Starting phenix.real_space_refine on Sun Jul 5 13:24:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7o85_12761/07_2026/7o85_12761.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o85_12761/07_2026/7o85_12761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7o85_12761/07_2026/7o85_12761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o85_12761/07_2026/7o85_12761.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o85_12761/07_2026/7o85_12761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o85_12761/07_2026/7o85_12761.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7o85_12761/07_2026/7o85_12761.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7o85_12761/07_2026/7o85_12761.cif" } resolution = 3.3 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: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 42 5.16 5 C 17892 2.51 5 N 4991 2.21 5 O 5586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 28525 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2620 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 17, 'TRANS': 314} Chain breaks: 4 Chain: "B" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 706 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 101} Chain: "C" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 747 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: D, G, J, M, P, S, E, H, K, N, Q, T, F, I, L, O, R, U Time building chain proxies: 3.97, per 1000 atoms: 0.14 Number of scatterers: 28525 At special positions: 0 Unit cell: (214.5, 217.8, 72.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 42 16.00 O 5586 8.00 N 4991 7.00 C 17892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.3 seconds 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7280 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 77 sheets defined 16.6% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 248 through 253 removed outlier: 4.060A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 removed outlier: 4.251A pdb=" N SER A 312 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 512 through 517 removed outlier: 3.816A pdb=" N THR A 517 " --> pdb=" O PRO A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 555 through 570 Processing helix chain 'A' and resid 577 through 581 removed outlier: 3.635A pdb=" N ILE A 581 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 614 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 98 through 102 removed outlier: 4.018A pdb=" N ALA C 102 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 234 through 241 Processing helix chain 'D' and resid 248 through 253 removed outlier: 4.060A pdb=" N HIS D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 314 removed outlier: 4.251A pdb=" N SER D 312 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'D' and resid 512 through 517 removed outlier: 3.816A pdb=" N THR D 517 " --> pdb=" O PRO D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 531 Processing helix chain 'D' and resid 555 through 570 Processing helix chain 'D' and resid 577 through 581 removed outlier: 3.635A pdb=" N ILE D 581 " --> pdb=" O LEU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 614 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 98 through 102 removed outlier: 4.018A pdb=" N ALA F 102 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 248 through 253 removed outlier: 4.060A pdb=" N HIS G 253 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 314 removed outlier: 4.250A pdb=" N SER G 312 " --> pdb=" O VAL G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 480 through 487 Processing helix chain 'G' and resid 512 through 517 removed outlier: 3.817A pdb=" N THR G 517 " --> pdb=" O PRO G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 531 Processing helix chain 'G' and resid 555 through 570 Processing helix chain 'G' and resid 577 through 581 removed outlier: 3.635A pdb=" N ILE G 581 " --> pdb=" O LEU G 578 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 614 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 98 through 102 removed outlier: 4.018A pdb=" N ALA I 102 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 191 Processing helix chain 'J' and resid 234 through 241 Processing helix chain 'J' and resid 248 through 253 removed outlier: 4.060A pdb=" N HIS J 253 " --> pdb=" O GLU J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 314 removed outlier: 4.251A pdb=" N SER J 312 " --> pdb=" O VAL J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 480 through 487 Processing helix chain 'J' and resid 512 through 517 removed outlier: 3.817A pdb=" N THR J 517 " --> pdb=" O PRO J 513 " (cutoff:3.500A) Processing helix chain 'J' and resid 522 through 531 Processing helix chain 'J' and resid 555 through 570 Processing helix chain 'J' and resid 577 through 581 removed