Starting phenix.real_space_refine on Sat Jul 4 00:33:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7scn_25039/07_2026/7scn_25039.cif Found real_map, /net/cci-nas-00/data/ceres_data/7scn_25039/07_2026/7scn_25039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7scn_25039/07_2026/7scn_25039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7scn_25039/07_2026/7scn_25039.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7scn_25039/07_2026/7scn_25039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7scn_25039/07_2026/7scn_25039.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7scn_25039/07_2026/7scn_25039.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7scn_25039/07_2026/7scn_25039.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 78 5.16 5 C 10806 2.51 5 N 2919 2.21 5 O 3342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17145 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2522 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "B" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "C" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2522 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "D" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "F" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2522 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "I" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain: "J" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "K" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.01, per 1000 atoms: 0.23 Number of scatterers: 17145 At special positions: 0 Unit cell: (124.2, 129.95, 147.2, 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 78 16.00 O 3342 8.00 N 2919 7.00 C 10806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.05 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.02 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.05 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.02 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS H 529 " - pdb=" SG CYS H 602 " distance=2.01 Simple disulfide: pdb=" SG CYS L 646 " - pdb=" SG CYS L 712 " distance=2.02 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 467 " distance=2.04 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.05 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.02 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.05 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.02 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 529 " - pdb=" SG CYS E 602 " distance=2.01 Simple disulfide: pdb=" SG CYS F 646 " - pdb=" SG CYS F 712 " distance=2.02 Simple disulfide: pdb=" SG CYS G 8 " - pdb=" SG CYS I 467 " distance=2.04 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 278 " distance=2.05 Simple disulfide: pdb=" SG CYS G 59 " - pdb=" SG CYS G 71 " distance=2.02 Simple disulfide: pdb=" SG CYS G 94 " - pdb=" SG CYS G 139 " distance=2.05 Simple disulfide: pdb=" SG CYS G 282 " - pdb=" SG CYS G 306 " distance=2.02 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 478 " distance=2.03 Simple disulfide: pdb=" SG CYS J 529 " - pdb=" SG CYS J 602 " distance=2.01 Simple disulfide: pdb=" SG CYS K 646 " - pdb=" SG CYS K 712 " distance=2.02 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=1, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 58 " " NAG A 402 " - " ASN A 27 " " NAG A 403 " - " ASN A 91 " " NAG A 404 " - " ASN A 129 " " NAG A 405 " - " ASN A 290 " " NAG C 401 " - " ASN C 58 " " NAG C 402 " - " ASN C 27 " " NAG C 403 " - " ASN C 91 " " NAG C 404 " - " ASN C 129 " " NAG C 405 " - " ASN C 290 " " NAG G 401 " - " ASN G 58 " " NAG G 402 " - " ASN G 27 " " NAG G 403 " - " ASN G 91 " " NAG G 404 " - " ASN G 129 " " NAG G 405 " - " ASN G 290 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 805.6 milliseconds 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3948 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 51 sheets defined 22.4% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.899A pdb=" N GLU A 72 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU A 73 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.340A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 367 through 389 Processing helix chain 'B' and resid 404 through 457 removed outlier: 4.028A pdb=" N GLN B 455 " --> pdb=" O LYS B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 Processing helix chain 'B' and resid 488 through 503 removed outlier: 3.826A pdb=" N TYR B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU B 494 " --> pdb=" O PRO B 490 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU B 495 " --> pdb=" O LYS B 491 " (cutoff:3.500A) Processing helix chain 'H' and resid 535 through 539 Processing helix chain 'H' and resid 568 through 571 Processing helix chain 'L' and resid 653 through 655 No H-bonds generated for 'chain 'L' and resid 653 through 655' Processing helix chain 'L' and resid 703 through 707 Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 68 through 75 removed outlier: 3.898A pdb=" N GLU C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU C 73 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 109 Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.341A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 367 through 389 Processing helix chain 'D' and resid 404 through 457 removed outlier: 4.027A pdb=" N GLN D 455 " --> pdb=" O LYS D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'D' and resid 488 through 503 removed outlier: 3.827A pdb=" N TYR D 492 " --> pdb=" O ASP D 488 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU D 494 " --> pdb=" O PRO D 490 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU D 495 " --> pdb=" O LYS D 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 539 Processing helix chain 'E' and resid 568 through 571 Processing helix chain 'F' and resid 653 through 655 No H-bonds generated for 'chain 'F' and resid 653 through 655' Processing helix chain 'F' and resid 703 through 707 Processing helix chain 'G' and resid 60 through 67 Processing helix chain 'G' and resid 68 through 75 removed outlier: 3.898A pdb=" N GLU G 72 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU G 73 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 122 through 127 removed outlier: 4.340A pdb=" N TRP G 127 " --> pdb=" O