Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 02:44:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9g_20698/07_2023/6u9g_20698.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9g_20698/07_2023/6u9g_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_20698/07_2023/6u9g_20698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9g_20698/07_2023/6u9g_20698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9g_20698/07_2023/6u9g_20698.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9g_20698/07_2023/6u9g_20698.pdb" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-5013/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: 8.68, per 1000 atoms: 0.48 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: 6.19 Conformation dependent library (CDL) restraints added in 2.3 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: 1.43 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: 6.17 Time building geometry restraints manager: 6.83 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: 2.050 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: 0.020 Extract box with map and model: 10.140 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 44.530 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.090 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.112 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 outliers start: 0 outliers final: 0 residues processed: 531 average time/residue: 0.3404 time to fit residues: 260.4281 Evaluate side-chains 240 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.052 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8956 ------------------------------------------------------------------------------- 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: 2.9990 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 622 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 18465 Z= 0.240 Angle : 0.723 10.991 24909 Z= 0.380 Chirality : 0.051 0.205 2907 Planarity : 0.003 0.031 3210 Dihedral : 7.515 35.870 2439 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer Outliers : 3.30 % 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: -4.17 (0.15), residues: 2301 helix: -3.00 (0.20), residues: 300 sheet: -1.58 (0.20), residues: 603 loop : -3.45 (0.13), residues: 1398 *********************** 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 349 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 284 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 37 residues processed: 334 average time/residue: 0.2973 time to fit residues: 151.5872 Evaluate side-chains 230 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 193 time to evaluate : 2.142 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1701 time to fit residues: 14.7594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 176 optimal weight: 0.5980 chunk 144 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 229 optimal weight: 0.5980 chunk 189 optimal weight: 0.1980 chunk 211 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN A 723 ASN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN C 796 ASN E 294 ASN E 529 ASN B 114 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 18465 Z= 0.188 Angle : 0.656 10.604 24909 Z= 0.346 Chirality : 0.050 0.221 2907 Planarity : 0.003 0.044 3210 Dihedral : 6.762 35.745 2439 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer Outliers : 2.03 % 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: -3.79 (0.15), residues: 2301 helix: -1.97 (0.26), residues: 285 sheet: -1.45 (0.20), residues: 606 loop : -3.32 (0.14), residues: 1410 *********************** 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 256 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 216 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 10 residues processed: 248 average time/residue: 0.2889 time to fit residues: 111.2535 Evaluate side-chains 184 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 174 time to evaluate : 2.055 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1650 time to fit residues: 6.0269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 213 optimal weight: 0.3980 chunk 226 optimal weight: 0.0670 chunk 111 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 18465 Z= 0.213 Angle : 0.643 9.043 24909 Z= 0.340 Chirality : 0.049 0.196 2907 Planarity : 0.003 0.044 3210 Dihedral : 6.494 34.529 2439 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.16), residues: 2301 helix: -1.21 (0.28), residues: 303 sheet: -1.44 (0.20), residues: 615 loop : -3.28 (0.14), residues: 1383 *********************** 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 216 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 189 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 10 residues processed: 210 average time/residue: 0.3124 time to fit residues: 102.3831 Evaluate side-chains 175 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 2.256 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1635 time to fit residues: 6.1614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 0.0020 chunk 203 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.8990 ------------------------------------------------------------------------------- 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: 0.7988 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 18465 Z= 0.218 Angle : 0.629 8.058 24909 Z= 0.334 Chirality : 0.049 0.189 2907 Planarity : 0.003 0.040 3210 Dihedral : 6.375 35.199 2439 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.91 % Favored : 88.09 % Rotamer Outliers : 1.12 % 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: -3.42 (0.16), residues: 2301 helix: -0.76 (0.29), residues: 303 sheet: -1.32 (0.20), residues: 603 loop : -3.25 (0.14), residues: 1395 *********************** 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 209 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 187 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 207 average time/residue: 0.2796 time to fit residues: 92.4691 Evaluate side-chains 180 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 2.263 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1912 time to fit residues: 7.0464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 55 optimal weight: 0.4980 