outlier: 3.635A pdb=" N ILE J 581 " --> pdb=" O LEU J 578 " (cutoff:3.500A) Processing helix chain 'J' and resid 608 through 614 Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'L' and resid 98 through 102 removed outlier: 4.018A pdb=" N ALA L 102 " --> pdb=" O ASP L 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 191 Processing helix chain 'M' and resid 234 through 241 Processing helix chain 'M' and resid 248 through 253 removed outlier: 4.060A pdb=" N HIS M 253 " --> pdb=" O GLU M 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 314 removed outlier: 4.250A pdb=" N SER M 312 " --> pdb=" O VAL M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 480 through 487 Processing helix chain 'M' and resid 512 through 517 removed outlier: 3.817A pdb=" N THR M 517 " --> pdb=" O PRO M 513 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 531 Processing helix chain 'M' and resid 555 through 570 Processing helix chain 'M' and resid 577 through 581 removed outlier: 3.635A pdb=" N ILE M 581 " --> pdb=" O LEU M 578 " (cutoff:3.500A) Processing helix chain 'M' and resid 608 through 614 Processing helix chain 'O' and resid 87 through 91 Processing helix chain 'O' and resid 98 through 102 removed outlier: 4.017A pdb=" N ALA O 102 " --> pdb=" O ASP O 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 191 Processing helix chain 'P' and resid 234 through 241 Processing helix chain 'P' and resid 248 through 253 removed outlier: 4.060A pdb=" N HIS P 253 " --> pdb=" O GLU P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 308 through 314 removed outlier: 4.251A pdb=" N SER P 312 " --> pdb=" O VAL P 309 " (cutoff:3.500A) Processing helix chain 'P' and resid 480 through 487 Processing helix chain 'P' and resid 512 through 517 removed outlier: 3.816A pdb=" N THR P 517 " --> pdb=" O PRO P 513 " (cutoff:3.500A) Processing helix chain 'P' and resid 522 through 531 Processing helix chain 'P' and resid 555 through 570 Processing helix chain 'P' and resid 577 through 581 removed outlier: 3.635A pdb=" N ILE P 581 " --> pdb=" O LEU P 578 " (cutoff:3.500A) Processing helix chain 'P' and resid 608 through 614 Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'R' and resid 98 through 102 removed outlier: 4.018A pdb=" N ALA R 102 " --> pdb=" O ASP R 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 184 through 191 Processing helix chain 'S' and resid 234 through 241 Processing helix chain 'S' and resid 248 through 253 removed outlier: 4.060A pdb=" N HIS S 253 " --> pdb=" O GLU S 250 " (cutoff:3.500A) Processing helix chain 'S' and resid 308 through 314 removed outlier: 4.250A pdb=" N SER S 312 " --> pdb=" O VAL S 309 " (cutoff:3.500A) Processing helix chain 'S' and resid 480 through 487 Processing helix chain 'S' and resid 512 through 517 removed outlier: 3.816A pdb=" N THR S 517 " --> pdb=" O PRO S 513 " (cutoff:3.500A) Processing helix chain 'S' and resid 522 through 531 Processing helix chain 'S' and resid 555 through 570 Processing helix chain 'S' and resid 577 through 581 removed outlier: 3.635A pdb=" N ILE S 581 " --> pdb=" O LEU S 578 " (cutoff:3.500A) Processing helix chain 'S' and resid 608 through 614 Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'U' and resid 98 through 102 removed outlier: 4.018A pdb=" N ALA U 102 " --> pdb=" O ASP U 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 196 removed outlier: 3.520A pdb=" N ASP A 195 " --> pdb=" O PHE A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 3.819A pdb=" N ASN A 409 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA4, first strand: chain 'A' and resid 458 through 462 removed outlier: 4.155A pdb=" N ILE A 459 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 470 " --> pdb=" O THR A 461 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.765A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASP A 593 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA7, first strand: chain 'A' and resid 596 through 597 removed outlier: 3.550A pdb=" N GLY A 606 " --> pdb=" O HIS A 597 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 4 through 5 removed outlier: 4.297A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 67 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER B 63 " --> pdb=" O THR B 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 removed outlier: 5.547A pdb=" N ALA B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 39 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 36 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE B 87 " --> pdb=" O TYR B 36 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA B 38 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ALA B 85 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60 removed outlier: 5.168A pdb=" N TRP C 47 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA