Starting phenix.real_space_refine on Thu Mar 5 09:59:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qun_14149/03_2026/7qun_14149_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qun_14149/03_2026/7qun_14149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qun_14149/03_2026/7qun_14149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qun_14149/03_2026/7qun_14149.map" model { file = "/net/cci-nas-00/data/ceres_data/7qun_14149/03_2026/7qun_14149_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qun_14149/03_2026/7qun_14149_trim.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.097 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 140 5.16 5 C 13570 2.51 5 N 3598 2.21 5 O 3786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21094 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5236 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 694, 5231 Classifications: {'peptide': 694} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 648} Chain breaks: 3 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 21, 'GLN:plan1': 7, 'TYR:plan': 1, 'ASP:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 149 Conformer: "B" Number of residues, atoms: 694, 5231 Classifications: {'peptide': 694} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 648} Chain breaks: 3 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 21, 'GLN:plan1': 7, 'TYR:plan': 1, 'ASP:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 149 bond proxies already assigned to first conformer: 5366 Chain: "B" Number of atoms: 5240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5240 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 19, 'GLN:plan1': 7, 'TYR:plan': 1, 'ASP:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 5248 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 693, 5243 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 10, 'TYR:plan': 1, 'ASP:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 138 Conformer: "B" Number of residues, atoms: 693, 5243 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 10, 'TYR:plan': 1, 'ASP:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 138 bond proxies already assigned to first conformer: 5379 Chain: "D" Number of atoms: 5266 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 693, 5255 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 16, 'GLN:plan1': 8, 'TYR:plan': 1, 'ASP:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 120 Conformer: "B" Number of residues, atoms: 693, 5255 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 16, 'GLN:plan1': 8, 'TYR:plan': 1, 'ASP:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 120 bond proxies already assigned to first conformer: 5384 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 7.87, per 1000 atoms: 0.37 Number of scatterers: 21094 At special positions: 0 Unit cell: (131.52, 111.36, 136.32, 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 140 16.00 O 3786 8.00 N 3598 7.00 C 13570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 1.3 seconds 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5144 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 40 sheets defined 21.8% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.538A pdb=" N GLU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 443 through 447 removed outlier: 3.705A pdb=" N VAL A 447 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 544 through 551 removed outlier: 4.043A pdb=" N LEU A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 575 Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 615 through 621 removed outlier: 4.222A pdb=" N GLY A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 634 removed outlier: 4.312A pdb=" N CYS A 629 " --> pdb=" O ILE A 625 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET A 630 " --> pdb=" O PRO A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 654 removed outlier: 3.551A pdb=" N LYS A 654 " --> pdb=" O ALA A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 663 Proline residue: A 661 - end of helix Processing helix chain 'A' and resid 680 through 692 Processing helix chain 'A' and resid 711 through 730 Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.532A pdb=" N GLU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 139' Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 443 through 447 removed outlier: 3.630A pdb=" N VAL B 447 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 475 Processing helix chain 'B' and resid 519 through 527 Processing helix chain 'B' and resid 544 through 551 removed outlier: 4.065A pdb=" N LEU B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 575 removed outlier: 3.563A pdb=" N GLU B 573 " --> pdb=" O GLN B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 600 Processing helix chain 'B' and resid 615 through 621 removed outlier: 4.188A pdb=" N GLY B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 634 removed outlier: 4.267A pdb=" N CYS B 629 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B 630 " --> pdb=" O PRO B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 655 through 663 Proline residue: B 661 - end of helix Processing helix chain 'B' and resid 680 through 693 Processing helix chain 'B' and resid 711 through 730 Processing helix chain 'C' and resid 10 through 22 removed outlier: 3.977A pdb=" N ARG C 22 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.853A pdb=" N GLU C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 135 through 139' Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 443 through 447 removed outlier: 3.588A pdb=" N VAL C 447 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 475 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 551 removed outlier: 4.206A pdb=" N LEU C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 575 Processing helix chain 'C' and resid 587 through 600 Processing helix chain 'C' and resid 615 through 620 Processing helix chain 'C' and resid 625 through 634 removed outlier: 4.245A pdb=" N CYS C 629 " --> pdb=" O ILE C 625 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET C 630 " --> pdb=" O PRO C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 654 removed outlier: 3.667A pdb=" N ALA C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 663 Proline residue: C 661 - end of helix Processing helix chain 'C' and resid 680 through 692 removed outlier: 3.500A pdb=" N MET C 684 " --> pdb=" O PHE C 680 