Starting phenix.real_space_refine on Wed Jun 18 15:14:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qun_14149/06_2025/7qun_14149_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qun_14149/06_2025/7qun_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_14149/06_2025/7qun_14149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qun_14149/06_2025/7qun_14149.map" model { file = "/net/cci-nas-00/data/ceres_data/7qun_14149/06_2025/7qun_14149_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qun_14149/06_2025/7qun_14149_trim.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.097 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 21, 'ARG:plan': 3} 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: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 21, 'ARG:plan': 3} 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: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7, 'GLU:plan': 19, 'ARG:plan': 2} 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: {'GLN:plan1': 10, 'GLU:plan': 18, 'ASP:plan': 5, 'ARG:plan': 2, 'TYR:plan': 1} 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: {'GLN:plan1': 10, 'GLU:plan': 18, 'ASP:plan': 5, 'ARG:plan': 2, 'TYR:plan': 1} 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: {'GLN:plan1': 8, 'GLU:plan': 16, 'ASP:plan': 4, 'ARG:plan': 2, 'TYR:plan': 1} 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: {'GLN:plan1': 8, 'GLU:plan': 16, 'ASP:plan': 4, 'ARG:plan': 2, 'TYR:plan': 1} 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: 20.53, per 1000 atoms: 0.97 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: 4.78 Conformation dependent library (CDL) restraints added in 4.4 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: 2.82 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: 8.21 Time building geometry restraints manager: 5.68 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 730 or resid 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 730 or resid 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 730 or res \ id 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 730 or resid 80 \ 1)) } 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 59.130 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.070 ------------------------------------------------------------------------------- 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 : 4.57 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.012 0.001 TRP D 155 HIS 0.007 0.001 HIS A 588 PHE 0.021 0.001 PHE C 591 TYR 0.009 0.001 TYR C 686 ARG 0.004 0.000 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.15147 ( 839) hydrogen bonds : angle 5.81992 ( 2471) covalent geometry : bond 0.00457 (21669) covalent geometry : angle 0.71826 (29561) 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 : 2.547 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: 1.6613 time to fit residues: 382.9780 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 : 2.319 ------------------------------------------------------------------------------- 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 233 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.118656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.104746 restraints weight = 29432.675| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.21 r_work: 0.3075 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 2.44 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 = 0.50 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 = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21673 Z= 0.242 Angle : 0.799 9.826 29561 Z= 0.432 Chirality : 0.054 0.193 3312 Planarity : 0.006 0.055 3785 Dihedral : 10.324 113.230 3181 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.43 % Allowed : 6.92 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 2745 helix: 1.15 (0.24), residues: 479 sheet: 1.19 (0.17), residues: 808 loop : -1.00 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 369 HIS 0.008 0.002 HIS C 557 PHE 0.036 0.003 PHE D 591 TYR 0.016 0.002 TYR A 337 ARG 0.006 0.001 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.07842 ( 839) hydrogen bonds : angle 5.62925 ( 2471) covalent geometry : bond 0.00453 (21669) covalent geometry : angle 0.79901 (29561) Misc. bond : bond 0.00092 ( 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 198 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 2.627 Fit side-chains REVERT: B 118 LYS cc_start: 0.8954 (mmtp) cc_final: 0.8574 (mtpp) REVERT: B 326 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8629 (mt0) REVERT: C 42 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7672 (mtm-85) REVERT: C 139 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: C 528 MET cc_start: 0.8836 (mtp) cc_final: 0.8583 (mtp) REVERT: C 676 ARG cc_start: 0.8469 (mtm180) cc_final: 0.8231 (mtp85) REVERT: C 688 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7680 (mtp85) REVERT: D 42 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7163 (mtm-85) REVERT: D 528 MET cc_start: 0.8839 (mtp) cc_final: 0.8610 (mtp) outliers start: 30 outliers final: 14 residues processed: 184 average time/residue: 1.6853 time to fit residues: 344.6852 Evaluate side-chains 183 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 227 LEU 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 227 LEU 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 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 