C 93 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 68 through 73 Processing sheet with id=AB3, first strand: chain 'D' and resid 192 through 196 removed outlier: 3.519A pdb=" N ASP D 195 " --> pdb=" O PHE D 202 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 262 through 263 removed outlier: 3.819A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 296 through 297 Processing sheet with id=AB6, first strand: chain 'D' and resid 458 through 462 removed outlier: 4.155A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 470 " --> pdb=" O THR D 461 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 501 through 506 removed outlier: 8.766A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AB9, first strand: chain 'D' and resid 596 through 597 removed outlier: 3.549A pdb=" N GLY D 606 " --> pdb=" O HIS D 597 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 4 through 5 removed outlier: 4.296A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER E 63 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 53 through 54 removed outlier: 5.547A pdb=" N ALA E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA E 39 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR E 36 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE E 87 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA E 38 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA E 85 " --> pdb=" O ALA E 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.168A pdb=" N TRP F 47 " --> pdb=" O ALA F 38 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA F 93 " --> pdb=" O ALA F 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 68 through 73 Processing sheet with id=AC5, first strand: chain 'G' and resid 192 through 196 removed outlier: 3.520A pdb=" N ASP G 195 " --> pdb=" O PHE G 202 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 262 through 263 removed outlier: 3.819A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 296 through 297 Processing sheet with id=AC8, first strand: chain 'G' and resid 458 through 462 removed outlier: 4.155A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG G 470 " --> pdb=" O THR G 461 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.766A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 541 through 542 Processing sheet with id=AD2, first strand: chain 'G' and resid 596 through 597 removed outlier: 3.549A pdb=" N GLY G 606 " --> pdb=" O HIS G 597 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 4 through 5 removed outlier: 4.297A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER H 63 " --> pdb=" O THR H 74 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 53 through 54 removed outlier: 5.547A pdb=" N ALA H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA H 39 " --> pdb=" O ALA H 43 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR H 36 " --> pdb=" O PHE H 87 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE H 87 " --> pdb=" O TYR H 36 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA H 38 " --> pdb=" O ALA H 85 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA H 85 " --> pdb=" O ALA H 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 58 through 60 removed outlier: 5.168A pdb=" N TRP I 47 " --> pdb=" O ALA I 38 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA I 93 " --> pdb=" O ALA I 39 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 68 through 73 Processing sheet with id=AD7, first strand: chain 'J' and resid 192 through 196 removed outlier: 3.519A pdb=" N ASP J 195 " --> pdb=" O PHE J 202 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 262 through 263 removed outlier: 3.818A pdb=" N ASN J 409 " --> pdb=" O ASN J 368 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 296 through 297 Processing sheet with id=AE1, first strand: chain 'J' and resid 458 through 462 removed outlier: 4.156A pdb=" N ILE J 459 " --> pdb=" O ASP J 472 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG J 470 " --> pdb=" O THR J 461 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 501 through 506 removed outlier: 8.765A pdb=" N ILE J 589 " --> pdb=" O THR J 488 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG J 490 " --> pdb=" O ILE J 589 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE J 591 " --> pdb=" O ARG J 490 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE J 492 " --> pdb=" O ILE J 591 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASP J 593 " --> pdb=" O ILE J 492 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 541 through 542 Processing sheet with id=AE4, first strand: chain 'J' and resid 596 through 597 removed outlier: 3.550A pdb=" N GLY J 606 " --> pdb=" O HIS J 597 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 5 removed outlier: 4.297A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER K 67 " --> pdb=" O ASP K 70 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER K 63 " --> pdb=" O THR K 74 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 53 through 54 removed outlier: 5.547A pdb=" N ALA K 43 " --> pdb=" O ALA K 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA K 39 " --> pdb=" O ALA K 43 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR K 36 " --> pdb=" O PHE K 87 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE K 87 " --> pdb=" O TYR K 36 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA K 38 " --> pdb=" O ALA K 85 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA K 85 " --> pdb=" O ALA K 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 58 through 60 removed outlier: 5.168A pdb=" N TRP L 47 " --> pdb=" O ALA L 38 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA L 93 " --> pdb=" O ALA L 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 68 through 73 Processing sheet with id=AE9, first strand: chain 'M' and resid 192 through 196 removed outlier: 3.520A pdb=" N ASP M 195 " --> pdb=" O PHE M 202 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 262 through 263 removed outlier: 3.819A pdb=" N ASN M 409 " --> pdb=" O ASN M 368 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 296 through 297 Processing sheet with id=AF3, first strand: chain 'M' and resid 458 through 462 removed outlier: 4.155A pdb=" N ILE M 459 " --> pdb=" O ASP M 472 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG M 470 " --> pdb=" O THR M 461 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 501 through 506 removed outlier: 8.765A pdb=" N ILE M 589 " --> pdb=" O THR M 488 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG M 490 " --> pdb=" O ILE M 589 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE M 591 " --> pdb=" O ARG M 490 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE M 492 " --> pdb=" O ILE M 591 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASP M 593 " --> pdb=" O ILE M 492 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 541 through 542 Processing sheet with id=AF6, first strand: chain 'M' and resid 596 through 597 removed outlier: 3.550A pdb=" N GLY M 606 " --> pdb=" O HIS M 597 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 4 through 5 removed outlier: 4.297A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER N 67 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER N 63 " --> pdb=" O THR N 74 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 53 through 54 removed outlier: 5.547A pdb=" N ALA N 43 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA N 39 " --> pdb=" O ALA N 43 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR N 36 " --> pdb=" O PHE N 87 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA N 38 " --> pdb=" O ALA N 85 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA N 85 " --> pdb=" O ALA N 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 58 through 60 removed outlier: 5.168A pdb=" N TRP O 47 " --> pdb=" O ALA O 38 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA O 93 " --> pdb=" O ALA O 39 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 68 through 73 Processing sheet with id=AG2, first strand: chain 'P' and resid 192 through 196 removed outlier: 3.519A pdb=" N ASP P 195 " --> pdb=" O PHE P 202 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 262 through 263 removed outlier: 3.819A pdb=" N ASN P 409 " --> pdb=" O ASN P 368 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 296 through 297 Processing sheet with id=AG5, first strand: chain 'P' and resid 458 through 462 removed outlier: 4.155A pdb=" N ILE P 459 " --> pdb=" O ASP P 472 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG P 470 " --> pdb=" O THR P 461 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 501 through 506 removed outlier: 8.766A pdb=" N ILE P 589 " --> pdb=" O THR P 488 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG P 490 " --> pdb=" O ILE P 589 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE P 591 " --> pdb=" O ARG P 490 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE P 492 " --> pdb=" O ILE P 591 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASP P 593 " --> pdb=" O ILE P 492 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 541 through 542 Processing sheet with id=AG8, first strand: chain 'P' and resid 596 through 597 removed outlier: 3.550A pdb=" N GLY P 606 " --> pdb=" O HIS P 597 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 4 through 5 removed outlier: 4.297A pdb=" N ASP Q 70 " --> pdb=" O SER Q 67 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER Q 67 " --> pdb=" O ASP Q 70 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER Q 63 " --> pdb=" O THR Q 74 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 53 through 