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 686 " --> pdb=" O GLN C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 730 Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.516A pdb=" N GLU D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 135 through 139' Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 443 through 447 removed outlier: 3.621A pdb=" N VAL D 447 " --> pdb=" O GLU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 475 Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'D' and resid 544 through 551 removed outlier: 4.091A pdb=" N LEU D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 575 removed outlier: 3.521A pdb=" N LYS D 561 " --> pdb=" O HIS D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 600 Processing helix chain 'D' and resid 615 through 620 Processing helix chain 'D' and resid 625 through 634 removed outlier: 4.237A pdb=" N CYS D 629 " --> pdb=" O ILE D 625 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET D 630 " --> pdb=" O PRO D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 654 Processing helix chain 'D' and resid 655 through 663 Proline residue: D 661 - end of helix Processing helix chain 'D' and resid 680 through 692 removed outlier: 3.516A pdb=" N MET D 684 " --> pdb=" O PHE D 680 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR D 686 " --> pdb=" O GLN D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 730 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 31 removed outlier: 5.745A pdb=" N LEU A 26 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR A 51 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 28 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG A 42 " --> pdb=" O HIS A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 removed outlier: 4.089A pdb=" N ARG A 42 " --> pdb=" O HIS A 71 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG A 62 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 96 removed outlier: 5.863A pdb=" N GLU A 91 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS A 108 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 93 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU A 125 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LYS A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 251 removed outlier: 4.273A pdb=" N ALA A 249 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 259 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TRP A 251 " --> pdb=" O GLY A 257 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLY A 257 " --> pdb=" O TRP A 251 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 307 removed outlier: 6.588A pdb=" N VAL A 315 " --> pdb=" O PRO A 305 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU A 307 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ARG A 313 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 333 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL A 343 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASP A 335 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR A 341 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 382 Processing sheet with id=AA9, first strand: chain 'A' and resid 409 through 416 removed outlier: 6.855A pdb=" N VAL A 421 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE A 415 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N THR A 426 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU A 433 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 461 through 468 removed outlier: 3.506A pdb=" N GLU A 485 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY A 586 " --> pdb=" O PRO A 506 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A 606 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 25 through 31 removed outlier: 5.726A pdb=" N LEU B 26 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR B 51 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 28 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG B 42 " --> pdb=" O HIS B 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 35 through 36 removed outlier: 4.184A pdb=" N ARG B 42 " --> pdb=" O HIS B 71 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG B 62 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 91 through 96 removed outlier: 5.946A pdb=" N GLU B 91 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 108 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 93 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU B 125 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LYS B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AB6, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB7, first strand: chain 'B' and resid 244 through 251 removed outlier: 4.272A pdb=" N ALA B 249 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 259 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TRP B 251 " --> pdb=" O GLY B 257 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLY B 257 " --> pdb=" O TRP B 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 301 through 307 removed outlier: 6.653A pdb=" N VAL B 315 " --> pdb=" O PRO B 305 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU B 307 " --> pdb=" O ARG B 313 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG B 313 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 333 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL B 343 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASP B 335 " --> pdb=" O THR B 341 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR B 341 " --> pdb=" O ASP B 335 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 375 through 382 Processing sheet with id=AC1, first strand: chain 'B' and resid 409 through 416 removed outlier: 6.841A pdb=" N VAL B 421 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE B 415 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N THR B 426 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 433 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 461 through 468 removed outlier: 3.501A pdb=" N GLU B 485 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLY B 586 " --> pdb=" O PRO B 506 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA B 606 " --> pdb=" O VAL B 581 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 25 through 31 removed outlier: 5.581A pdb=" N LEU C 26 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N THR C 51 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 28 