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 144 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 13 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 213 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 = 0.118797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.105811 restraints weight = 23945.908| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.06 r_work: 0.3095 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21673 Z= 0.230 Angle : 0.773 9.447 29561 Z= 0.419 Chirality : 0.052 0.162 3312 Planarity : 0.006 0.054 3785 Dihedral : 9.972 112.338 3167 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.43 % Allowed : 6.78 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 2745 helix: 1.08 (0.24), residues: 479 sheet: 1.20 (0.17), residues: 801 loop : -1.01 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 369 HIS 0.007 0.002 HIS C 557 PHE 0.033 0.003 PHE D 591 TYR 0.015 0.002 TYR A 337 ARG 0.006 0.001 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.07482 ( 839) hydrogen bonds : angle 5.56158 ( 2471) covalent geometry : bond 0.00427 (21669) covalent geometry : angle 0.77345 (29561) Misc. bond : bond 0.00095 ( 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 201 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 2.386 Fit side-chains REVERT: A 326 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8634 (mt0) REVERT: B 118 LYS cc_start: 0.8971 (mmtp) cc_final: 0.8611 (mtpp) REVERT: B 273 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8175 (tpt170) REVERT: B 326 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8613 (mt0) REVERT: C 42 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7662 (mtm-85) REVERT: C 139 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: C 524 MET cc_start: 0.8855 (ttt) cc_final: 0.8642 (ttm) REVERT: C 688 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7624 (mtp85) REVERT: D 42 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7142 (mtm-85) REVERT: D 524 MET cc_start: 0.8828 (ttt) cc_final: 0.8613 (ttm) outliers start: 30 outliers final: 12 residues processed: 189 average time/residue: 1.8200 time to fit residues: 381.5664 Evaluate side-chains 184 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 326 GLN 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 273 ARG Chi-restraints excluded: chain B residue 326 GLN 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 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 C residue 724 LEU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 724 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 193 optimal weight: 4.9990 chunk 258 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 49 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 108 optimal weight: 0.0870 chunk 6 optimal weight: 7.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.121764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.107167 restraints weight = 36038.341| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.37 r_work: 0.3106 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21673 Z= 0.159 Angle : 0.640 8.431 29561 Z= 0.344 Chirality : 0.048 0.152 3312 Planarity : 0.005 0.038 3785 Dihedral : 9.169 107.765 3163 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.29 % Allowed : 7.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 2745 helix: 1.32 (0.24), residues: 477 sheet: 1.09 (0.17), residues: 861 loop : -0.96 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 369 HIS 0.006 0.001 HIS A 325 PHE 0.028 0.002 PHE D 591 TYR 0.011 0.001 TYR C 686 ARG 0.006 0.000 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.05633 ( 839) hydrogen bonds : angle 5.25305 ( 2471) covalent geometry : bond 0.00290 (21669) covalent geometry : angle 0.63982 (29561) Misc. bond : bond 0.00093 ( 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 200 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 2.631 Fit side-chains REVERT: A 273 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8203 (tpt170) REVERT: B 118 LYS cc_start: 0.8989 (mmtp) cc_final: 0.8582 (mtpp) REVERT: B 273 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8196 (tpt170) REVERT: C 42 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7675 (mtm-85) REVERT: C 139 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: C 524 MET cc_start: 0.8883 (ttt) cc_final: 0.8670 (ttm) REVERT: C 528 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8344 (mtp) REVERT: C 688 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7635 (mtp85) REVERT: D 42 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7177 (mtm-85) REVERT: D 524 MET cc_start: 0.8872 (ttt) cc_final: 0.8653 (ttm) REVERT: D 528 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8416 (mtp) outliers start: 27 outliers final: 8 residues processed: 184 average time/residue: 1.7177 time to fit residues: 350.6200 Evaluate side-chains 186 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 2.552 ------------------------------------------------------------------------------- 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 139 GLU Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 688 ARG Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 528 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 199 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 140 optimal weight: 0.0980 chunk 130 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 210 optimal weight: 8.9990 chunk 51 optimal