54 removed outlier: 5.547A pdb=" N ALA Q 43 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA Q 39 " --> pdb=" O ALA Q 43 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR Q 49 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR Q 36 " --> pdb=" O PHE Q 87 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE Q 87 " --> pdb=" O TYR Q 36 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA Q 38 " --> pdb=" O ALA Q 85 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA Q 85 " --> pdb=" O ALA Q 38 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'R' and resid 58 through 60 removed outlier: 5.167A pdb=" N TRP R 47 " --> pdb=" O ALA R 38 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA R 93 " --> pdb=" O ALA R 39 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'R' and resid 68 through 73 Processing sheet with id=AH4, first strand: chain 'S' and resid 192 through 196 removed outlier: 3.520A pdb=" N ASP S 195 " --> pdb=" O PHE S 202 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'S' and resid 262 through 263 removed outlier: 3.819A pdb=" N ASN S 409 " --> pdb=" O ASN S 368 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'S' and resid 296 through 297 Processing sheet with id=AH7, first strand: chain 'S' and resid 458 through 462 removed outlier: 4.156A pdb=" N ILE S 459 " --> pdb=" O ASP S 472 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG S 470 " --> pdb=" O THR S 461 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'S' and resid 501 through 506 removed outlier: 8.765A pdb=" N ILE S 589 " --> pdb=" O THR S 488 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG S 490 " --> pdb=" O ILE S 589 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE S 591 " --> pdb=" O ARG S 490 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE S 492 " --> pdb=" O ILE S 591 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASP S 593 " --> pdb=" O ILE S 492 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'S' and resid 541 through 542 Processing sheet with id=AI1, first strand: chain 'S' and resid 596 through 597 removed outlier: 3.550A pdb=" N GLY S 606 " --> pdb=" O HIS S 597 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'T' and resid 4 through 5 removed outlier: 4.297A pdb=" N ASP T 70 " --> pdb=" O SER T 67 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER T 67 " --> pdb=" O ASP T 70 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER T 63 " --> pdb=" O THR T 74 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'T' and resid 53 through 54 removed outlier: 5.547A pdb=" N ALA T 43 " --> pdb=" O ALA T 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA T 39 " --> pdb=" O ALA T 43 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR T 36 " --> pdb=" O PHE T 87 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE T 87 " --> pdb=" O TYR T 36 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA T 38 " --> pdb=" O ALA T 85 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA T 85 " --> pdb=" O ALA T 38 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'U' and resid 58 through 60 removed outlier: 5.168A pdb=" N TRP U 47 " --> pdb=" O ALA U 38 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA U 93 " --> pdb=" O ALA U 39 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'U' and resid 68 through 73 707 hydrogen bonds defined for protein. 1743 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.49 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9542 1.34 - 1.46: 5888 1.46 - 1.57: 13585 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 29078 Sorted by residual: bond pdb=" CA ILE K 48 " pdb=" CB ILE K 48 " ideal model delta sigma weight residual 1.540 1.551 -0.010 1.23e-02 6.61e+03 7.23e-01 bond pdb=" CA ILE T 48 " pdb=" CB ILE T 48 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.23e-02 6.61e+03 6.68e-01 bond pdb=" CA ILE B 48 " pdb=" CB ILE B 48 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.23e-02 6.61e+03 6.50e-01 bond pdb=" CA ILE E 48 " pdb=" CB ILE E 48 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.23e-02 6.61e+03 6.26e-01 bond pdb=" CA ILE Q 48 " pdb=" CB ILE Q 48 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.23e-02 6.61e+03 6.09e-01 ... (remaining 29073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 38552 1.28 - 2.57: 855 2.57 - 3.85: 170 3.85 - 5.13: 28 5.13 - 6.42: 1 Bond angle restraints: 39606 Sorted by residual: angle pdb=" C HIS T 55 " pdb=" N SER T 56 " pdb=" CA SER T 56 " ideal model delta sigma weight residual 121.54 127.96 -6.42 1.91e+00 2.74e-01 1.13e+01 angle pdb=" N SER D 402 " pdb=" CA SER D 402 " pdb=" C SER D 402 " ideal model delta sigma weight residual 114.56 111.02 3.54 1.27e+00 6.20e-01 7.77e+00 angle pdb=" N SER G 402 " pdb=" CA SER G 402 " pdb=" C SER G 402 " ideal model