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG C 42 " --> pdb=" O HIS C 71 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 35 through 36 removed outlier: 3.870A pdb=" N ARG C 42 " --> pdb=" O HIS C 71 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARG C 62 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 91 through 96 removed outlier: 6.756A pdb=" N LEU C 106 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER C 94 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA C 104 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU C 125 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AC7, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AC8, first strand: chain 'C' and resid 244 through 251 removed outlier: 4.315A pdb=" N ALA C 249 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL C 259 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TRP C 251 " --> pdb=" O GLY C 257 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLY C 257 " --> pdb=" O TRP C 251 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 301 through 307 removed outlier: 6.552A pdb=" N VAL C 315 " --> pdb=" O PRO C 305 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU C 307 " --> pdb=" O ARG C 313 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ARG C 313 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU C 331 " --> pdb=" O VAL C 344 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 375 through 382 Processing sheet with id=AD2, first strand: chain 'C' and resid 409 through 416 removed outlier: 6.858A pdb=" N VAL C 421 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE C 415 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N THR C 426 " --> pdb=" O PRO C 430 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU C 433 " --> pdb=" O LEU C 452 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 461 through 468 removed outlier: 3.552A pdb=" N GLU C 485 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N MET C 502 " --> pdb=" O ALA C 582 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N MET C 584 " --> pdb=" O MET C 502 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL C 504 " --> pdb=" O MET C 584 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 25 through 31 removed outlier: 6.727A pdb=" N GLU D 49 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA D 29 " --> pdb=" O HIS D 47 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS D 47 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU D 31 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR D 45 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG D 42 " --> pdb=" O HIS D 71 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.876A pdb=" N ARG D 42 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ARG D 62 " --> pdb=" O THR D 88 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 91 through 96 removed outlier: 6.783A pdb=" N LEU D 106 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER D 94 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA D 104 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS D 131 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU D 125 " --> pdb=" O LYS D 129 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AD8, first strand: chain 'D' and resid 173 through 174 Processing sheet with id=AD9, first strand: chain 'D' and resid 244 through 251 removed outlier: 4.305A pdb=" N ALA D 249 " --> pdb=" O VAL D 259 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL D 259 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N TRP D 251 " --> pdb=" O GLY D 257 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY D 257 " --> pdb=" O TRP D 251 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 301 through 307 removed outlier: 6.632A pdb=" N VAL D 315 " --> pdb=" O PRO D 305 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU D 307 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG D 313 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 331 " --> pdb=" O VAL D 344 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 375 through 382 Processing sheet with id=AE3, first strand: chain 'D' and resid 409 through 416 removed outlier: 6.851A pdb=" N VAL D 421 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE D 415 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N THR D 426 " --> pdb=" O PRO D 430 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU D 433 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 461 through 468 removed outlier: 3.551A pdb=" N GLU D 485 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET D 502 " --> pdb=" O ALA D 582 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N MET D 584 " --> pdb=" O MET D 502 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL D 504 " --> pdb=" O MET D 584 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLY D 586 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA D 606 " --> pdb=" O VAL D 581 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU D 667 " --> pdb=" O ARG D 698 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU D 700 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU D 669 " --> pdb=" O LEU D 700 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR D 702 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU D 671 " --> pdb=" O TYR D 702 " (cutoff:3.500A) 891 hydrogen bonds defined for protein. 2471 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.29: 3368 1.29 - 1.45: 6008 1.45 - 1.60: 12081 1.60 - 1.76: 0 1.76 - 1.91: 212 Bond restraints: 21669 Sorted by residual: bond pdb=" CAM DWZ C 801 " pdb=" OAT DWZ C 801 " ideal model delta sigma weight residual 1.246 1.134 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" CAM DWZ A 801 " pdb=" OAT DWZ A 801 " ideal model delta sigma weight residual 1.246 1.138 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" CAM DWZ B 801 " pdb=" OAT DWZ B 801 " ideal model delta sigma weight residual 1.246 1.138 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" CAM DWZ D 801 " pdb=" OAT DWZ D 801 " ideal model delta sigma weight residual 1.246 1.140 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" CA SER C 587 " pdb=" C SER C 587 " ideal model delta sigma weight residual 1.524 1.573 -0.049 9.50e-03 1.11e+04 2.64e+01 ... (remaining 21664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 29234 2.86 - 5.72: 271 5.72 - 8.58: 46 8.58 - 11.44: 4 11.44 - 14.31: 6 Bond angle restraints: 29561 Sorted by residual: angle