weight: 0.0040 chunk 269 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.6198 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.121172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.107100 restraints weight = 31915.638| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.26 r_work: 0.3108 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1370 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= 0.169 Angle : 0.660 8.472 29561 Z= 0.354 Chirality : 0.049 0.150 3312 Planarity : 0.005 0.038 3785 Dihedral : 9.168 106.492 3163 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.15 % Allowed : 7.71 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 2745 helix: 1.33 (0.24), residues: 477 sheet: 1.09 (0.17), residues: 861 loop : -0.98 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 369 HIS 0.006 0.001 HIS B 325 PHE 0.029 0.002 PHE D 591 TYR 0.012 0.002 TYR D 283 ARG 0.006 0.000 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.05984 ( 839) hydrogen bonds : angle 5.26273 ( 2471) covalent geometry : bond 0.00308 (21669) covalent geometry : angle 0.65966 (29561) Misc. bond : bond 0.00078 ( 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 195 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 2.556 Fit side-chains REVERT: B 118 LYS cc_start: 0.8988 (mmtp) cc_final: 0.8596 (mtpp) REVERT: B 273 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8193 (tpt170) REVERT: C 42 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7609 (mtm-85) REVERT: C 139 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: C 524 MET cc_start: 0.8877 (ttt) cc_final: 0.8667 (ttm) REVERT: C 688 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7645 (mtp85) REVERT: D 42 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7177 (mtm-85) REVERT: D 524 MET cc_start: 0.8874 (ttt) cc_final: 0.8652 (ttm) outliers start: 24 outliers final: 12 residues processed: 184 average time/residue: 1.7488 time to fit residues: 357.4019 Evaluate side-chains 184 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 2.586 ------------------------------------------------------------------------------- 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 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 C residue 724 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 118 optimal weight: 1.9990 chunk 228 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 268 optimal weight: 8.9990 chunk 264 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 237 optimal weight: 0.0980 chunk 14 optimal weight: 6.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.118705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.105436 restraints weight = 25535.956| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.10 r_work: 0.3088 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 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 = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21673 Z= 0.235 Angle : 0.781 9.182 29561 Z= 0.423 Chirality : 0.053 0.171 3312 Planarity : 0.006 0.058 3785 Dihedral : 9.780 111.100 3163 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.29 % Allowed : 7.71 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 2745 helix: 1.12 (0.24), residues: 479 sheet: 1.20 (0.17), residues: 801 loop : -1.01 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 369 HIS 0.007 0.002 HIS B 265 PHE 0.037 0.003 PHE D 591 TYR 0.014 0.002 TYR B 337 ARG 0.005 0.001 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.07519 ( 839) hydrogen bonds : angle 5.54228 ( 2471) covalent geometry : bond 0.00435 (21669) covalent geometry : angle 0.78112 (29561) Misc. bond : bond 0.00084 ( 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 199 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 2.491 Fit side-chains REVERT: A 273 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8180 (tpt170) REVERT: B 118 LYS cc_start: 0.8992 (mmtp) cc_final: 0.8605 (mtpp) REVERT: B 273 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8188 (tpt170) REVERT: C 42 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7662 (mtm-85) REVERT: C 139 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: C 688 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7632 (mtp85) REVERT: D 42 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7142 (mtm-85) REVERT: D 524 MET cc_start: 0.8865 (ttt) cc_final: 0.8662 (ttm) outliers start: 27 outliers final: 16 residues processed: 187 average time/residue: 1.7554 time to fit residues: 364.5940 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 : 2.339 ------------------------------------------------------------------------------- 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 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 201 ILE Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 724 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 256 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 0.3980 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.119821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106258 restraints weight = 28006.508| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.16 r_work: 0.3099 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- 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 = 0.37 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 = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21673 Z= 0.200 Angle : 0.715 8.783 29561 Z= 0.387 Chirality : 0.050 0.157 3312 Planarity : 0.005 0.040 3785 Dihedral : 9.569 110.533 3163 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.43 % Allowed : 7.