delta sigma weight residual 114.56 111.02 3.54 1.27e+00 6.20e-01 7.77e+00 angle pdb=" N SER A 402 " pdb=" CA SER A 402 " pdb=" C SER A 402 " ideal model delta sigma weight residual 114.56 111.04 3.52 1.27e+00 6.20e-01 7.68e+00 angle pdb=" N SER P 402 " pdb=" CA SER P 402 " pdb=" C SER P 402 " ideal model delta sigma weight residual 114.56 111.05 3.51 1.27e+00 6.20e-01 7.65e+00 ... (remaining 39601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.48: 15327 15.48 - 30.97: 1494 30.97 - 46.45: 336 46.45 - 61.93: 77 61.93 - 77.42: 28 Dihedral angle restraints: 17262 sinusoidal: 6020 harmonic: 11242 Sorted by residual: dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 88 " pdb=" CB CYS H 88 " ideal model delta sinusoidal sigma weight residual 93.00 141.91 -48.91 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 141.91 -48.91 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 88 " pdb=" CB CYS N 88 " ideal model delta sinusoidal sigma weight residual 93.00 141.89 -48.89 1 1.00e+01 1.00e-02 3.29e+01 ... (remaining 17259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2530 0.027 - 0.055: 1292 0.055 - 0.082: 346 0.082 - 0.110: 224 0.110 - 0.137: 109 Chirality restraints: 4501 Sorted by residual: chirality pdb=" CA ILE M 374 " pdb=" N ILE M 374 " pdb=" C ILE M 374 " pdb=" CB ILE M 374 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE S 374 " pdb=" N ILE S 374 " pdb=" C ILE S 374 " pdb=" CB ILE S 374 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE G 374 " pdb=" N ILE G 374 " pdb=" C ILE G 374 " pdb=" CB ILE G 374 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 4498 not shown) Planarity restraints: 5180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 411 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 412 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR J 411 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO J 412 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO J 412 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 412 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 411 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.22e+00 pdb=" N PRO S 412 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO S 412 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO S 412 " 0.025 5.00e-02 4.00e+02 ... (remaining 5177 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 14 2.16 - 2.84: 9726 2.84 - 3.53: 37585 3.53 - 4.21: 63524 4.21 - 4.90: 113241 Nonbonded interactions: 224090 Sorted by model distance: nonbonded pdb=" OD2 ASP D 181 " pdb=" OE2 GLU D 188 " model vdw 1.470 3.040 nonbonded pdb=" OD2 ASP P 181 " pdb=" OE2 GLU P 188 " model vdw 1.470 3.040 nonbonded pdb=" OD2 ASP G 181 " pdb=" OE2 GLU G 188 " model vdw 1.470 3.040 nonbonded pdb=" OD2 ASP M 181 " pdb=" OE2 GLU M 188 " model vdw 1.470 3.040 nonbonded pdb=" OD2 ASP S 181 " pdb=" OE2 GLU S 188 " model vdw 1.470 3.040 ... (remaining 224085 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' } 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: 5.560 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: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 23.590 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.002 0.030 29085 Z= 0.091 Angle : 0.480 6.416 39620 Z= 0.263 Chirality : 0.041 0.137 4501 Planarity : 0.004 0.045 5180 Dihedral : 13.511 77.416 9961 Min Nonbonded Distance : 1.470 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3745 helix: 0.49 (0.26), residues: 462 sheet: 0.17 (0.19), residues: 875 loop : -0.39 (0.13), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 24 TYR 0.011 0.001 TYR H 50 PHE 0.009 0.001 PHE D 493 TRP 0.010 0.001 TRP K 96 HIS 0.001 0.000 HIS M 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.09 (29078) covalent geometry : angle 0.48011 / 0.26 (39606) SS BOND : bond 0.00037 / 0.02 ( 7) SS BOND : angle 0.39170 / 0.20 ( 14) hydrogen bonds : bond 0.24094 / 15.99 ( 707) hydrogen bonds : angle 8.54255 / 6.00 ( 1743) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.6882 (mtm180) cc_final: 0.6405 (pmt-80) REVERT: D 590 LEU cc_start: 0.7806 (tp) cc_final: 0.7516 (tp) REVERT: E 35 TRP cc_start: 0.6151 (m100) cc_final: 0.5912 (m100) REVERT: H 35 TRP cc_start: 0.6295 (m100) cc_final: 0.6052 (m100) REVERT: P 602 ASN cc_start: 0.6488 (t0) cc_final: 0.6070 (t0) REVERT: R 31 ASN cc_start: 0.7763 (t0) cc_final: 0.7556 (t0) REVERT: S 449 ARG cc_start: 0.6849 (mtm180) cc_final: 0.6296 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.1697 time to fit residues: 118.3924 Evaluate side-chains 297 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.0000 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 GLN ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN A 601 ASN C 35 HIS D 485 GLN F 35 HIS G 454 GLN G 602 ASN I 35 HIS L 35 HIS M 454 GLN M 541 GLN M 570 