 0.2914 time to fit residues: 150.1233 Evaluate side-chains 250 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 213 time to evaluate : 2.114 ------------------------------------------------------------------------------- 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 485 SER Chi-restraints excluded: chain A residue 506 ILE 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 671 GLU Chi-restraints excluded: chain A residue 732 ASP 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 374 ILE Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 527 SER Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 544 ASP Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 651 ASP 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 530 THR Chi-restraints excluded: chain E residue 544 ASP 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 732 ASP Chi-restraints excluded: chain E residue 764 GLN Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain D residue 58 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 0.1980 chunk 65 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 229 optimal weight: 0.0770 chunk 189 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN E 294 ASN E 529 ASN B 114 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18465 Z= 0.179 Angle : 0.645 10.705 24909 Z= 0.340 Chirality : 0.049 0.220 2907 Planarity : 0.003 0.044 3210 Dihedral : 6.729 36.062 2439 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 3.09 % Allowed : 13.19 % Favored : 83.71 % 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: -3.76 (0.15), residues: 2301 helix: -1.92 (0.26), residues: 285 sheet: -1.45 (0.20), residues: 615 loop : -3.30 (0.14), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 236 HIS 0.004 0.001 HIS F 6 PHE 0.013 0.002 PHE C 356 TYR 0.019 0.001 TYR A 692 ARG 0.004 0.001 ARG A 570 *********************** 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 295 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 234 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ASP cc_start: 0.8044 (p0) cc_final: 0.7578 (p0) REVERT: A 458 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8279 (ptmt) REVERT: A 498 ASP cc_start: 0.8564 (m-30) cc_final: 0.8219 (m-30) REVERT: A 612 SER cc_start: 0.8673 (m) cc_final: 0.8430 (t) REVERT: A 650 ASN cc_start: 0.7418 (m-40) cc_final: 0.7171 (m110) REVERT: A 703 ASP cc_start: 0.7789 (m-30) cc_final: 0.7516 (t70) REVERT: A 721 SER cc_start: 0.8259 (p) cc_final: 0.8030 (p) REVERT: A 732 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8443 (t0) REVERT: C 225 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7561 (tt0) REVERT: C 253 LEU cc_start: 0.9257 (mt) cc_final: 0.8985 (mt) REVERT: C 458 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8136 (ttmt) REVERT: C 498 ASP cc_start: 0.8494 (m-30) cc_final: 0.8046 (m-30) REVERT: C 703 ASP cc_start: 0.7763 (m-30) cc_final: 0.7285 (t70) REVERT: E 299 ASP cc_start: 0.7882 (t0) cc_final: 0.7659 (t0) REVERT: E 300 ILE cc_start: 0.9538 (mt) cc_final: 0.9316 (mt) REVERT: E 409 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7583 (mtpp) REVERT: E 436 ASP cc_start: 0.6687 (t0) cc_final: 0.6463 (t0) REVERT: E 498 ASP cc_start: 0.8449 (m-30) cc_final: 0.8156 (m-30) REVERT: E 703 ASP cc_start: 0.7826 (m-30) cc_final: 0.7468 (t70) REVERT: B 49 ASP cc_start: 0.7523 (m-30) cc_final: 0.7002 (t0) REVERT: B 60 LYS cc_start: 0.8077 (mttt) cc_final: 0.7728 (mttp) REVERT: D 12 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7234 (tt0) REVERT: D 126 LYS cc_start: 0.8236 (mttm) cc_final: 0.7973 (tttt) REVERT: F 12 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7266 (tt0) REVERT: F 126 LYS cc_start: 0.8014 (mttm) cc_final: 0.7262 (tmtt) outliers start: 61 outliers final: 33 residues processed: 284 average time/residue: 0.2852 time to fit residues: 124.9390 Evaluate side-chains 227 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 192 time to evaluate : 2.258 ------------------------------------------------------------------------------- 