pdb=" CA GLY D 589 " pdb=" C GLY D 589 " pdb=" O GLY D 589 " ideal model delta sigma weight residual 120.75 113.30 7.45 1.03e+00 9.43e-01 5.23e+01 angle pdb=" CA GLY D 589 " pdb=" C GLY D 589 " pdb=" N GLY D 590 " ideal model delta sigma weight residual 117.04 123.98 -6.94 9.90e-01 1.02e+00 4.92e+01 angle pdb=" C GLY D 589 " pdb=" N GLY D 590 " pdb=" CA GLY D 590 " ideal model delta sigma weight residual 120.00 127.12 -7.12 1.10e+00 8.26e-01 4.19e+01 angle pdb=" C GLU C 573 " pdb=" N GLU C 574 " pdb=" CA GLU C 574 " ideal model delta sigma weight residual 122.26 112.80 9.46 1.59e+00 3.96e-01 3.54e+01 angle pdb=" O VAL C 570 " pdb=" C VAL C 570 " pdb=" N LEU C 571 " ideal model delta sigma weight residual 121.87 115.86 6.01 1.01e+00 9.80e-01 3.54e+01 ... (remaining 29556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.44: 12202 26.44 - 52.88: 600 52.88 - 79.31: 70 79.31 - 105.75: 13 105.75 - 132.19: 8 Dihedral angle restraints: 12893 sinusoidal: 4900 harmonic: 7993 Sorted by residual: dihedral pdb=" CAD DWZ A 801 " pdb=" CAB DWZ A 801 " pdb=" CAE DWZ A 801 " pdb=" OAG DWZ A 801 " ideal model delta sinusoidal sigma weight residual 71.26 -60.93 132.19 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" CAD DWZ B 801 " pdb=" CAB DWZ B 801 " pdb=" CAE DWZ B 801 " pdb=" OAG DWZ B 801 " ideal model delta sinusoidal sigma weight residual 71.26 -59.51 130.77 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CAD DWZ D 801 " pdb=" CAB DWZ D 801 " pdb=" CAE DWZ D 801 " pdb=" OAG DWZ D 801 " ideal model delta sinusoidal sigma weight residual 71.26 -53.55 124.81 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 12890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2923 0.075 - 0.149: 359 0.149 - 0.224: 19 0.224 - 0.298: 8 0.298 - 0.373: 3 Chirality restraints: 3312 Sorted by residual: chirality pdb=" CB VAL C 560 " pdb=" CA VAL C 560 " pdb=" CG1 VAL C 560 " pdb=" CG2 VAL C 560 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB VAL C 46 " pdb=" CA VAL C 46 " pdb=" CG1 VAL C 46 " pdb=" CG2 VAL C 46 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CAB DWZ D 801 " pdb=" CAA DWZ D 801 " pdb=" CAD DWZ D 801 " pdb=" CAE DWZ D 801 " both_signs ideal model delta sigma weight residual False -2.48 -2.78 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 3309 not shown) Planarity restraints: 3785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 120 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C PHE B 120 " -0.058 2.00e-02 2.50e+03 pdb=" O PHE B 120 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU B 121 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 338 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C THR C 338 " -0.051 2.00e-02 2.50e+03 pdb=" O THR C 338 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG C 339 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 44 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C ARG C 44 " -0.047 2.00e-02 2.50e+03 pdb=" O ARG C 44 " 0.018 2.00e-02 2.50e+03 pdb=" N THR C 45 " 0.016 2.00e-02 2.50e+03 ... (remaining 3782 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2888 2.76 - 3.30: 17792 3.30 - 3.83: 33020 3.83 - 4.37: 40258 4.37 - 4.90: 71307 Nonbonded interactions: 165265 Sorted by model distance: nonbonded pdb=" OG SER C 370 " pdb=" OD1 ASP C 372 " model vdw 2.230 3.040 nonbonded pdb=" OG SER D 370 " pdb=" OD1 ASP D 372 " model vdw 2.249 3.040 nonbonded pdb=" O VAL D 217 " pdb=" OG SER D 218 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 370 " pdb=" OD1 ASP A 372 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR C 67 " pdb=" OE1 GLU C 453 " model vdw 2.267 3.040 ... (remaining 165260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 55 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 through 67 or resid 69 through 88 or (resid \ 89 and (name N or name CA or name C or name O or name CB )) or resid 90 through \ 105 or resid 107 or (resid 108 through 109 and (name N or name CA or name C or \ name O or name CB )) or resid 117 through 130 or resid 132 through 292 or (resid \ 293 and (name N or name CA or name C or name O or name CB )) or resid 294 throu \ gh 410 or (resid 411 and (name N or name CA or name C or name O or name CB or na \ me CG )) or resid 412 through 444 or (resid 445 through 446 and (name N or name \ CA or name C or name O or name CB )) or resid 447 through 477 or (resid 478 and \ (name N or name CA or name C or name O or name CB )) or resid 479 through 498 or \ (resid 499 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 0 through 638 or (resid 639 through 642 and (name N or name CA or name C or name \ O or name CB )) or resid 643 through 652 or (resid 653 and (name N or name CA o \ r name C or name O or name CB )) or resid 654 through 663 or (resid 664 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE ) \ ) or resid 665 through 693 or (resid 694 and (name N or name CA or name C or nam \ e O or name CB )) or resid 695 through 709 or (resid 710 and (name N or name CA \ or name C or name O or name CB )) or resid 711 through 801)) selection = (chain 'B' and (resid 9 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 55 or (resid 56 and (n \ ame N or name CA or name C or name O or name CB )) or resid 57 through 67 or res \ id 69 through 105 or resid 107 or (resid 108 through 117 and (name N or name CA \ or name C or name O or name CB )) or resid 118 through 130 or resid 132 through \ 173 or (resid 174 and (name N or name CA or name C or name O or name CB or name \ CG )) or resid 175 through 232 or (resid 233 and (name N or name CA or name C or \ name O or name CB )) or resid 234 through 290 or (resid 291 and (name N or name \ CA or name C or name O or name CB )) or resid 292 or (resid 293 and (name N or \ name CA or name C or name O or name CB )) or resid 294 through 298 or (resid 299 \ and (name N or name CA or name C or name O or name CB )) or resid 300 through 4 \ 10 or (resid 411 and (name N or name CA or name C or name O or name CB or name C \ G )) or resid 412 through 416 or (resid 417 and (name N or name CA or name C or \ name O or name CB or name CG or name CD )) or resid 418 through 444 or (resid 44 \ 5 through 446 and (name N or name CA or name C or name O or name CB )) or resid \ 447 through 477 or (resid 478 and (name N or name CA or name C or name O or name \ CB )) or resid 479 through 571 or (resid 572 and (name N or name CA or name C o \ r name O or name CB or name