chunk 226 optimal weight: 1.9990 chunk 187 optimal weight: 0.0980 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 74 optimal weight: 0.0010 chunk 118 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 796 ASN E 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 18465 Z= 0.182 Angle : 0.610 7.568 24909 Z= 0.324 Chirality : 0.048 0.199 2907 Planarity : 0.003 0.038 3210 Dihedral : 6.087 34.345 2439 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer Outliers : 1.12 % 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: -3.23 (0.16), residues: 2301 helix: -0.39 (0.30), residues: 303 sheet: -1.20 (0.20), residues: 603 loop : -3.18 (0.14), residues: 1395 *********************** 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 204 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 194 average time/residue: 0.2773 time to fit residues: 87.9872 Evaluate side-chains 174 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 2.385 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1766 time to fit residues: 7.3978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 139 optimal weight: 0.0000 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN E 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 18465 Z= 0.191 Angle : 0.609 7.660 24909 Z= 0.323 Chirality : 0.048 0.188 2907 Planarity : 0.003 0.040 3210 Dihedral : 6.041 35.348 2439 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.91 % Favored : 88.09 % Rotamer Outliers : 1.01 % 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: -3.18 (0.16), residues: 2301 helix: -0.21 (0.31), residues: 285 sheet: -1.18 (0.20), residues: 606 loop : -3.15 (0.14), residues: 1410 *********************** 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 188 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 181 average time/residue: 0.2623 time to fit residues: 77.5494 Evaluate side-chains 164 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1677 time to fit residues: 6.2902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 0.8980 chunk 134 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7998 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 18465 Z= 0.221 Angle : 0.628 10.286 24909 Z= 0.330 Chirality : 0.049 0.194 2907 Planarity : 0.003 0.041 3210 Dihedral : 6.161 34.972 2439 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.47 % Favored : 87.53 % Rotamer Outliers : 0.71 % 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: -3.13 (0.16), residues: 2301 helix: -0.06 (0.31), residues: 303 sheet: -1.21 (0.20), residues: 618 loop : -3.15 (0.14), residues: 1380 *********************** 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 176 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 168 average time/residue: 0.2671 time to fit residues: 73.6428 Evaluate side-chains 159 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 2.164 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1674 time to fit residues: 5.4320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 91 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 189 optimal weight: 0.7980 chunk 198 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 18465 Z= 0.289 Angle : 0.676 10.894 24909 Z= 0.354 Chirality : 0.050 0.193 2907 Planarity : 0.003 0.044 3210 Dihedral : 6.518 35.671 2439 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.82 % Favored : 86.18 % Rotamer Outliers : 0.51 % 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: -3.23 (0.16), residues: 2301 helix: -0.14 (0.31), residues: 303 sheet: -1.33 (0.20), residues: 621 loop : -3.20 (0.14), residues: 1377 *********************** 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 172 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 168 average time/residue: 0.2734 time to fit residues: 74.3216 Evaluate side-chains 154 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 2.256 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1714 time to fit residues: 4.7168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 233 optimal weight: 7.9990 chunk 214 optimal weight: 0.0980 chunk 185 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 143 optimal weight: 0.0070 chunk 113 optimal weight: 4.9990 chunk 147 optimal weight: 0.1980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 ASN E 399 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 18465 Z= 0.147 Angle : 0.603 9.856 24909 Z= 0.316 Chirality : 0.048 0.192 2907 Planarity : 0.003 0.043 3210 Dihedral : 5.761 33.926 2439 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer Outliers : 0.15 % 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: -3.07 (0.16), residues: 2301 helix: 0.15 (0.33), residues: 285 sheet: -1.18 (0.20), residues: 642 loop : -3.14 (0.14), residues: 1374 ********************** 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 187 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 186 average time/residue: 0.2657 time to fit residues: 81.0504 Evaluate side-chains 158 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 2.156 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1618 time to fit residues: 3.3666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 171 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 0.0050 chunk 185 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.121208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.105944 restraints weight = 30921.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.107863 restraints weight = 19426.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109255 restraints weight = 13878.071| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4965 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= 0.162 Angle : 0.603 9.972 24909 Z= 0.317 Chirality : 0.048 0.191 2907 Planarity : 0.003 0.042 3210 Dihedral : 5.715 34.873 2439 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer Outliers : 0.25 % 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: -2.95 (0.16), residues: 2301 helix: 0.39 (0.32), residues: 303 sheet: -1.03 (0.21), residues: 615 loop : -3.15 (0.14), residues: 1383 =============================================================================== Job complete usr+sys time: 3202.29 seconds wall clock time: 60 minutes 1.73 seconds (3601.73 seconds total)