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 460 ASN Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 544 ASP 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 671 GLU Chi-restraints excluded: chain A residue 732 ASP 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 415 SER Chi-restraints excluded: chain C residue 475 ASN Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 527 SER Chi-restraints excluded: chain C residue 544 ASP Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain E residue 409 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 527 SER Chi-restraints excluded: chain E residue 544 ASP Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 634 SER Chi-restraints excluded: chain E residue 671 GLU Chi-restraints excluded: chain D residue 58 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 ASN A 796 ASN C 796 ASN E 764 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18465 Z= 0.356 Angle : 0.740 8.662 24909 Z= 0.389 Chirality : 0.051 0.207 2907 Planarity : 0.003 0.044 3210 Dihedral : 7.213 36.011 2439 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.99 % Favored : 85.01 % Rotamer: Outliers : 3.75 % Allowed : 14.26 % Favored : 81.99 % 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: -3.70 (0.16), residues: 2301 helix: -1.29 (0.28), residues: 300 sheet: -1.57 (0.20), residues: 627 loop : -3.34 (0.14), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 236 HIS 0.005 0.002 HIS A 220 PHE 0.037 0.002 PHE E 250 TYR 0.019 0.002 TYR A 692 ARG 0.007 0.001 ARG E 287 *********************** 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 270 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 196 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8144 (p0) REVERT: A 458 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8334 (ptmt) REVERT: A 498 ASP cc_start: 0.8563 (m-30) cc_final: 0.8272 (m-30) REVERT: A 703 ASP cc_start: 0.7869 (m-30) cc_final: 0.7504 (t70) REVERT: A 721 SER cc_start: 0.8478 (p) cc_final: 0.8259 (p) REVERT: C 225 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7619 (tt0) REVERT: C 240 ASP cc_start: 0.8275 (m-30) cc_final: 0.7976 (m-30) REVERT: C 458 LYS cc_start: 0.8849 (ttpt) cc_final: 0.8178 (ttmt) REVERT: C 498 ASP cc_start: 0.8549 (m-30) cc_final: 0.8171 (m-30) REVERT: C 612 SER cc_start: 0.8832 (m) cc_final: 0.8598 (t) REVERT: C 703 ASP cc_start: 0.7872 (m-30) cc_final: 0.7292 (t70) REVERT: E 225 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7774 (tt0) REVERT: E 436 ASP cc_start: 0.6631 (t0) cc_final: 0.6207 (t0) REVERT: E 438 LYS cc_start: 0.8289 (mttt) cc_final: 0.7959 (mmtp) REVERT: E 498 ASP cc_start: 0.8460 (m-30) cc_final: 0.8170 (m-30) REVERT: E 703 ASP cc_start: 0.7861 (m-30) cc_final: 0.7492 (t70) REVERT: E 721 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8301 (m) REVERT: E 732 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8271 (t0) REVERT: E 775 GLU cc_start: 0.7656 (pp20) cc_final: 0.7336 (pp20) REVERT: B 7 ILE cc_start: 0.8982 (mt) cc_final: 0.8742 (mt) REVERT: B 49 ASP cc_start: 0.7703 (m-30) cc_final: 0.7192 (t0) REVERT: B 60 LYS cc_start: 0.8310 (mttt) cc_final: 0.7999 (mttp) REVERT: B 126 LYS cc_start: 0.8591 (mttm) cc_final: 0.8286 (mtpt) REVERT: D 12 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7279 (tt0) REVERT: D 60 LYS cc_start: 0.8195 (mttt) cc_final: 0.7939 (mttp) REVERT: D 126 LYS cc_start: 0.8370 (mttm) cc_final: 0.8090 (tttt) REVERT: F 12 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7182 (tt0) REVERT: F 60 LYS cc_start: 0.8295 (mttt) cc_final: 0.7994 (mttp) outliers start: 74 outliers final: 49 residues processed: 261 average time/residue: 0.2888 time to fit residues: 117.7125 Evaluate side-chains 229 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 177 time to evaluate : 2.321 ------------------------------------------------------------------------------- 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 404 LYS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 475 ASN 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 