CG )) or (resid 573 through 575 and (name N or name \ CA or name C or name O or name CB )) or resid 576 through 638 or (resid 639 thro \ ugh 642 and (name N or name CA or name C or name O or name CB )) or resid 643 th \ rough 801)) selection = (chain 'C' and (resid 9 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB )) or resid 37 through 67 or resid 69 through 95 or (resid \ 96 and (name N or name CA or name C or name O or name CB or name CG )) or resid \ 97 through 105 or resid 107 or (resid 108 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 through 130 or resid 132 through 13 \ 8 or (resid 139 and (name N or name CA or name C or name O or name CB )) or resi \ d 140 through 147 or (resid 148 and (name N or name CA or name C or name O or na \ me CB )) or resid 149 through 173 or (resid 174 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 175 through 232 or (resid 233 and ( \ name N or name CA or name C or name O or name CB )) or resid 234 through 290 or \ (resid 291 and (name N or name CA or name C or name O or name CB )) or resid 292 \ or (resid 293 and (name N or name CA or name C or name O or name CB )) or resid \ 294 through 410 or (resid 411 and (name N or name CA or name C or name O or nam \ e CB or name CG )) or resid 412 through 416 or (resid 417 and (name N or name CA \ or name C or name O or name CB or name CG or name CD )) or resid 418 through 57 \ 4 or (resid 575 and (name N or name CA or name C or name O or name CB )) or resi \ d 576 through 621 or (resid 622 and (name N or name CA or name C or name O or na \ me CB )) or resid 623 through 643 or (resid 644 through 645 and (name N or name \ CA or name C or name O or name CB )) or resid 646 through 663 or (resid 664 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ CE )) or resid 665 through 693 or (resid 694 and (name N or name CA or name C or \ name O or name CB )) or resid 695 through 710 or (resid 711 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 712 through 801)) selection = (chain 'D' and (resid 9 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 55 or (resid 56 and (n \ ame N or name CA or name C or name O or name CB )) or resid 57 through 67 or res \ id 69 through 95 or (resid 96 and (name N or name CA or name C or name O or name \ CB or name CG )) or resid 97 through 105 or resid 107 through 130 or resid 132 \ through 147 or (resid 148 and (name N or name CA or name C or name O or name CB \ )) or resid 149 through 159 or (resid 160 and (name N or name CA or name C or na \ me O or name CB )) or resid 161 through 173 or (resid 174 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 175 through 232 or (resid \ 233 and (name N or name CA or name C or name O or name CB )) or resid 234 throu \ gh 237 or (resid 238 and (name N or name CA or name C or name O or name CB )) or \ resid 239 through 290 or (resid 291 and (name N or name CA or name C or name O \ or name CB )) or resid 292 through 416 or (resid 417 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD )) or resid 418 through 444 or \ (resid 445 through 446 and (name N or name CA or name C or name O or name CB )) \ or resid 447 through 571 or (resid 572 and (name N or name CA or name C or name \ O or name CB or name CG )) or (resid 573 through 575 and (name N or name CA or n \ ame C or name O or name CB )) or resid 576 through 638 or (resid 639 through 642 \ and (name N or name CA or name C or name O or name CB )) or resid 643 through 6 \ 52 or (resid 653 and (name N or name CA or name C or name O or name CB )) or res \ id 654 through 684 or (resid 685 and (name N or name CA or name C or name O or n \ ame CB )) or resid 686 through 693 or (resid 694 and (name N or name CA or name \ C or name O or name CB )) or resid 695 through 709 or (resid 710 and (name N or \ name CA or name C or name O or name CB )) or (resid 711 and (name N or name CA o \ r name C or name O or name CB or name CG )) or resid 712 through 801)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.040 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 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 0.112 21673 Z= 0.293 Angle : 0.718 14.306 29561 Z= 0.413 Chirality : 0.050 0.373 3312 Planarity : 0.004 0.037 3785 Dihedral : 15.644 132.190 7749 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.88 % Allowed : 6.88 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.16), residues: 2745 helix: 1.77 (0.25), residues: 467 sheet: 1.02 (0.17), residues: 887 loop : -0.95 (0.16), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 42 TYR 0.009 0.001 TYR C 686 PHE 0.021 0.001 PHE C 591 TRP 0.012 0.001 TRP D 155 HIS 0.007 0.001 HIS A 588 Details of bonding type rmsd covalent geometry : bond 0.00457 (21669) covalent geometry : angle 0.71826 (29561) hydrogen bonds : bond 0.15147 ( 839) hydrogen bonds : angle 5.81992 ( 2471) Misc. bond : bond 0.01381 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 0.841 Fit side-chains REVERT: A 118 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7346 (mttt) REVERT: A 557 HIS cc_start: 0.7408 (t-90) cc_final: 0.7150 (t70) REVERT: A 602 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6833 (mp0) REVERT: B 108 LYS cc_start: 0.7812 (ptmt) cc_final: 0.7584 (ptmm) REVERT: B 118 LYS cc_start: 0.8126 (mmtp) cc_final: 0.7508 (mtpp) REVERT: B 557 HIS cc_start: 0.7427 (t-90) cc_final: 0.7137 (t70) REVERT: C 42 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6952 (mtm-85) REVERT: C 108 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.8011 (ttpp) REVERT: C 528 MET cc_start: 0.8060 (mtp) cc_final: 0.7838 (mtp) REVERT: C 584 MET cc_start: 0.8402 (ttt) cc_final: 0.8191 (ttt) REVERT: D 528 MET cc_start: 0.8042 (mtp) cc_final: 0.7816 (mtp) REVERT: D 584 MET cc_start: 0.8386 (ttt) cc_final: 0.8168 (ttt) outliers start: 18 outliers final: 9 residues processed: 207 average time/residue: 0.7610 time to fit residues: 174.9967 Evaluate side-chains 174 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 47 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0170 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 overall best weight: 1.