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 2745 helix: 1.17 (0.24), residues: 479 sheet: 1.00 (0.17), residues: 861 loop : -1.03 (0.15), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 369 HIS 0.006 0.002 HIS B 265 PHE 0.031 0.002 PHE D 591 TYR 0.012 0.002 TYR D 283 ARG 0.006 0.000 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.06720 ( 839) hydrogen bonds : angle 5.42171 ( 2471) covalent geometry : bond 0.00366 (21669) covalent geometry : angle 0.71480 (29561) Misc. bond : bond 0.00083 ( 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 200 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 2.569 Fit side-chains REVERT: A 273 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8182 (tpt170) REVERT: B 118 LYS cc_start: 0.8986 (mmtp) cc_final: 0.8601 (mtpp) REVERT: B 273 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8173 (tpt170) REVERT: C 139 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: C 688 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7605 (mtp85) REVERT: D 42 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7168 (mtm-85) REVERT: D 524 MET cc_start: 0.8864 (ttt) cc_final: 0.8652 (ttm) outliers start: 30 outliers final: 16 residues processed: 187 average time/residue: 1.7815 time to fit residues: 371.2349 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 : 2.358 ------------------------------------------------------------------------------- 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 64 CYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 426 THR 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 75 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 724 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 99 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 150 optimal weight: 0.0060 chunk 215 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 68 optimal weight: 8.9990 chunk 239 optimal weight: 7.9990 chunk 249 optimal weight: 4.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.121688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.107694 restraints weight = 30773.314| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.25 r_work: 0.3117 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 2.53 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 = 0.37 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: 0.8522 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21673 Z= 0.158 Angle : 0.639 8.378 29561 Z= 0.344 Chirality : 0.048 0.152 3312 Planarity : 0.005 0.037 3785 Dihedral : 9.023 106.801 3159 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.11 % Allowed : 8.49 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 2745 helix: 1.33 (0.24), residues: 477 sheet: 1.09 (0.17), residues: 860 loop : -0.98 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 155 HIS 0.005 0.001 HIS A 325 PHE 0.027 0.002 PHE D 591 TYR 0.010 0.001 TYR C 686 ARG 0.007 0.000 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.05649 ( 839) hydrogen bonds : angle 5.23596 ( 2471) covalent geometry : bond 0.00288 (21669) covalent geometry : angle 0.63888 (29561) Misc. bond : bond 0.00093 ( 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 194 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 2.534 Fit side-chains REVERT: A 273 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8176 (tpt170) REVERT: B 118 LYS cc_start: 0.8981 (mmtp) cc_final: 0.8583 (mtpp) REVERT: B 273 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8170 (tpt170) REVERT: B 610 ARG cc_start: 0.8444 (ttp-110) cc_final: 0.8221 (ttp-110) REVERT: C 139 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: C 688 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7622 (mtp85) REVERT: D 42 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7191 (mtm-85) REVERT: D 524 MET cc_start: 0.8854 (ttt) cc_final: 0.8638 (ttm) outliers start: 23 outliers final: 15 residues processed: 183 average time/residue: 1.7776 time to fit residues: 360.6798 Evaluate side-chains 192 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 2.511 ------------------------------------------------------------------------------- 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 47 HIS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 426 THR 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 Chi-restraints excluded: chain D residue 426 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 13 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 268 optimal weight: 9.9990 chunk 61 optimal weight: 0.4980 chunk 7 optimal weight: 9.9990 chunk 59 optimal weight: 0.3980 chunk 179 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.120578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.106431 restraints weight = 32684.540| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.27 r_work: 0.3098 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- 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 = 0.38 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 = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21673 Z= 0.181 Angle : 0.683 8.693 29561 Z= 0.368 Chirality : 0.049 0.152 3312 Planarity : 0.005 0.039 3785 Dihedral : 9.170 107.063 3159 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.11 % Allowed : 8.58 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 