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 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 415 SER Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 527 SER Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 544 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 474 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 527 SER Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 544 ASP 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 732 ASP Chi-restraints excluded: chain E residue 789 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain D residue 58 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 188 optimal weight: 1.9990 chunk 128 optimal weight: 0.0270 chunk 3 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 57 optimal weight: 0.0030 overall best weight: 0.9852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18465 Z= 0.234 Angle : 0.647 8.127 24909 Z= 0.345 Chirality : 0.049 0.203 2907 Planarity : 0.003 0.040 3210 Dihedral : 6.668 35.245 2439 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 3.25 % Allowed : 16.18 % Favored : 80.57 % 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: -3.60 (0.16), residues: 2301 helix: -0.99 (0.29), residues: 303 sheet: -1.46 (0.20), residues: 624 loop : -3.36 (0.14), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 236 HIS 0.004 0.001 HIS A 220 PHE 0.026 0.002 PHE E 250 TYR 0.016 0.001 TYR A 692 ARG 0.005 0.001 ARG E 287 *********************** 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 261 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 197 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.8663 (ttpt) cc_final: 0.8263 (ptmt) REVERT: A 498 ASP cc_start: 0.8476 (m-30) cc_final: 0.8168 (m-30) REVERT: A 612 SER cc_start: 0.8791 (m) cc_final: 0.8509 (t) REVERT: A 703 ASP cc_start: 0.7815 (m-30) cc_final: 0.7515 (t70) REVERT: C 225 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7598 (tt0) REVERT: C 240 ASP cc_start: 0.8108 (m-30) cc_final: 0.7765 (m-30) REVERT: C 458 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8161 (ttmt) REVERT: C 498 ASP cc_start: 0.8482 (m-30) cc_final: 0.8108 (m-30) REVERT: C 612 SER cc_start: 0.8817 (m) cc_final: 0.8611 (t) REVERT: C 703 ASP cc_start: 0.7834 (m-30) cc_final: 0.7243 (t70) REVERT: E 436 ASP cc_start: 0.6602 (t0) cc_final: 0.6155 (t0) REVERT: E 438 LYS cc_start: 0.8225 (mttt) cc_final: 0.7940 (mmtp) REVERT: E 498 ASP cc_start: 0.8443 (m-30) cc_final: 0.8178 (m-30) REVERT: E 703 ASP cc_start: 0.7811 (m-30) cc_final: 0.7487 (t70) REVERT: E 732 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8265 (t0) REVERT: E 775 GLU cc_start: 0.7677 (pp20) cc_final: 0.7395 (pp20) REVERT: B 49 ASP cc_start: 0.7596 (m-30) cc_final: 0.7072 (t0) REVERT: B 60 LYS cc_start: 0.8129 (mttt) cc_final: 0.7832 (mttp) REVERT: B 126 LYS cc_start: 0.8570 (mttm) cc_final: 0.8299 (mtpt) REVERT: D 12 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7212 (tt0) REVERT: D 60 LYS cc_start: 0.8062 (mttt) cc_final: 0.7811 (mttp) REVERT: D 126 LYS cc_start: 0.8167 (mttm) cc_final: 0.7932 (tttt) REVERT: F 12 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7136 (tt0) REVERT: F 60 LYS cc_start: 0.8183 (mttt) cc_final: 0.7906 (mttp) REVERT: F 126 LYS cc_start: 0.8212 (mttm) cc_final: 0.7502 (tmtt) outliers start: 64 outliers final: 44 residues processed: 250 average time/residue: 0.3000 time to fit residues: 118.5719 Evaluate side-chains 225 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 180 time to evaluate : 2.278 ------------------------------------------------------------------------------- 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 460 ASN Chi-restraints excluded: chain A residue 465 GLU 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 751 ILE Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 527 SER Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 544 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 474 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 527 SER Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 