LYS G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 195 Processing helix chain 'I' and resid 367 through 389 Processing helix chain 'I' and resid 404 through 457 removed outlier: 4.027A pdb=" N GLN I 455 " --> pdb=" O LYS I 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 484 Processing helix chain 'I' and resid 488 through 503 removed outlier: 3.827A pdb=" N TYR I 492 " --> pdb=" O ASP I 488 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU I 494 " --> pdb=" O PRO I 490 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU I 495 " --> pdb=" O LYS I 491 " (cutoff:3.500A) Processing helix chain 'J' and resid 535 through 539 Processing helix chain 'J' and resid 568 through 571 Processing helix chain 'K' and resid 653 through 655 No H-bonds generated for 'chain 'K' and resid 653 through 655' Processing helix chain 'K' and resid 703 through 707 Processing sheet with id=AA1, first strand: chain 'B' and resid 361 through 366 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 48 removed outlier: 6.257A pdb=" N LEU A 45 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N CYS A 278 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.658A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER A 261 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE A 115 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA A 259 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG A 117 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA A 257 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER A 261 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE A 115 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA A 259 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG A 117 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA A 257 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.726A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 289 removed outlier: 4.137A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 512 through 513 Processing sheet with id=AB4, first strand: chain 'H' and resid 517 through 518 removed outlier: 6.656A pdb=" N GLU H 517 " --> pdb=" O THR H 624 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE H 541 " --> pdb=" O ARG H 557 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG H 557 " --> pdb=" O PHE H 541 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP H 543 " --> pdb=" O MET H 555 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 517 through 518 removed outlier: 6.656A pdb=" N GLU H 517 " --> pdb=" O THR H 624 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 627 through 630 Processing sheet with id=AB7, first strand: chain 'L' and resid 633 through 636 removed outlier: 6.707A pdb=" N LEU L 657 " --> pdb=" O TYR L 673 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR L 673 " --> pdb=" O LEU L 657 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP L 659 " --> pdb=" O LEU L 671 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 633 through 636 Processing sheet with id=AB9, first strand: chain 'D' and resid 361 through 366 Processing sheet with id=AC1, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AC2, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AC3, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AC4, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.256A pdb=" N LEU C 45 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N CYS C 278 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.660A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER C 261 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 115 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA C 259 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG C 117 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA C 257 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER C 261 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 115 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA C 259 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG C 117 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA C 257 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.725A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD1, first strand: chain 'C' and resid 287 through 289 removed outlier: 4.136A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 512 through 513 Processing sheet with id=AD3, first strand: chain 'E' and resid 517 through 518 removed outlier: 6.655A pdb=" N GLU E 517 " --> pdb=" O THR E 624 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE E 541 " --> pdb=" O ARG E 557 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG E 557 " --> pdb=" O PHE E 541 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP E 543 " --> pdb=" O MET E 555 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 517 through 518 removed outlier: 6.655A pdb=" N GLU E 517 " --> pdb=" O THR E 624 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 627 through 630 Processing sheet with id=AD6, first strand: chain 'F' and resid 633 through 636 removed outlier: 6.707A pdb=" N LEU F 657 " --> pdb=" O TYR F 673 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR F 673 " --> pdb=" O LEU F 657 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP F 659 " --> pdb=" O LEU F 671 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 633 through 636 Processing sheet with id=AD8, first strand: chain 'I' and resid 361 through 366 Processing sheet with id=AD9, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AE1, first strand: chain 'G' and resid 33 through 35 Processing sheet with id=AE2, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AE3, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.256A pdb=" N LEU G 45 " --> pdb=" O ASP G 276 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N CYS G 278 " --> pdb=" O LEU G 45 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.659A pdb=" N LEU G 54 " --> pdb=" O VAL G 84 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER G 261 " --> pdb=" O SER G 113 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE G 115 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA G 259 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG G 117 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA G 257 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER G 261 " --> pdb=" O SER G 113 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE G 115 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA G 259 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG G 117 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA G 257 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 136 through 141 removed outlier: 4.726A pdb=" N CYS G 139 " --> pdb=" O SER G 146 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER G 146 " --> pdb=" O CYS G 139 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AE9, first strand: chain 'G' and resid 287 through 289 removed outlier: 4.136A pdb=" N CYS G 282 " --> pdb=" O ILE G 289 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 512 through 513 Processing sheet with id=AF2, first strand: chain 'J' and resid 517 through 518 removed outlier: 6.656A pdb=" N GLU J 517 " --> pdb=" O THR J 624 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE J 541 " --> pdb=" O ARG J 557 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG J 557 " --> pdb=" O PHE J 541 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP J 543 " --> pdb=" O MET J 555 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 517 through 518 removed outlier: 6.656A pdb=" N GLU J 517 " --> pdb=" O THR J 624 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 627 through 630 Processing sheet with id=AF5, first strand: chain 'K' and resid 633 through 636 removed outlier: 6.707A pdb=" N LEU K 657 " --> pdb=" O TYR K 673 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR K 673 " --> pdb=" O LEU K 657 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP K 659 " --> pdb=" O LEU K 671 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 633 through 636 741 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 5141 1.33 - 1.48: 5396 1.48 - 1.62: 6887 1.62 - 1.76: 36 1.76 - 1.90: 93 Bond restraints: 17553 Sorted by residual: bond pdb=" CB ILE I 503 " pdb=" CG1 ILE I 503 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" CB ILE D 503 " pdb=" CG1 ILE D 503 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" CB ILE B 503 " pdb=" CG1 ILE B 503 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" CB ILE B 336 " pdb=" CG1 ILE B 336 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" CB ILE D 336 " pdb=" CG1 ILE D 336 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 17548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.76: 23727 6.76 - 13.52: 87 13.52 - 20.27: 3 20.27 - 27.03: 3 27.03 - 33.79: 3 Bond angle restraints: 23823 Sorted by residual: angle pdb=" N TYR H 609 " pdb=" CA TYR H 609 " pdb=" C TYR H 609 " ideal model delta sigma weight residual 113.12 90.54 22.58 1.25e+00 6.40e-01 3.26e+02 angle pdb=" N TYR E 609 " pdb=" CA TYR E 609 " pdb=" C TYR E 609 " ideal model delta sigma weight residual 113.12 90.57 22.55 1.25e+00 6.40e-01 3.25e+02 angle pdb=" N TYR J 609 " pdb=" CA TYR J 609 " pdb=" C TYR J 609 " ideal model delta sigma weight residual 113.12 90.58 22.54 1.25e+00 6.40e-01 3.25e+02 angle pdb=" C2 NAG G 404 " pdb=" N2 NAG G 404 " pdb=" C7 NAG G 404 " ideal model delta sigma weight residual 124.56 158.35 -33.79 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C2 NAG C 404 " pdb=" N2 NAG C 404 " pdb=" C7 NAG C 404 " ideal model delta sigma weight residual 124.56 158.32 -33.76 3.00e+00 1.11e-01 1.27e+02 ... (remaining 23818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 9931 17.16 - 34.32: 254 34.32 - 51.48: 63 51.48 - 68.64: 46 68.64 - 85.80: 17 Dihedral angle restraints: 10311 sinusoidal: 4119 harmonic: 6192 Sorted by residual: dihedral pdb=" CB CYS D 474 " pdb=" SG CYS D 474 " pdb=" SG CYS D 478 " pdb=" CB CYS D 478 " ideal model delta sinusoidal sigma weight residual 93.00 146.18 -53.18 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CB CYS B 474 " pdb=" SG CYS B 474 " pdb=" SG CYS B 478 " pdb=" CB CYS B 478 " ideal model delta sinusoidal sigma weight residual 93.00 146.15 -53.15 1 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" CB CYS I 474 " pdb=" SG CYS I 474 " pdb=" SG CYS I 478 " pdb=" CB CYS I 478 " ideal model delta sinusoidal sigma weight residual 93.00 146.14 -53.14 1 1.00e+01 1.00e-02 3.84e+01 ... (remaining 10308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1883 0.100 - 0.199: 555 0.199 - 0.299: 111 0.299 - 0.398: 32 0.398 - 0.498: 26 Chirality restraints: 2607 Sorted by residual: chirality pdb=" CB ILE B 336 " pdb=" CA ILE B 336 " pdb=" CG1 ILE B 336 " pdb=" CG2 ILE B 336 " both_signs ideal model delta sigma weight residual False 2.64 3.14 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CB ILE D 336 " pdb=" CA ILE D 336 " pdb=" CG1 ILE D 336 " pdb=" CG2 ILE D 336 " both_signs ideal model delta sigma weight residual False 2.64 3.14 -0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CB ILE I 336 " pdb=" CA ILE I 336 " pdb=" CG1 ILE I 336 " pdb=" CG2 ILE I 336 " both_signs ideal model delta sigma weight residual False 2.64 3.14 -0.49 2.00e-01 2.50e+01 6.09e+00 ... (remaining 2604 not shown) Planarity restraints: 3078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 449 " 0.063 2.00e-02 2.50e+03 3.46e-02 2.39e+01 pdb=" CG TYR D 449 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR D 449 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR D 449 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR D 449 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR D 449 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR D 449 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 449 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 449 " -0.062 2.00e-02 2.50e+03 3.44e-02 2.36e+01 pdb=" CG TYR B 449 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 449 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 449 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR B 449 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR B 449 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR B 449 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 449 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 449 " -0.062 2.00e-02 2.50e+03 3.44e-02 2.36e+01 pdb=" CG TYR I 449 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR I 449 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR I 449 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR I 449 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR I 449 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR I 449 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 449 " -0.053 2.00e-02 2.50e+03 ... (remaining 3075 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 8 2.38 - 3.01: 9676 3.01 - 3.64: 24158 3.64 - 4.27: 41932 4.27 - 4.90: 67441 Nonbonded interactions: 143215 Sorted by model distance: nonbonded pdb=" CD1 LEU L 627 " pdb=" OE1 GLN L 714 " model vdw 1.750 3.460 nonbonded pdb=" NE2 GLN B 372 " pdb=" OG SER H 607 " model vdw 2.099 3.120 nonbonded pdb=" N TYR E 609 " pdb=" N PHE E 610 " model vdw 2.215 2.560 nonbonded pdb=" N TYR H 609 " pdb=" N PHE H 610 " model vdw 2.215 2.560 nonbonded pdb=" N TYR J 609 " pdb=" N PHE J 610 " model vdw 2.215 2.560 ... (remaining 143210 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.400 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.022 0.288 17593 Z= 1.157 Angle : 1.793 33.790 23916 Z= 1.183 Chirality : 0.109 0.498 2607 Planarity : 0.009 0.055 3063 Dihedral : 10.470 85.803 6291 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.16 % Allowed : 0.32 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.17), residues: 2121 helix: 1.24 (0.24), residues: 363 sheet: 1.19 (0.23), residues: 504 loop : 0.65 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 619 TYR 0.063 0.009 TYR D 449 PHE 0.035 0.007 PHE F 722 TRP 0.037 0.008 TRP H 554 HIS 0.013 0.003 HIS I 472 Details of bonding type rmsd/Z covalent geometry : bond 0.02154 / 1.13 (17553) covalent geometry : angle 1.78552 / 1.18 (23823) SS BOND : bond 0.01490 / 0.95 ( 24) SS BOND : angle 3.51692 / 2.47 ( 48) hydrogen bonds : bond 0.14831 / 9.71 ( 708) hydrogen bonds : angle 7.05380 / 4.89 ( 1926) Misc. bond : bond 0.28833 / 15.18 ( 1) link_NAG-ASN : bond 0.07677 / 4.81 ( 15) link_NAG-ASN : angle 2.92393 / 1.83 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 422 time to evaluate : 0.652 Fit side-chains REVERT: A 275 MET cc_start: 0.8103 (tpt) cc_final: 0.7746 (tpt) REVERT: H 587 MET cc_start: 0.8019 (ttp) cc_final: 0.7807 (ttp) REVERT: D 347 MET cc_start: 0.8308 (ttp) cc_final: 0.7922 (ttm) REVERT: E 570 PHE cc_start: 0.7785 (m-80) cc_final: 0.7579 (m-80) REVERT: F 701 ARG cc_start: 0.6949 (mtm-85) cc_final: 0.6599 (mtm-85) REVERT: G 222 LYS cc_start: 0.9018 (mttt) cc_final: 0.8805 (mttm) REVERT: I 347 MET cc_start: 0.8207 (ttp) cc_final: 0.7832 (ttm) REVERT: I 484 ASN cc_start: 0.7638 (m-40) cc_final: 0.7402 (m-40) REVERT: K 630 SER cc_start: 0.6884 (t) cc_final: 0.6601 (p) outliers start: 3 outliers final: 3 residues processed: 425 average time/residue: 0.1576 time to fit residues: 97.1734 Evaluate side-chains 231 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 228 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain G residue 115 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 GLN C 55 GLN C 296 GLN G 55 GLN G 296 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.165454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136366 restraints weight = 20929.773| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.61 r_work: 0.3426 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17593 Z= 0.172 Angle : 0.642 9.102 23916 Z= 0.349 Chirality : 0.047 0.177 2607 Planarity : 0.004 0.035 3063 Dihedral : 6.366 87.216 2346 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.26 % Allowed : 6.84 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.18), residues: 2121 helix: 2.19 (0.25), residues: 369 sheet: 0.59 (0.19), residues: 645 loop : 0.52 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 619 TYR 0.015 0.002 TYR J 609 PHE 0.017 0.002 PHE A 115 TRP 0.013 0.002 TRP J 554 HIS 0.004 0.001 HIS C 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (17553) covalent geometry : angle 0.63117 / 0.35 (23823) SS BOND : bond 0.00574 / 0.36 ( 24) SS BOND : angle 1.36636 / 1.00 ( 48) hydrogen bonds : bond 0.05327 / 3.54 ( 708) hydrogen bonds : angle 5.41298 / 3.81 ( 1926) Misc. bond : bond 0.00223 / 0.12 ( 1) link_NAG-ASN : bond 0.00453 / 0.28 ( 15) link_NAG-ASN : angle 2.44366 / 1.54 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8434 (m-70) cc_final: 0.8014 (m-70) REVERT: A 317 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8507 (ttt) REVERT: B 369 LYS cc_start: 0.8312 (mttt) cc_final: 0.8003 (mmtm) REVERT: B 396 VAL cc_start: 0.7864 (t) cc_final: 0.7314 (p) REVERT: L 701 ARG cc_start: 0.7277 (ptp90) cc_final: 0.6913 (ptp90) REVERT: D 347 MET cc_start: 0.8457 (ttp) cc_final: 0.8083 (ttm) REVERT: D 477 GLU cc_start: 0.6953 (mp0) cc_final: 0.6681 (mp0) REVERT: E 587 MET cc_start: 0.8466 (ttp) cc_final: 0.8211 (ttp) REVERT: F 666 GLN cc_start: 0.7945 (mt0) cc_final: 0.7608 (mm-40) REVERT: I 347 MET cc_start: 0.8435 (ttp) cc_final: 0.8089 (ttm) REVERT: I 349 ASP cc_start: 0.8071 (p0) cc_final: 0.7817 (p0) outliers start: 42 outliers final: 26 residues processed: 296 average time/residue: 0.1384 time to fit residues: 62.0098 Evaluate side-chains 268 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain H residue 621 THR Chi-restraints excluded: chain L residue 628 THR Chi-restraints excluded: chain L residue 645 SER Chi-restraints excluded: chain L residue 698 THR Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain E residue 624 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 689 SER Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain I residue 402 LYS Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 624 THR Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 698 THR Chi-restraints excluded: chain K residue 709 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 204 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 23 optimal weight: 0.0010 chunk 156 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN B 376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.167368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139160 restraints weight = 21036.143| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.70 r_work: 0.3438 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17593 Z= 0.125 Angle : 0.539 9.739 23916 Z= 0.287 Chirality : 0.044 0.241 2607 Planarity : 0.004 0.035 3063 Dihedral : 5.927 85.040 2346 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.72 % Allowed : 9.32 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.18), residues: 2121 helix: 2.48 (0.26), residues: 372 sheet: 0.61 (0.21), residues: 582 loop : 0.42 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 701 TYR 0.016 0.002 TYR H 609 PHE 0.017 0.002 PHE A 115 TRP 0.010 0.001 TRP I 351 HIS 0.003 0.001 HIS G 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (17553) covalent geometry : angle 0.53103 / 0.29 (23823) SS BOND : bond 0.00331 / 0.22 ( 24) SS BOND : angle 0.94536 / 0.71 ( 48) hydrogen bonds : bond 0.04156 / 2.75 ( 708) hydrogen bonds : angle 4.97800 / 3.51 ( 1926) Misc. bond : bond 0.00058 / 0.03 ( 1) link_NAG-ASN : bond 0.00531 / 0.31 ( 15) link_NAG-ASN : angle 2.07886 / 1.28 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 268 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8438 (m-70) cc_final: 0.8072 (m-70) REVERT: A 317 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8394 (ttt) REVERT: B 369 LYS cc_start: 0.8318 (mttt) cc_final: 0.8013 (mptt) REVERT: B 396 VAL cc_start: 0.7955 (t) cc_final: 0.7427 (p) REVERT: H 517 GLU cc_start: 0.7348 (mp0) cc_final: 0.7084 (mp0) REVERT: H 561 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8239 (pt) REVERT: H 565 ASP cc_start: 0.8012 (t0) cc_final: 0.7708 (t0) REVERT: L 701 ARG cc_start: 0.7145 (ptp90) cc_final: 0.6864 (ptp90) REVERT: D 347 MET cc_start: 0.8409 (ttp) cc_final: 0.8075 (ttm) REVERT: E 587 MET cc_start: 0.8384 (ttp) cc_final: 0.8176 (ttp) REVERT: I 347 MET cc_start: 0.8405 (ttp) cc_final: 0.8098 (ttm) REVERT: I 349 ASP cc_start: 0.8022 (p0) cc_final: 0.7791 (p0) REVERT: I 480 GLU cc_start: 0.7767 (tp30) cc_final: 0.7486 (tp30) REVERT: I 484 ASN cc_start: 0.7959 (m-40) cc_final: 0.7617 (m110) outliers start: 32 outliers final: 19 residues processed: 285 average time/residue: 0.1361 time to fit residues: 58.5549 Evaluate side-chains 253 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain H residue 561 ILE Chi-restraints excluded: chain H residue 621 THR Chi-restraints excluded: chain L residue 645 SER Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain F residue 689 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain I residue 402 LYS Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain K residue 626 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 2 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 713 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.163620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134923 restraints weight = 20817.548| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.63 r_work: 0.3300 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17593 Z= 0.165 Angle : 0.597 12.465 23916 Z= 0.307 Chirality : 0.045 0.281 2607 Planarity : 0.004 0.051 3063 Dihedral : 5.985 82.943 2346 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.42 % Allowed : 9.10 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.18), residues: 2121 helix: 2.58 (0.26), residues: 372 sheet: 0.62 (0.21), residues: 612 loop : 0.29 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 619 TYR 0.016 0.002 TYR J 609 PHE 0.016 0.002 PHE C 115 TRP 0.009 0.001 TRP B 422 HIS 0.005 0.001 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (17553) covalent geometry : angle 0.57545 / 0.30 (23823) SS BOND : bond 0.00403 / 0.25 ( 24) SS BOND : angle 1.06472 / 0.81 ( 48) hydrogen bonds : bond 0.04179 / 2.77 ( 708) hydrogen bonds : angle 5.02831 / 3.52 ( 1926) Misc. bond : bond 0.00570 / 0.30 ( 1) link_NAG-ASN : bond 0.00367 / 0.21 ( 15) link_NAG-ASN : angle 3.54827 / 2.34 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 251 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8499 (m-70) cc_final: 0.8171 (m-70) REVERT: A 317 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8427 (ttt) REVERT: B 396 VAL cc_start: 0.8152 (t) cc_final: 0.7608 (p) REVERT: H 517 GLU cc_start: 0.7407 (mp0) cc_final: 0.7111 (mp0) REVERT: H 565 ASP cc_start: 0.8037 (t0) cc_final: 0.7677 (t0) REVERT: H 571 ARG cc_start: 0.7358 (mtt90) cc_final: 0.6771 (mtt90) REVERT: L 701 ARG cc_start: 0.7228 (ptp90) cc_final: 0.6789 (ptp90) REVERT: D 347 MET cc_start: 0.8457 (ttp) cc_final: 0.8112 (ttm) REVERT: I 347 MET cc_start: 0.8456 (ttp) cc_final: 0.8106 (ttm) REVERT: I 349 ASP cc_start: 0.8012 (p0) cc_final: 0.7798 (p0) REVERT: I 367 ASP cc_start: 0.8206 (t0) cc_final: 0.8000 (t70) REVERT: I 480 GLU cc_start: 0.7690 (tp30) cc_final: 0.7376 (tp30) REVERT: I 484 ASN cc_start: 0.7965 (m-40) cc_final: 0.7634 (m110) REVERT: J 608 MET cc_start: 0.6051 (tpp) cc_final: 0.5678 (tpt) outliers start: 45 outliers final: 34 residues processed: 270 average time/residue: 0.1391 time to fit residues: 56.6542 Evaluate side-chains 273 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 542 SER Chi-restraints excluded: chain H residue 561 ILE Chi-restraints excluded: chain H residue 624 THR Chi-restraints excluded: chain L residue 628 THR Chi-restraints excluded: chain L residue 698 THR Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain E residue 608 MET Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 689 SER Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain K residue 626 VAL Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 696 THR Chi-restraints excluded: chain K residue 698 THR Chi-restraints excluded: chain K residue 709 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 59 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 372 GLN G 41 HIS I 355 HIS K 713 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.164351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135952 restraints weight = 20811.619| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.72 r_work: 0.3325 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17593 Z= 0.140 Angle : 0.578 13.266 23916 Z= 0.291 Chirality : 0.044 0.234 2607 Planarity : 0.004 0.035 3063 Dihedral : 5.807 79.704 2346 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.37 % Allowed : 9.80 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.18), residues: 2121 helix: 2.76 (0.26), residues: 372 sheet: 0.55 (0.21), residues: 582 loop : 0.20 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 619 TYR 0.013 0.002 TYR H 609 PHE 0.016 0.002 PHE C 115 TRP 0.008 0.001 TRP B 422 HIS 0.004 0.001 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (17553) covalent