2745 helix: 1.26 (0.24), residues: 479 sheet: 1.08 (0.17), residues: 860 loop : -0.99 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 369 HIS 0.006 0.001 HIS B 265 PHE 0.030 0.002 PHE D 591 TYR 0.012 0.002 TYR D 283 ARG 0.006 0.000 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.06270 ( 839) hydrogen bonds : angle 5.32191 ( 2471) covalent geometry : bond 0.00331 (21669) covalent geometry : angle 0.68272 (29561) Misc. bond : bond 0.00077 ( 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 195 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 2.300 Fit side-chains REVERT: A 273 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8209 (tpt170) REVERT: B 118 LYS cc_start: 0.8996 (mmtp) cc_final: 0.8600 (mtpp) REVERT: B 273 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8199 (tpt170) REVERT: B 610 ARG cc_start: 0.8474 (ttp-110) cc_final: 0.8252 (ttp-110) REVERT: C 139 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: C 688 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7663 (mtp85) REVERT: D 42 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7215 (mtm-85) REVERT: D 524 MET cc_start: 0.8863 (ttt) cc_final: 0.8648 (ttm) outliers start: 23 outliers final: 16 residues processed: 184 average time/residue: 1.6989 time to fit residues: 347.0040 Evaluate side-chains 191 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 2.566 ------------------------------------------------------------------------------- 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 47 HIS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 426 THR 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 Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 475 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 253 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 268 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 205 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 = 0.3335 r_free = 0.3335 target = 0.117336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.104022 restraints weight = 25831.703| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.11 r_work: 0.3067 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 21673 Z= 0.298 Angle : 0.892 10.747 29561 Z= 0.485 Chirality : 0.057 0.199 3312 Planarity : 0.007 0.079 3785 Dihedral : 10.089 113.760 3159 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.11 % Allowed : 8.72 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 2745 helix: 0.93 (0.23), residues: 479 sheet: 1.16 (0.17), residues: 796 loop : -1.05 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 648 HIS 0.010 0.002 HIS B 265 PHE 0.043 0.003 PHE D 591 TYR 0.016 0.003 TYR D 283 ARG 0.009 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.08707 ( 839) hydrogen bonds : angle 5.76364 ( 2471) covalent geometry : bond 0.00565 (21669) covalent geometry : angle 0.89191 (29561) Misc. bond : bond 0.00084 ( 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 189 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 2.378 Fit side-chains REVERT: A 273 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8197 (tpt170) REVERT: B 118 LYS cc_start: 0.9003 (mmtp) cc_final: 0.8619 (mtpp) REVERT: B 273 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8201 (tpt90) REVERT: C 139 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: C 688 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7648 (mtp85) REVERT: D 42 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7186 (mtm-85) REVERT: D 524 MET cc_start: 0.8861 (ttt) cc_final: 0.8658 (ttm) outliers start: 23 outliers final: 13 residues processed: 180 average time/residue: 1.7010 time to fit residues: 340.2127 Evaluate side-chains 183 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 2.341 ------------------------------------------------------------------------------- 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 64 CYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 426 THR 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 426 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 107 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 chunk 256 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 219 optimal weight: 0.0870 chunk 65 optimal weight: 0.8980 chunk 130 optimal weight: 0.0870 chunk 268 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.122559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.108551 restraints weight = 32327.928| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.27 r_work: 0.3129 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21673 Z= 0.143 Angle : 0.616 8.383 29561 Z= 0.330 Chirality : 0.047 0.149 3312 Planarity : 0.005 0.037 3785 Dihedral : 8.993 107.845 3159 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.83 % Allowed : 8.72 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 2745 helix: 1.32 (0.24), residues: 481 sheet: 1.02 (0.17), residues: 878 loop : -0.91 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 155 HIS 0.006 0.001 HIS B 265 PHE 0.026 0.002 PHE D 591 TYR 0.011 0.001 TYR D 686 ARG 0.006 0.000 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.05229 ( 839) hydrogen bonds : angle 5.21240 ( 2471) covalent geometry : bond 0.00261 (21669) covalent geometry : angle 0.61592 (29561) Misc. bond : bond 0.00093 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20362.41 seconds wall clock time: 354 minutes 9.72 seconds (21249.72 seconds total)