544 ASP 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 732 ASP Chi-restraints excluded: chain E residue 735 ILE Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain D residue 58 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 187 optimal weight: 0.0870 chunk 104 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4321 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= 0.177 Angle : 0.613 7.637 24909 Z= 0.327 Chirality : 0.049 0.195 2907 Planarity : 0.003 0.039 3210 Dihedral : 6.211 35.319 2439 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 2.99 % Allowed : 17.25 % Favored : 79.76 % 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: -3.45 (0.16), residues: 2301 helix: -0.77 (0.30), residues: 285 sheet: -1.32 (0.20), residues: 621 loop : -3.28 (0.14), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E 236 HIS 0.003 0.001 HIS A 220 PHE 0.026 0.001 PHE E 250 TYR 0.015 0.001 TYR A 692 ARG 0.010 0.001 ARG E 287 *********************** 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 260 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 201 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 ASN cc_start: 0.7447 (m-40) cc_final: 0.7181 (p0) REVERT: A 458 LYS cc_start: 0.8614 (ttpt) cc_final: 0.8251 (ptmt) REVERT: A 498 ASP cc_start: 0.8414 (m-30) cc_final: 0.8101 (m-30) REVERT: A 612 SER cc_start: 0.8760 (m) cc_final: 0.8509 (t) REVERT: A 703 ASP cc_start: 0.7873 (m-30) cc_final: 0.7417 (t70) REVERT: C 225 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7569 (tt0) REVERT: C 240 ASP cc_start: 0.8025 (m-30) cc_final: 0.7707 (m-30) REVERT: C 330 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9066 (mt) REVERT: C 458 LYS cc_start: 0.8830 (ttpt) cc_final: 0.8154 (ttmt) REVERT: C 474 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6839 (tt) REVERT: C 498 ASP cc_start: 0.8415 (m-30) cc_final: 0.8107 (m-30) REVERT: C 612 SER cc_start: 0.8742 (m) cc_final: 0.8507 (t) REVERT: C 685 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.7766 (t0) REVERT: C 703 ASP cc_start: 0.7707 (m-30) cc_final: 0.7153 (t70) REVERT: C 775 GLU cc_start: 0.7782 (pp20) cc_final: 0.7470 (pp20) REVERT: E 436 ASP cc_start: 0.6621 (t0) cc_final: 0.6102 (t0) REVERT: E 438 LYS cc_start: 0.8183 (mttt) cc_final: 0.7895 (mmtp) REVERT: E 498 ASP cc_start: 0.8315 (m-30) cc_final: 0.8016 (m-30) REVERT: E 703 ASP cc_start: 0.7823 (m-30) cc_final: 0.7543 (t70) REVERT: E 732 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8230 (t0) REVERT: E 775 GLU cc_start: 0.7693 (pp20) cc_final: 0.7384 (pp20) REVERT: B 49 ASP cc_start: 0.7452 (m-30) cc_final: 0.7070 (t0) REVERT: B 60 LYS cc_start: 0.8087 (mttt) cc_final: 0.7719 (mttp) REVERT: D 12 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7164 (tt0) REVERT: D 60 LYS cc_start: 0.7967 (mttt) cc_final: 0.7741 (mttp) REVERT: D 126 LYS cc_start: 0.8131 (mttm) cc_final: 0.7883 (tttt) REVERT: F 12 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7152 (tt0) REVERT: F 60 LYS cc_start: 0.8048 (mttt) cc_final: 0.7737 (mttp) REVERT: F 126 LYS cc_start: 0.8097 (mttm) cc_final: 0.7399 (tmtt) outliers start: 59 outliers final: 43 residues processed: 251 average time/residue: 0.2697 time to fit residues: 106.7589 Evaluate side-chains 226 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 179 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 475 ASN 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 751 ILE Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 422 VAL 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 527 SER Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 544 ASP Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 685 ASN Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 415 SER 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 506 ILE Chi-restraints excluded: chain E residue 527 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 732 ASP 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 58 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain D residue 58 