geometry : angle 0.54412 / 0.28 (23823) SS BOND : bond 0.00377 / 0.24 ( 24) SS BOND : angle 0.90748 / 0.68 ( 48) hydrogen bonds : bond 0.03978 / 2.64 ( 708) hydrogen bonds : angle 4.94850 / 3.47 ( 1926) Misc. bond : bond 0.00481 / 0.25 ( 1) link_NAG-ASN : bond 0.00524 / 0.30 ( 15) link_NAG-ASN : angle 4.44483 / 2.89 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 245 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8488 (m-70) cc_final: 0.8159 (m-70) REVERT: A 317 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8420 (ttt) REVERT: B 357 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: B 396 VAL cc_start: 0.8136 (t) cc_final: 0.7561 (p) REVERT: B 480 GLU cc_start: 0.7861 (tp30) cc_final: 0.7539 (tp30) REVERT: H 571 ARG cc_start: 0.7347 (mtt90) cc_final: 0.6765 (mtt90) REVERT: D 347 MET cc_start: 0.8456 (ttp) cc_final: 0.8087 (ttm) REVERT: I 347 MET cc_start: 0.8451 (ttp) cc_final: 0.8066 (ttm) REVERT: I 349 ASP cc_start: 0.8186 (p0) cc_final: 0.7939 (p0) REVERT: I 484 ASN cc_start: 0.7877 (m-40) cc_final: 0.7370 (t0) REVERT: J 553 GLU cc_start: 0.8346 (tt0) cc_final: 0.7954 (tt0) REVERT: J 608 MET cc_start: 0.5925 (tpp) cc_final: 0.5664 (tpt) outliers start: 44 outliers final: 38 residues processed: 264 average time/residue: 0.1251 time to fit residues: 51.4355 Evaluate side-chains 275 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 235 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 542 SER Chi-restraints excluded: chain H residue 561 ILE Chi-restraints excluded: chain H residue 624 THR Chi-restraints excluded: chain L residue 626 VAL Chi-restraints excluded: chain L residue 698 THR Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain E residue 608 MET Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 689 SER Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain K residue 626 VAL Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 696 THR Chi-restraints excluded: chain K residue 698 THR Chi-restraints excluded: chain K residue 709 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 135 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 ASN C 231 ASN G 231 ASN G 248 ASN ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 372 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.158832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.129499 restraints weight = 20797.597| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.65 r_work: 0.3226 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17593 Z= 0.248 Angle : 0.673 13.252 23916 Z= 0.342 Chirality : 0.048 0.258 2607 Planarity : 0.005 0.050 3063 Dihedral : 6.304 85.005 2346 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.02 % Allowed : 9.64 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 2121 helix: 2.53 (0.26), residues: 369 sheet: 0.36 (0.20), residues: 612 loop : -0.06 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 406 TYR 0.018 0.002 TYR E 609 PHE 0.016 0.002 PHE C 115 TRP 0.011 0.002 TRP J 581 HIS 0.009 0.002 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.25 (17553) covalent geometry : angle 0.64745 / 0.34 (23823) SS BOND : bond 0.00557 / 0.35 ( 24) SS BOND : angle 1.20965 / 0.84 ( 48) hydrogen bonds : bond 0.04518 / 3.00 ( 708) hydrogen bonds : angle 5.30558 / 3.72 ( 1926) Misc. bond : bond 0.00490 / 0.26 ( 1) link_NAG-ASN : bond 0.00471 / 0.26 ( 15) link_NAG-ASN : angle 4.12124 / 2.70 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8643 (m-70) cc_final: 0.8426 (m-70) REVERT: A 317 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8545 (ttt) REVERT: B 480 GLU cc_start: 0.7996 (tp30) cc_final: 0.7363 (pt0) REVERT: H 571 ARG cc_start: 0.7410 (mtt90) cc_final: 0.6936 (mtt90) REVERT: H 573 ARG cc_start: 0.7285 (ttp80) cc_final: 0.6969 (ttt-90) REVERT: C 120 ILE cc_start: 0.8653 (mt) cc_final: 0.8383 (mt) REVERT: E 573 ARG cc_start: 0.6870 (ttp80) cc_final: 0.6355 (ttt-90) REVERT: E 587 MET cc_start: 0.8280 (ttp) cc_final: 0.7477 (ttp) REVERT: F 660 TYR cc_start: 0.7973 (m-80) cc_final: 0.7561 (m-80) REVERT: I 484 ASN cc_start: 0.8041 (m-40) cc_final: 0.7341 (t0) REVERT: J 608 MET cc_start: 0.6156 (tpp) cc_final: 0.5876 (tpt) outliers start: 56 outliers final: 49 residues processed: 273 average time/residue: 0.1172 time to fit residues: 48.3719 Evaluate side-chains 285 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 235 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 542 SER Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 624 THR Chi-restraints excluded: chain L residue 626 VAL Chi-restraints excluded: chain L residue 628 THR Chi-restraints excluded: chain L residue 698 THR Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain L residue 721 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain E residue 608 MET Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 689 SER Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain F residue 709 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain K residue 626 VAL Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 698 THR Chi-restraints excluded: chain K residue 709 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 206 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS B 356 HIS G 248 ASN ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.160225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131468 restraints weight = 20798.815| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.64 r_work: 0.3257 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17593 Z= 0.179 Angle : 0.601 12.889 23916 Z= 0.307 Chirality : 0.045 0.222 2607 Planarity : 0.004 0.044 3063 Dihedral : 6.072 84.309 2346 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.02 % Allowed : 10.29 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 2121 helix: 2.65 (0.26), residues: 369 sheet: 0.34 (0.21), residues: 582 loop : -0.12 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 619 TYR 0.015 0.002 TYR K 673 PHE 0.015 0.002 PHE C 115 TRP 0.010 0.001 TRP J 581 HIS 0.009 0.001 HIS B 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (17553) covalent geometry : angle 0.57697 / 0.30 (23823) SS BOND : bond 0.00446 / 0.29 ( 24) SS BOND : angle 1.01122 / 0.71 ( 48) hydrogen bonds : bond 0.04143 / 2.76 ( 708) hydrogen bonds : angle 5.13627 / 3.61 ( 1926) Misc. bond : bond 0.00407 / 0.21 ( 1) link_NAG-ASN : bond 0.00553 / 0.33 ( 15) link_NAG-ASN : angle 3.79530 / 2.49 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 241 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8608 (m-70) cc_final: 0.8375 (m-70) REVERT: A 317 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8498 (ttt) REVERT: B 480 GLU cc_start: 0.7896 (tp30) cc_final: 0.7301 (pt0) REVERT: H 571 ARG cc_start: 0.7386 (mtt90) cc_final: 0.6848 (mtt90) REVERT: H 573 ARG cc_start: 0.7247 (ttp80) cc_final: 0.6905 (ttt-90) REVERT: C 120 ILE cc_start: 0.8558 (mt) cc_final: 0.8310 (mt) REVERT: E 573 ARG cc_start: 0.6870 (ttp80) cc_final: 0.6211 (ttt-90) REVERT: E 587 MET cc_start: 0.8125 (ttp) cc_final: 0.7832 (ttp) REVERT: F 636 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.6973 (mp) REVERT: I 484 ASN cc_start: 0.7832 (m-40) cc_final: 0.7192 (t0) REVERT: J 608 MET cc_start: 0.6133 (tpp) cc_final: 0.5915 (tpt) REVERT: K 636 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7102 (mp) outliers start: 56 outliers final: 46 residues processed: 273 average time/residue: 0.1204 time to fit residues: 49.3994 Evaluate side-chains 282 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 542 SER Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 561 ILE Chi-restraints excluded: chain H residue 624 THR Chi-restraints excluded: chain L residue 628 THR Chi-restraints excluded: chain L residue 698 THR Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain L residue 721 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain E residue 608 MET Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain F residue 689 SER Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain F residue 709 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 445 VAL Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain K residue 626 VAL Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 636 LEU Chi-restraints excluded: chain K residue 691 SER Chi-restraints excluded: chain K residue 698 THR Chi-restraints excluded: chain K residue 709 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 172 optimal weight: 0.2980 chunk 105 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.162723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134066 restraints weight = 20822.929| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.69 r_work: 0.3281 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17593 Z= 0.126 Angle : 0.572 12.430 23916 Z= 0.289 Chirality : 0.044 0.240 2607 Planarity : 0.004 0.035 3063 Dihedral : 5.800 81.356 2346 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.75 % Allowed : 10.82 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.18), residues: 2121 helix: 2.84 (0.26), residues: 372 sheet: 0.43 (0.21), residues: 612 loop : 0.00 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 619 TYR 0.017 0.002 TYR K 673 PHE 0.015 0.002 PHE C 115 TRP 0.014 0.001 TRP D 351 HIS 0.003 0.001 HIS G 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (17553) covalent geometry : angle 0.54816 / 0.28 (23823) SS BOND : bond 0.00345 / 0.23 ( 24) SS BOND : angle 0.73155 / 0.51 ( 48) hydrogen bonds : bond 0.03814 / 2.55 ( 708) hydrogen bonds : angle 4.90484 / 3.45 ( 1926) Misc. bond : bond 0.00336 / 0.18 ( 1) link_NAG-ASN : bond 0.00799 / 0.48 ( 15) link_NAG-ASN : angle 3.77655 / 2.50 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8575 (m-70) cc_final: 0.8303 (m-70) REVERT: B 449 TYR cc_start: 0.8430 (t80) cc_final: 0.8196 (t80) REVERT: B 480 GLU cc_start: 0.7830 (tp30) cc_final: 0.7277 (pt0) REVERT: H 571 ARG cc_start: 0.7284 (mtt90) cc_final: 0.6728 (mtt90) REVERT: H 573 ARG cc_start: 0.7136 (ttp80) cc_final: 0.6542 (ttt-90) REVERT: L 636 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.6936 (mp) REVERT: C 120 ILE cc_start: 0.8399 (mt) cc_final: 0.8164 (mt) REVERT: E 587 MET cc_start: 0.8054 (ttp) cc_final: 0.7299 (ttp) REVERT: E 593 ARG cc_start: 0.6375 (mtt90) cc_final: 0.6173 (mtt90) REVERT: F 636 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.6888 (mp) REVERT: G 311 ARG cc_start: 0.8422 (mtm-85) cc_final: 0.8065 (mtm180) REVERT: I 484 ASN cc_start: 0.7817 (m-40) cc_final: 0.7123 (t0) REVERT: J 608 MET cc_start: 0.6104 (tpp) cc_final: 0.5854 (tpt) REVERT: K 636 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7006 (mp) outliers start: 51 outliers final: 40 residues processed: 267 average time/residue: 0.1241 time to fit residues: 50.6169 Evaluate side-chains 274 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 542 SER Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 561 ILE Chi-restraints excluded: chain L residue 628 THR Chi-restraints excluded: chain L residue 636 LEU Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain E residue 608 MET Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain F residue 689 SER Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain F residue 709 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 445 VAL Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain K residue 626 VAL Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 636 LEU Chi-restraints excluded: chain K residue 698 THR Chi-restraints excluded: chain K residue 709 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 355 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.162944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134327 restraints weight = 20820.483| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.68 r_work: 0.3258 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17593 Z= 0.143 Angle : 0.581 12.674 23916 Z= 0.295 Chirality : 0.046 0.502 2607 Planarity : 0.004 0.034 3063 Dihedral : 5.790 81.073 2346 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.53 % Allowed : 11.04 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.18), residues: 2121 helix: 2.87 (0.26), residues: 372 sheet: 0.46 (0.21), residues: 612 loop : -0.02 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 593 TYR 0.017 0.002 TYR K 673 PHE 0.015 0.002 PHE C 115 TRP 0.013 0.001 TRP H 543 HIS 0.003 0.001 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (17553) covalent geometry : angle 0.56368 / 0.29 (23823) SS BOND : bond 0.00373 / 0.25 ( 24) SS BOND : angle 0.81037 / 0.56 ( 48) hydrogen bonds : bond 0.03862 / 2.57 ( 