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN B 557 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.106721 restraints weight = 33973.427| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.31 r_work: 0.3100 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21673 Z= 0.183 Angle : 0.689 8.615 29561 Z= 0.369 Chirality : 0.050 0.169 3312 Planarity : 0.005 0.038 3785 Dihedral : 9.814 112.755 3181 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.11 % Allowed : 7.38 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.16), residues: 2745 helix: 1.33 (0.24), residues: 483 sheet: 1.17 (0.17), residues: 825 loop : -0.97 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 44 TYR 0.013 0.002 TYR C 686 PHE 0.033 0.002 PHE D 591 TRP 0.016 0.002 TRP C 369 HIS 0.005 0.001 HIS C 557 Details of bonding type rmsd covalent geometry : bond 0.00336 (21669) covalent geometry : angle 0.68886 (29561) hydrogen bonds : bond 0.06347 ( 839) hydrogen bonds : angle 5.35312 ( 2471) Misc. bond : bond 0.00089 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.657 Fit side-chains REVERT: B 118 LYS cc_start: 0.8939 (mmtp) cc_final: 0.8542 (mtpp) REVERT: C 42 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7654 (mtm-85) REVERT: C 139 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: C 528 MET cc_start: 0.8830 (mtp) cc_final: 0.8578 (mtp) REVERT: C 688 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7699 (mtp85) REVERT: D 42 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7125 (mtm-85) REVERT: D 528 MET cc_start: 0.8827 (mtp) cc_final: 0.8571 (mtp) outliers start: 23 outliers final: 9 residues processed: 178 average time/residue: 0.7772 time to fit residues: 153.7134 Evaluate side-chains 177 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 688 ARG Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 75 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 80 optimal weight: 7.9990 chunk 227 optimal weight: 0.0670 chunk 224 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 273 optimal weight: 9.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104996 restraints weight = 21206.963| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 0.99 r_work: 0.3086 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21673 Z= 0.282 Angle : 0.865 10.764 29561 Z= 0.470 Chirality : 0.056 0.197 3312 Planarity : 0.007 0.077 3785 Dihedral : 10.320 114.341 3165 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.34 % Allowed : 6.83 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.15), residues: 2745 helix: 1.00 (0.23), residues: 479 sheet: 1.20 (0.17), residues: 799 loop : -1.02 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 44 TYR 0.017 0.003 TYR B 337 PHE 0.038 0.003 PHE D 591 TRP 0.018 0.003 TRP A 369 HIS 0.007 0.002 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00535 (21669) covalent geometry : angle 0.86459 (29561) hydrogen bonds : bond 0.08509 ( 839) hydrogen bonds : angle 5.72706 ( 2471) Misc. bond : bond 0.00093 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.950 Fit side-chains REVERT: B 118 LYS cc_start: 0.8954 (mmtp) cc_final: 0.8586 (mtpp) REVERT: B 326 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8611 (mt0) REVERT: C 42 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7663 (mtm-85) REVERT: C 139 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6632 (mp0) REVERT: C 524 MET cc_start: 0.8860 (ttt) cc_final: 0.8638 (ttm) REVERT: C 688 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7619 (mtp85) REVERT: D 42 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7129 (mtm-85) outliers start: 28 outliers final: 16 residues processed: 185 average time/residue: 0.8388 time to fit residues: 171.8458 Evaluate side-chains 188 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 688 ARG Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 524 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 153 optimal weight: 0.0370 chunk 83 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 275 optimal weight: 7.9990 chunk 106 optimal weight: 30.0000 chunk 268 optimal weight: 9.9990 chunk 181 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 overall best weight: 1.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 HIS C 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.105769 restraints weight = 37714.084| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.38 r_work: 0.3085 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21673 Z= 0.180 Angle : 0.684 8.784 29561 Z= 0.369 Chirality : 0.049 0.154 3312 Planarity : 0.005 0.039 3785 Dihedral : 9.511 110.892 3163 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.52 % Allowed : 6.88 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 2745 helix: 1.23 (0.24), residues: 477 sheet: 1.04 (0.17), residues: 861 loop : -1.01 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 417 TYR 0.012 0.002 TYR B 337 PHE 0.029 0.002 PHE D 591 TRP 0.014 0.002 TRP D 369 HIS 0.006 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00326 (21669) covalent geometry : angle 0.68377 (29561) hydrogen bonds : bond 0.06299 ( 839) hydrogen bonds : angle 5.38249 ( 2471) Misc. bond : bond 0.00097 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.837 Fit side-chains REVERT: A 273 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8220 (tpt170) REVERT: B 118 LYS cc_start: 0.8991 (mmtp) cc_final: 0.8599 (mtpp) REVERT: B 273 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8216 (tpt170) REVERT: C 42 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7638 (mtm-85) REVERT: C 139 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6632 (mp0) REVERT: C 524 MET cc_start: 0.8938 (ttt) cc_final: 0.8713 (ttm) REVERT: C 688 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7655 (mtp85) REVERT: D 42 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7186 (mtm-85) outliers start: 32 outliers final: 13 residues processed: 188 average time/residue: 0.8529 time to fit residues: 176.9715 Evaluate side-chains 188 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 688 ARG Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 724 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 176 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 219 optimal weight: 0.2980 chunk 187 optimal weight: 3.9990 chunk 101 optimal weight: 0.1980 chunk 236 optimal weight: 0.9990 chunk 270 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 HIS C 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109852 restraints weight = 34883.488| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.32 r_work: 0.3146 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21673 Z= 0.126 Angle : 0.577 7.942 29561 Z= 0.307 Chirality : 0.046 0.144 3312 Planarity : 0.004 