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 190 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 GLN E 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4449 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= 0.225 Angle : 0.635 10.186 24909 Z= 0.337 Chirality : 0.049 0.187 2907 Planarity : 0.003 0.040 3210 Dihedral : 6.298 35.512 2439 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 3.40 % Allowed : 17.91 % Favored : 78.69 % 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: -3.32 (0.16), residues: 2301 helix: -0.43 (0.30), residues: 303 sheet: -1.27 (0.20), residues: 618 loop : -3.27 (0.14), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 236 HIS 0.004 0.001 HIS A 220 PHE 0.030 0.002 PHE A 250 TYR 0.016 0.001 TYR A 692 ARG 0.004 0.001 ARG A 570 *********************** 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 248 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 181 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 ASN cc_start: 0.7339 (m-40) cc_final: 0.7138 (p0) REVERT: A 458 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8316 (ptmt) REVERT: A 498 ASP cc_start: 0.8403 (m-30) cc_final: 0.8107 (m-30) REVERT: A 537 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 612 SER cc_start: 0.8780 (m) cc_final: 0.8519 (t) REVERT: A 703 ASP cc_start: 0.7855 (m-30) cc_final: 0.7428 (t70) REVERT: A 775 GLU cc_start: 0.7653 (pp20) cc_final: 0.7164 (pp20) REVERT: C 225 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7615 (tt0) REVERT: C 240 ASP cc_start: 0.8098 (m-30) cc_final: 0.7796 (m-30) REVERT: C 458 LYS cc_start: 0.8794 (ttpt) cc_final: 0.8192 (ttmt) REVERT: C 474 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6861 (tt) REVERT: C 498 ASP cc_start: 0.8433 (m-30) cc_final: 0.8140 (m-30) REVERT: C 703 ASP cc_start: 0.7762 (m-30) cc_final: 0.7219 (t70) REVERT: E 396 LEU cc_start: 0.9458 (tp) cc_final: 0.9145 (tp) REVERT: E 436 ASP cc_start: 0.6605 (t0) cc_final: 0.6039 (t0) REVERT: E 438 LYS cc_start: 0.8215 (mttt) cc_final: 0.7893 (mmtp) REVERT: E 498 ASP cc_start: 0.8332 (m-30) cc_final: 0.8033 (m-30) REVERT: E 523 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8555 (tt) REVERT: E 703 ASP cc_start: 0.7782 (m-30) cc_final: 0.7523 (t70) REVERT: B 49 ASP cc_start: 0.7468 (m-30) cc_final: 0.7263 (t0) REVERT: B 60 LYS cc_start: 0.8139 (mttt) cc_final: 0.7787 (mttp) REVERT: D 12 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7176 (tt0) REVERT: D 60 LYS cc_start: 0.8023 (mttt) cc_final: 0.7781 (mttp) REVERT: D 126 LYS cc_start: 0.8086 (mttm) cc_final: 0.7782 (tttt) REVERT: F 12 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7189 (tt0) REVERT: F 60 LYS cc_start: 0.8065 (mttt) cc_final: 0.7755 (mttp) outliers start: 67 outliers final: 55 residues processed: 236 average time/residue: 0.2675 time to fit residues: 100.7079 Evaluate side-chains 232 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 175 time to evaluate : 2.351 ------------------------------------------------------------------------------- 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 302 GLU Chi-restraints excluded: chain A residue 460 ASN 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 530 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 555 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 751 ILE Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 430 ILE 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 527 SER Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 544 ASP 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 683 ILE Chi-restraints excluded: chain C residue 721 SER 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 506 ILE Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 544 ASP Chi-restraints excluded: chain E residue 617 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 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 58 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain D residue 58 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 Chi-restraints excluded: chain F