708) hydrogen bonds : angle 4.89456 / 3.44 ( 1926) Misc. bond : bond 0.00947 / 0.50 ( 1) link_NAG-ASN : bond 0.00836 / 0.60 ( 15) link_NAG-ASN : angle 3.20395 / 2.07 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 229 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8567 (m-70) cc_final: 0.8304 (m-70) REVERT: B 480 GLU cc_start: 0.7809 (tp30) cc_final: 0.7103 (pt0) REVERT: H 571 ARG cc_start: 0.7215 (mtt90) cc_final: 0.6718 (mtt90) REVERT: L 636 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.6930 (mp) REVERT: C 120 ILE cc_start: 0.8468 (mt) cc_final: 0.8246 (mt) REVERT: E 587 MET cc_start: 0.8042 (ttp) cc_final: 0.7287 (ttp) REVERT: E 593 ARG cc_start: 0.6264 (mtt90) cc_final: 0.6050 (mtt90) REVERT: F 636 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6834 (mp) REVERT: I 484 ASN cc_start: 0.7820 (m-40) cc_final: 0.7073 (t0) REVERT: J 608 MET cc_start: 0.5946 (tpp) cc_final: 0.5731 (tpt) REVERT: K 636 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.6993 (mp) outliers start: 47 outliers final: 42 residues processed: 259 average time/residue: 0.1181 time to fit residues: 47.4337 Evaluate side-chains 269 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 542 SER Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 561 ILE Chi-restraints excluded: chain L residue 628 THR Chi-restraints excluded: chain L residue 636 LEU Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain E residue 608 MET Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain F residue 689 SER Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain F residue 709 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 445 VAL Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain K residue 626 VAL Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 636 LEU Chi-restraints excluded: chain K residue 698 THR Chi-restraints excluded: chain K residue 709 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 165 optimal weight: 1.9990 chunk 170 optimal weight: 0.0470 chunk 66 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 0.0060 chunk 144 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 overall best weight: 0.4294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.166233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137694 restraints weight = 20822.147| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.60 r_work: 0.3413 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17593 Z= 0.107 Angle : 0.540 12.564 23916 Z= 0.275 Chirality : 0.044 0.416 2607 Planarity : 0.004 0.042 3063 Dihedral : 5.438 76.226 2346 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.10 % Allowed : 11.47 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.18), residues: 2121 helix: 3.01 (0.26), residues: 375 sheet: 0.57 (0.21), residues: 612 loop : 0.08 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 685 TYR 0.018 0.001 TYR K 673 PHE 0.015 0.001 PHE C 115 TRP 0.011 0.001 TRP H 543 HIS 0.002 0.000 HIS G 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (17553) covalent geometry : angle 0.52362 / 0.27 (23823) SS BOND : bond 0.00308 / 0.22 ( 24) SS BOND : angle 0.59690 / 0.42 ( 48) hydrogen bonds : bond 0.03559 / 2.37 ( 708) hydrogen bonds : angle 4.67277 / 3.29 ( 1926) Misc. bond : bond 0.00691 / 0.36 ( 1) link_NAG-ASN : bond 0.00773 / 0.51 ( 15) link_NAG-ASN : angle 3.07480 / 2.00 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 250 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8544 (m-70) cc_final: 0.8237 (m-70) REVERT: B 396 VAL cc_start: 0.8073 (t) cc_final: 0.7559 (p) REVERT: B 480 GLU cc_start: 0.7916 (tp30) cc_final: 0.7115 (pt0) REVERT: H 565 ASP cc_start: 0.7995 (t0) cc_final: 0.7552 (t0) REVERT: L 636 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.6900 (mp) REVERT: C 120 ILE cc_start: 0.8178 (mt) cc_final: 0.7960 (mt) REVERT: E 587 MET cc_start: 0.7797 (ttp) cc_final: 0.7049 (ttp) REVERT: F 636 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6704 (mp) REVERT: F 685 ARG cc_start: 0.5901 (ttp-110) cc_final: 0.5674 (ttp-110) REVERT: I 484 ASN cc_start: 0.7933 (m-40) cc_final: 0.7136 (t0) REVERT: J 553 GLU cc_start: 0.8405 (tt0) cc_final: 0.7984 (tt0) REVERT: J 591 SER cc_start: 0.7343 (m) cc_final: 0.7021 (m) REVERT: K 636 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.6888 (mp) outliers start: 39 outliers final: 29 residues processed: 276 average time/residue: 0.1199 time to fit residues: 51.6149 Evaluate side-chains 263 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 542 SER Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 561 ILE Chi-restraints excluded: chain L residue 628 THR Chi-restraints excluded: chain L residue 636 LEU Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain F residue 709 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 445 VAL Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain K residue 626 VAL Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 636 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 85 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.159809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131323 restraints weight = 20855.821| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.72 r_work: 0.3234 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17593 Z= 0.225 Angle : 0.659 12.675 23916 Z= 0.334 Chirality : 0.048 0.484 2607 Planarity : 0.005 0.039 3063 Dihedral : 6.050 83.355 2346 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.37 % Allowed : 11.15 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.18), residues: 2121 helix: 2.73 (0.26), residues: 372 sheet: 0.41 (0.21), residues: 612 loop : -0.11 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 685 TYR 0.014 0.002 TYR H 609 PHE 0.016 0.002 PHE C 115 TRP 0.011 0.002 TRP J 581 HIS 0.008 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 (17553) covalent geometry : angle 0.64287 / 0.33 (23823) SS BOND : bond 0.00521 / 0.32 ( 24) SS BOND : angle 1.17998 / 0.80 ( 48) hydrogen bonds : bond 0.04293 / 2.85 ( 708) hydrogen bonds : angle 5.11155 / 3.59 ( 1926) Misc. bond : bond 0.00856 / 0.45 ( 1) link_NAG-ASN : bond 0.00680 / 0.41 ( 15) link_NAG-ASN : angle 3.26560 / 2.14 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4417.57 seconds wall clock time: 76 minutes 27.26 seconds (4587.26 seconds total)