0.036 3785 Dihedral : 8.717 103.692 3163 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.97 % Allowed : 7.84 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.16), residues: 2745 helix: 1.47 (0.24), residues: 481 sheet: 1.07 (0.17), residues: 889 loop : -0.88 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 417 TYR 0.009 0.001 TYR C 686 PHE 0.025 0.002 PHE D 591 TRP 0.013 0.001 TRP C 124 HIS 0.005 0.001 HIS B 557 Details of bonding type rmsd covalent geometry : bond 0.00234 (21669) covalent geometry : angle 0.57669 (29561) hydrogen bonds : bond 0.04684 ( 839) hydrogen bonds : angle 5.05834 ( 2471) Misc. bond : bond 0.00081 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.899 Fit side-chains REVERT: B 118 LYS cc_start: 0.8983 (mmtp) cc_final: 0.8592 (mtpp) REVERT: B 273 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8212 (tpt170) REVERT: B 602 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: C 42 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7631 (mtm-85) REVERT: C 139 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: C 524 MET cc_start: 0.8860 (ttt) cc_final: 0.8646 (ttm) REVERT: C 528 MET cc_start: 0.8659 (mtp) cc_final: 0.8286 (mtp) REVERT: D 42 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7160 (mtm-85) REVERT: D 528 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8280 (mtp) outliers start: 20 outliers final: 11 residues processed: 180 average time/residue: 0.8122 time to fit residues: 162.0206 Evaluate side-chains 186 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 528 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 240 optimal weight: 0.9990 chunk 218 optimal weight: 0.4980 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 275 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 HIS C 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106221 restraints weight = 33146.075| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.28 r_work: 0.3095 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21673 Z= 0.187 Angle : 0.689 8.691 29561 Z= 0.371 Chirality : 0.050 0.153 3312 Planarity : 0.005 0.042 3785 Dihedral : 9.236 106.301 3163 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.06 % Allowed : 8.08 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 2745 helix: 1.31 (0.24), residues: 479 sheet: 1.10 (0.17), residues: 861 loop : -0.97 (0.15), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 417 TYR 0.013 0.002 TYR D 283 PHE 0.031 0.002 PHE D 591 TRP 0.013 0.002 TRP C 369 HIS 0.006 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00342 (21669) covalent geometry : angle 0.68855 (29561) hydrogen bonds : bond 0.06404 ( 839) hydrogen bonds : angle 5.31767 ( 2471) Misc. bond : bond 0.00075 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.800 Fit side-chains REVERT: A 273 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8216 (tpt170) REVERT: B 118 LYS cc_start: 0.8995 (mmtp) cc_final: 0.8600 (mtpp) REVERT: B 273 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8209 (tpt170) REVERT: C 42 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7647 (mtm-85) REVERT: C 139 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: C 688 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7658 (mtp85) REVERT: D 42 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7182 (mtm-85) outliers start: 22 outliers final: 12 residues processed: 178 average time/residue: 0.8620 time to fit residues: 169.8349 Evaluate side-chains 185 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 688 ARG Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 75 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 128 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 255 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 HIS C 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107855 restraints weight = 35025.932| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.32 r_work: 0.3118 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21673 Z= 0.152 Angle : 0.623 8.323 29561 Z= 0.335 Chirality : 0.047 0.147 3312 Planarity : 0.005 0.037 3785 Dihedral : 8.945 104.600 3163 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.11 % Allowed : 8.08 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 2745 helix: 1.40 (0.24), residues: 477 sheet: 1.13 (0.17), residues: 861 loop : -0.95 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 417 TYR 0.010 0.001 TYR D 283 PHE 0.028 0.002 PHE D 591 TRP 0.012 0.002 TRP C 155 HIS 0.005 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00278 (21669) covalent geometry : angle 0.62349 (29561) hydrogen bonds : bond 0.05462 ( 839) hydrogen bonds : angle 5.17624 ( 2471) Misc. bond : bond 0.00082 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.847 Fit side-chains REVERT: A 273 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8207 (tpt170) REVERT: B 118 LYS cc_start: 0.9001 (mmtp) cc_final: 0.8608 (mtpp) REVERT: B 273 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8216 (tpt170) REVERT: C 42 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7643 (mtm-85) REVERT: C 139 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: C 688 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7644 (mtp85) REVERT: D 42 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7185 (mtm-85) REVERT: D 524 MET cc_start: 0.8860 (ttt) cc_final: 0.8651 (ttm) outliers start: 23 outliers final: 11 residues processed: 190 average time/residue: 0.8563 time to fit residues: 179.7748 Evaluate side-chains 187 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 688 ARG Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 75 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 147 optimal weight: 7.9990 chunk 225 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 274 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 228 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 86 optimal weight: 0.0980 chunk 199 optimal weight: 6.