residue 122 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 0.6980 chunk 134 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 143 optimal weight: 0.0770 chunk 153 optimal weight: 0.0030 chunk 111 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 205 optimal weight: 0.7980 overall best weight: 0.4748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 ASN A 796 ASN C 796 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18465 Z= 0.155 Angle : 0.595 10.038 24909 Z= 0.315 Chirality : 0.048 0.204 2907 Planarity : 0.003 0.042 3210 Dihedral : 5.827 34.500 2439 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 2.74 % Allowed : 18.92 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.09 % 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: -3.19 (0.16), residues: 2301 helix: -0.25 (0.31), residues: 285 sheet: -1.07 (0.21), residues: 621 loop : -3.23 (0.14), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP E 236 HIS 0.002 0.001 HIS A 220 PHE 0.026 0.001 PHE A 250 TYR 0.015 0.001 TYR A 692 ARG 0.005 0.000 ARG A 570 *********************** 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 248 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 194 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 ASN cc_start: 0.7403 (m-40) cc_final: 0.7161 (p0) REVERT: A 498 ASP cc_start: 0.8272 (m-30) cc_final: 0.7967 (m-30) REVERT: A 612 SER cc_start: 0.8709 (m) cc_final: 0.8503 (t) REVERT: A 703 ASP cc_start: 0.7821 (m-30) cc_final: 0.7514 (t70) REVERT: A 775 GLU cc_start: 0.7577 (pp20) cc_final: 0.7148 (pp20) REVERT: C 225 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7524 (tt0) REVERT: C 240 ASP cc_start: 0.8060 (m-30) cc_final: 0.7751 (m-30) REVERT: C 289 ILE cc_start: 0.8924 (mt) cc_final: 0.8599 (mp) REVERT: C 330 LEU cc_start: 0.9452 (tp) cc_final: 0.9099 (mt) REVERT: C 458 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8164 (ttmt) REVERT: C 498 ASP cc_start: 0.8372 (m-30) cc_final: 0.8061 (m-30) REVERT: C 703 ASP cc_start: 0.7797 (m-30) cc_final: 0.7253 (t70) REVERT: C 775 GLU cc_start: 0.7765 (pp20) cc_final: 0.7523 (pp20) REVERT: E 289 ILE cc_start: 0.8938 (mt) cc_final: 0.8698 (mp) REVERT: E 436 ASP cc_start: 0.6592 (t0) cc_final: 0.6028 (t0) REVERT: E 438 LYS cc_start: 0.8112 (mttt) cc_final: 0.7800 (mmtp) REVERT: E 498 ASP cc_start: 0.8216 (m-30) cc_final: 0.7909 (m-30) REVERT: E 523 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8480 (tt) REVERT: E 703 ASP cc_start: 0.7895 (m-30) cc_final: 0.7597 (t70) REVERT: E 775 GLU cc_start: 0.7553 (pp20) cc_final: 0.7240 (pp20) REVERT: D 12 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7112 (tt0) REVERT: D 126 LYS cc_start: 0.8056 (mttm) cc_final: 0.7658 (tmtt) REVERT: F 12 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7091 (tt0) REVERT: F 126 LYS cc_start: 0.7996 (mttm) cc_final: 0.7269 (tmtt) outliers start: 54 outliers final: 45 residues processed: 238 average time/residue: 0.2611 time to fit residues: 101.0992 Evaluate side-chains 218 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 2.308 ------------------------------------------------------------------------------- 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 302 GLU Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 522 GLU 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 669 ILE 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 422 VAL Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 527 SER Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 544 ASP 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 422 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 536 THR Chi-restraints excluded: chain E residue 617 ILE 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 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 79 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 165 optimal weight: 0.0270 chunk 64 optimal weight: 1.9990 chunk 189 optimal weight: 0.0870 chunk 198 optimal weight: 1.9990 chunk 209 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4718 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= 0.174 Angle : 0.602 9.308 24909 Z= 0.319 Chirality : 0.048 0.191 2907 Planarity : 0.003 0.042 3210 Dihedral : 5.804 34.752 2439 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 2.74 % Allowed : 19.48 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.09 % 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: -3.01 (0.16), residues: 2301 helix: 0.11 (0.31), residues: 303 sheet: -0.98 (0.21), residues: 618 loop : -3.19 (0.14), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP E 236 HIS 0.003 0.001 HIS A 220 PHE 0.026 0.001 PHE A 250 TYR 0.015 0.001 TYR E 692 ARG 0.005 0.000 ARG A 570 *********************** 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 236 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 182 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 LYS cc_start: 0.8289 (tmtt) cc_final: 0.7881 (tmtt) REVERT: A 498 ASP cc_start: 0.8281 (m-30) cc_final: 0.7976 (m-30) REVERT: A 612 SER cc_start: 0.8734 (m) cc_final: 0.8510 (t) REVERT: A 703 ASP cc_start: 0.7846 (m-30) cc_final: 0.7519 (t70) REVERT: A 775 GLU cc_start: 0.7639 (pp20) cc_final: 0.7222 (pp20) REVERT: C 225 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7620 (tt0) REVERT: C 240 ASP cc_start: 0.8002 (m-30) cc_final: 0.7757 (m-30) REVERT: C 330 LEU cc_start: 0.9425 (tp) cc_final: 0.9075 (mt) REVERT: C 458 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8119 (ttmt) REVERT: C 498 ASP cc_start: 0.8375 (m-30) cc_final: 0.8078 (m-30) REVERT: C 703 ASP cc_start: 0.7811 (m-30) cc_final: 0.7247 (t70) REVERT: C 775 GLU cc_start: 0.7780 (pp20) cc_final: 0.7541 (pp20) REVERT: E 289 ILE cc_start: 0.8938 (mt) cc_final: 0.8720 (mp) REVERT: E 436 ASP cc_start: 0.6588 (t0) cc_final: 0.5983 (t0) REVERT: E 438 LYS cc_start: 0.8113 (mttt) cc_final: 0.7775 (mmtp) REVERT: E 498 ASP cc_start: 0.8228 (m-30) cc_final: 0.7904 (m-30) REVERT: E 523 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8524 (tt) REVERT: E 703 ASP cc_start: 0.7898 (m-30) cc_final: 0.7559 (t70) REVERT: E 775 GLU cc_start: 0.7668 (pp20) cc_final: 0.7355 (pp20) REVERT: E 779 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.7907 (tmm) REVERT: D 12 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7105 (tt0) REVERT: D 126 LYS cc_start: 0.8088 (mttm) cc_final: 0.7652 (tmtt) REVERT: F 12 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7064 (tt0) REVERT: F 60 LYS cc_start: 0.8012 (mttt) cc_final: 0.7740 (mttp) REVERT: F 126 LYS cc_start: 0.8053 (mttm) cc_final: 0.7437 (tmtt) outliers start: 54 outliers final: 45 residues processed: 225 average time/residue: 0.2736 time to fit residues: 99.2015 Evaluate side-chains 222 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 175 time to evaluate : 2.228 ------------------------------------------------------------------------------- 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 302 GLU Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 485 SER 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 669 ILE 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 422 VAL Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 527 SER Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 544 ASP 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 422 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 536 THR Chi-restraints excluded: chain E residue 617 ILE Chi-restraints excluded: chain E residue 634 SER Chi-restraints excluded: chain E residue 671 GLU 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 E residue 789 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain D residue 58 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 105 optimal weight: 0.0870 chunk 154 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 185 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 143 optimal weight: 0.1980 chunk 113 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18465 Z= 0.156 Angle : 0.588 8.834 24909 Z= 0.311 Chirality : 0.048 0.193 2907 Planarity : 0.003 0.044 3210 Dihedral : 5.606 33.858 2439 