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 HIS C 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.105579 restraints weight = 24013.830| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.06 r_work: 0.3091 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21673 Z= 0.243 Angle : 0.794 9.300 29561 Z= 0.430 Chirality : 0.053 0.171 3312 Planarity : 0.006 0.061 3785 Dihedral : 9.802 111.359 3163 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.20 % Allowed : 8.17 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 2745 helix: 1.14 (0.24), residues: 479 sheet: 1.20 (0.17), residues: 801 loop : -1.00 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 18 TYR 0.015 0.002 TYR D 283 PHE 0.037 0.003 PHE D 591 TRP 0.016 0.002 TRP A 369 HIS 0.007 0.002 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00453 (21669) covalent geometry : angle 0.79409 (29561) hydrogen bonds : bond 0.07680 ( 839) hydrogen bonds : angle 5.56487 ( 2471) Misc. bond : bond 0.00076 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.986 Fit side-chains REVERT: A 273 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8176 (tpt170) REVERT: B 47 HIS cc_start: 0.8706 (OUTLIER) cc_final: 0.8497 (m90) REVERT: B 118 LYS cc_start: 0.8988 (mmtp) cc_final: 0.8608 (mtpp) REVERT: B 273 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8176 (tpt170) REVERT: C 42 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7655 (mtm-85) REVERT: C 139 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: C 688 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7619 (mtp85) REVERT: D 42 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7122 (mtm-85) outliers start: 25 outliers final: 11 residues processed: 182 average time/residue: 0.8421 time to fit residues: 169.0609 Evaluate side-chains 188 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 688 ARG Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 75 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 199 optimal weight: 6.9990 chunk 249 optimal weight: 0.1980 chunk 82 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 170 optimal weight: 0.2980 chunk 4 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 237 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 HIS C 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.124970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111346 restraints weight = 30080.091| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.21 r_work: 0.3171 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21673 Z= 0.118 Angle : 0.563 7.860 29561 Z= 0.300 Chirality : 0.046 0.151 3312 Planarity : 0.004 0.034 3785 Dihedral : 8.636 103.600 3163 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 8.63 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 2745 helix: 1.47 (0.24), residues: 481 sheet: 1.08 (0.17), residues: 888 loop : -0.87 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 417 TYR 0.010 0.001 TYR D 686 PHE 0.024 0.001 PHE D 591 TRP 0.016 0.001 TRP C 155 HIS 0.004 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00223 (21669) covalent geometry : angle 0.56350 (29561) hydrogen bonds : bond 0.04388 ( 839) hydrogen bonds : angle 5.03718 ( 2471) Misc. bond : bond 0.00090 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.830 Fit side-chains REVERT: A 273 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8174 (tpt170) REVERT: B 118 LYS cc_start: 0.8978 (mmtp) cc_final: 0.8596 (mtpp) REVERT: B 273 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8199 (tpt170) REVERT: C 139 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6567 (mp0) REVERT: D 524 MET cc_start: 0.8835 (ttt) cc_final: 0.8630 (ttm) outliers start: 13 outliers final: 8 residues processed: 177 average time/residue: 0.8822 time to fit residues: 172.5127 Evaluate side-chains 180 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain D residue 75 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 38 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 HIS C 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.104878 restraints weight = 30187.270| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.22 r_work: 0.3077 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21673 Z= 0.240 Angle : 0.785 9.068 29561 Z= 0.425 Chirality : 0.053 0.175 3312 Planarity : 0.006 0.061 3785 Dihedral : 9.572 109.695 3159 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.83 % Allowed : 8.58 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 2745 helix: 1.14 (0.24), residues: 479 sheet: 1.24 (0.17), residues: 801 loop : -0.98 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 417 TYR 0.016 0.002 TYR A 337 PHE 0.038 0.003 PHE D 591 TRP 0.015 0.002 TRP A 369 HIS 0.006 0.002 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00448 (21669) covalent geometry : angle 0.78544 (29561) hydrogen bonds : bond 0.07553 ( 839) hydrogen bonds : angle 5.53304 ( 2471) Misc. bond : bond 0.00083 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.816 Fit side-chains REVERT: A 273 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8198 (tpt170) REVERT: B 47 HIS cc_start: 0.8748 (OUTLIER) cc_final: 0.8533 (m90) REVERT: B 118 LYS cc_start: 0.9003 (mmtp) cc_final: 0.8614 (mtpp) REVERT: B 273 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8211 (tpt170) REVERT: C 139 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: D 42 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7195 (mtm-85) outliers start: 17 outliers final: 9 residues processed: 179 average time/residue: 0.8716 time to fit residues: 172.5838 Evaluate side-chains 184 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 201 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 266 optimal weight: 0.8980 chunk 153 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 182 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 HIS C 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.105915 restraints weight = 34679.261| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.32 r_work: 0.3089 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21673 Z= 0.190 Angle : 0.697 8.756 29561 Z= 0.377 Chirality : 0.050 0.156 3312 Planarity : 0.005 0.038 3785 Dihedral : 9.342 109.341 3159 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.83 % Allowed : 8.44 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 2745 helix: 1.18 (0.24), residues: 479 sheet: 1.09 (0.17), residues: 827 loop : -1.01 (0.15), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 417 TYR 0.012 0.002 TYR D 283 PHE 0.030 0.002 PHE D 591 TRP 0.015 0.002 TRP C 648 HIS 0.006 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00346 (21669) covalent geometry : angle 0.69671 (29561) hydrogen bonds : bond 0.06469 ( 839) hydrogen bonds : angle 5.38508 ( 2471) Misc. bond : bond 0.00081 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9489.94 seconds wall clock time: 161 minutes 35.36 seconds (9695.36 seconds total)