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 2.28 % Allowed : 20.04 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.09 % 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: -2.95 (0.17), residues: 2301 helix: 0.32 (0.32), residues: 303 sheet: -1.08 (0.20), residues: 681 loop : -3.17 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP E 236 HIS 0.002 0.001 HIS F 6 PHE 0.024 0.001 PHE A 326 TYR 0.018 0.001 TYR A 692 ARG 0.005 0.000 ARG A 570 ********************** 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 246 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 201 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 LYS cc_start: 0.8194 (tmtt) cc_final: 0.7881 (tmtt) REVERT: A 498 ASP cc_start: 0.8253 (m-30) cc_final: 0.7970 (m-30) REVERT: A 612 SER cc_start: 0.8703 (m) cc_final: 0.8490 (t) REVERT: A 703 ASP cc_start: 0.7871 (m-30) cc_final: 0.7526 (t70) REVERT: A 775 GLU cc_start: 0.7637 (pp20) cc_final: 0.7201 (pp20) REVERT: C 240 ASP cc_start: 0.7950 (m-30) cc_final: 0.7719 (m-30) REVERT: C 330 LEU cc_start: 0.9404 (tp) cc_final: 0.9094 (mt) REVERT: C 498 ASP cc_start: 0.8324 (m-30) cc_final: 0.8029 (m-30) REVERT: C 703 ASP cc_start: 0.7732 (m-30) cc_final: 0.7189 (t70) REVERT: E 289 ILE cc_start: 0.8972 (mt) cc_final: 0.8729 (mp) REVERT: E 436 ASP cc_start: 0.6525 (t0) cc_final: 0.5926 (t0) REVERT: E 438 LYS cc_start: 0.8022 (mttt) cc_final: 0.7720 (mmtp) REVERT: E 523 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8522 (tt) REVERT: E 703 ASP cc_start: 0.7869 (m-30) cc_final: 0.7578 (t70) REVERT: E 775 GLU cc_start: 0.7660 (pp20) cc_final: 0.7366 (pp20) REVERT: E 779 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7931 (tmm) REVERT: D 12 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7076 (tt0) REVERT: D 126 LYS cc_start: 0.8084 (mttm) cc_final: 0.7660 (tmtt) REVERT: F 12 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7079 (tt0) REVERT: F 126 LYS cc_start: 0.7995 (mttm) cc_final: 0.7366 (tmtt) outliers start: 45 outliers final: 36 residues processed: 236 average time/residue: 0.2633 time to fit residues: 99.8111 Evaluate side-chains 214 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 176 time to evaluate : 2.252 ------------------------------------------------------------------------------- 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 302 GLU Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 522 GLU 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 751 ILE Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 527 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 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 617 ILE 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 B residue 79 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 97 ASP 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 197 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 171 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 chunk 34 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.120875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.105636 restraints weight = 31128.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.107544 restraints weight = 21629.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.108714 restraints weight = 15425.651| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18465 Z= 0.190 Angle : 0.608 8.865 24909 Z= 0.322 Chirality : 0.048 0.192 2907 Planarity : 0.003 0.043 3210 Dihedral : 5.719 34.580 2439 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 2.64 % Allowed : 20.19 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.09 % 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: -2.92 (0.17), residues: 2301 helix: 0.36 (0.32), residues: 303 sheet: -1.06 (0.20), residues: 681 loop : -3.16 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 236 HIS 0.003 0.001 HIS C 220 PHE 0.025 0.002 PHE A 250 TYR 0.019 0.001 TYR A 692 ARG 0.005 0.000 ARG A 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3601.60 seconds wall clock time: 66 minutes 49.23 seconds (4009.23 seconds total)