ASN O 35 HIS P 408 ASN P 454 GLN P 557 GLN R 35 HIS S 541 GLN ** S 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 35 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.194612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.156693 restraints weight = 36323.166| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.84 r_work: 0.3511 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29085 Z= 0.145 Angle : 0.530 5.980 39620 Z= 0.280 Chirality : 0.045 0.151 4501 Planarity : 0.005 0.051 5180 Dihedral : 3.897 17.145 4102 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.15 % Allowed : 7.07 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3745 helix: 0.09 (0.25), residues: 504 sheet: 0.46 (0.18), residues: 917 loop : -0.67 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 297 TYR 0.013 0.001 TYR A 233 PHE 0.010 0.001 PHE D 493 TRP 0.019 0.001 TRP B 35 HIS 0.004 0.001 HIS D 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.14 (29078) covalent geometry : angle 0.52959 / 0.28 (39606) SS BOND : bond 0.00047 / 0.02 ( 7) SS BOND : angle 0.96769 / 0.57 ( 14) hydrogen bonds : bond 0.03474 / 2.31 ( 707) hydrogen bonds : angle 5.69317 / 4.00 ( 1743) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 352 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7450 (mtm180) cc_final: 0.6368 (pmt-80) REVERT: A 539 ASN cc_start: 0.7622 (m-40) cc_final: 0.7256 (p0) REVERT: C 98 ARG cc_start: 0.8045 (ttp-170) cc_final: 0.7834 (ttp-170) REVERT: C 99 ASP cc_start: 0.6063 (t0) cc_final: 0.5748 (t70) REVERT: D 539 ASN cc_start: 0.7383 (m-40) cc_final: 0.6895 (p0) REVERT: D 541 GLN cc_start: 0.8895 (mt0) cc_final: 0.8597 (mt0) REVERT: G 539 ASN cc_start: 0.7428 (m-40) cc_final: 0.7020 (p0) REVERT: G 541 GLN cc_start: 0.8664 (mt0) cc_final: 0.7774 (mt0) REVERT: G 601 ASN cc_start: 0.6930 (OUTLIER) cc_final: 0.6666 (t0) REVERT: G 602 ASN cc_start: 0.6260 (t0) cc_final: 0.5611 (t0) REVERT: J 214 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8183 (mtpt) REVERT: J 539 ASN cc_start: 0.7354 (m-40) cc_final: 0.7082 (p0) REVERT: M 602 ASN cc_start: 0.6710 (t0) cc_final: 0.6498 (t0) REVERT: O 98 ARG cc_start: 0.7978 (ttp-170) cc_final: 0.7715 (ttp-170) REVERT: P 449 ARG cc_start: 0.7453 (mtm180) cc_final: 0.6301 (pmt-80) REVERT: P 539 ASN cc_start: 0.7424 (m-40) cc_final: 0.7085 (p0) REVERT: R 98 ARG cc_start: 0.8027 (ttp-170) cc_final: 0.7613 (ttp-170) REVERT: S 449 ARG cc_start: 0.7347 (mtm180) cc_final: 0.6416 (pmt-80) REVERT: S 541 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8594 (mt0) REVERT: S 602 ASN cc_start: 0.6687 (t0) cc_final: 0.6394 (t0) outliers start: 32 outliers final: 24 residues processed: 371 average time/residue: 0.1878 time to fit residues: 106.5888 Evaluate side-chains 341 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 315 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 570 ASN Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 570 ASN Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 541 GLN Chi-restraints excluded: chain U residue 30 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 46 optimal weight: 0.6980 chunk 274 optimal weight: 0.0980 chunk 210 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 197 optimal weight: 0.3980 chunk 342 optimal weight: 0.9990 chunk 142 optimal weight: 0.0770 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 330 optimal weight: 0.9980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN D 485 GLN ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 ASN ** G 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 408 ASN ** J 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 597 HIS M 408 ASN ** M 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 557 GLN R 31 ASN S 454 GLN ** S 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.195846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.159123 restraints weight = 36260.034| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.65 r_work: 0.3552 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29085 Z= 0.105 Angle : 0.486 5.652 39620 Z= 0.257 Chirality : 0.043 0.143 4501 Planarity : 0.004 0.051 5180 Dihedral : 3.741 17.283 4102 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.41 % Allowed : 8.77 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.14), residues: 3745 helix: 0.14 (0.25), residues: 504 sheet: 0.52 (0.18), residues: 917 loop : -0.66 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 297 TYR 0.014 0.001 TYR O 52 PHE 0.009 0.001 PHE D 493 TRP 0.011 0.001 TRP B 35 HIS 0.006 0.001 HIS J 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.10 (29078) covalent geometry : angle 0.48578 / 0.26 (39606) SS BOND : bond 0.00094 / 0.05 ( 7) SS BOND : angle 0.79443 / 0.47 ( 14) hydrogen bonds : bond 0.03040 / 2.02 ( 707) hydrogen bonds : angle 5.28474 / 3.71 ( 1743) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 351 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7323 (mtm180) cc_final: 0.6285 (pmt-80) REVERT: A 539 ASN cc_start: 0.7376 (m-40) cc_final: 0.7122 (p0) REVERT: A 541 GLN cc_start: 0.8812 (mt0) cc_final: 0.8347 (mt0) REVERT: B 52 SER cc_start: 0.7720 (OUTLIER) cc_final: 0.7330 (t) REVERT: C 98 ARG cc_start: 0.8043 (ttp-170) cc_final: 0.7835 (ttp-170) REVERT: C 99 ASP cc_start: 0.5916 (t0) cc_final: 0.5566 (t70) REVERT: D 539 ASN cc_start: 0.7365 (m-40) cc_final: 0.6843 (p0) REVERT: D 541 GLN cc_start: 0.8923 (mt0) cc_final: 0.8543 (mt0) REVERT: G 472 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: G 539 ASN cc_start: 0.7407 (m-40) cc_final: 0.6941 (p0) REVERT: G 601 ASN cc_start: 0.6652 (OUTLIER) cc_final: 0.6390 (t0) REVERT: J 214 LYS cc_start: 0.8441 (mtpt) cc_final: 0.8089 (mtpt) REVERT: J 451 ASP cc_start: 0.7614 (p0) cc_final: 0.7410 (m-30) REVERT: J 539 ASN cc_start: 0.7251 (m-40) cc_final: 0.6799 (p0) REVERT: M 602 ASN cc_start: 0.6852 (t0) cc_final: 0.6579 (t0) REVERT: O 98 ARG cc_start: 0.7898 (ttp-170) cc_final: 0.7634 (ttp-170) REVERT: P 449 ARG cc_start: 0.7375 (mtm180) cc_final: 0.6320 (pmt-80) REVERT: P 539 ASN cc_start: 0.7421 (m-40) cc_final: 0.7043 (p0) REVERT: P 602 ASN cc_start: 0.6111 (t0) cc_final: 0.5710 (t0) REVERT: Q 52 SER cc_start: 0.7861 (t) cc_final: 0.7639 (t) REVERT: R 98 ARG cc_start: 0.7891 (ttp-170) cc_final: 0.7533 (ttp-170) REVERT: R 103 TYR cc_start: 0.8429 (m-10) cc_final: 0.8227 (m-10) REVERT: S 449 ARG cc_start: 0.7328 (mtm180) cc_final: 0.6378 (pmt-80) REVERT: S 602 ASN cc_start: 0.6620 (t0) cc_final: 0.6348 (t0) outliers start: 39 outliers final: 25 residues processed: 368 average time/residue: 0.1756 time to fit residues: 100.8652 Evaluate side-chains 343 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 315 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 213 LYS Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 587 MET Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain T residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 19 optimal weight: 0.6980 chunk 140 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 374 optimal weight: 0.7980 chunk 260 optimal weight: 2.9990 chunk 321 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 200 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 HIS A 553 ASN D 408 ASN D 454 GLN D 553 ASN G 299 HIS G 408 ASN G 553 ASN G 597 HIS J 299 HIS J 408 ASN J 454 GLN J 553 ASN J 570 ASN M 299 HIS M 408 ASN ** M 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 597 HIS P 299 HIS P 553 ASN P 597 HIS R 31 ASN S 541 GLN ** S 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.192584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.143012 restraints weight = 36270.668| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.54 r_work: 0.3504 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29085 Z= 0.132 Angle : 0.508 6.510 39620 Z= 0.266 Chirality : 0.044 0.148 4501 Planarity : 0.004 0.055 5180 Dihedral : 3.873 18.466 4102 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.27 % Allowed : 9.45 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3745 helix: 0.00 (0.25), residues: 504 sheet: 0.41 (0.17), residues: 917 loop : -0.75 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 449 TYR 0.015 0.001 TYR F 32 PHE 0.010 0.001 PHE G 531 TRP 0.012 0.001 TRP B 35 HIS 0.007 0.001 HIS P 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.13 (29078) covalent geometry : angle 0.50791 / 0.27 (39606) SS BOND : bond 0.00123 / 0.09 ( 7) SS BOND : angle 0.79069 / 0.47 ( 14) hydrogen bonds : bond 0.02876 / 1.90 ( 707) hydrogen bonds : angle 4.85953 / 3.40 ( 1743) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 338 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7494 (mtm180) cc_final: 0.6324 (pmt-80) REVERT: A 539 ASN cc_start: 0.7472 (m-40) cc_final: 0.7177 (p0) REVERT: A 541 GLN cc_start: 0.8932 (mt0) cc_final: 0.8455 (mt0) REVERT: B 52 SER cc_start: 0.7935 (t) cc_final: 0.7552 (t) REVERT: C 98 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7652 (ttp-170) REVERT: D 539 ASN cc_start: 0.7481 (m-40) cc_final: 0.6987 (p0) REVERT: D 541 GLN cc_start: 0.8981 (mt0) cc_final: 0.8704 (mt0) REVERT: G 472 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7022 (m-30) REVERT: G 539 ASN cc_start: 0.7364 (m-40) cc_final: 0.6898 (p0) REVERT: G 541 GLN cc_start: 0.8734 (mt0) cc_final: 0.7997 (mt0) REVERT: G 601 ASN cc_start: 0.6616 (OUTLIER) cc_final: 0.6365 (t0) REVERT: J 214 LYS cc_start: 0.8429 (mtpt) cc_final: 0.7934 (mtpt) REVERT: J 451 ASP cc_start: 0.7700 (p0) cc_final: 0.7338 (m-30) REVERT: J 472 ASP cc_start: 0.7554 (m-30) cc_final: 0.6859 (m-30) REVERT: J 539 ASN cc_start: 0.7427 (m-40) cc_final: 0.6924 (p0) REVERT: O 98 ARG cc_start: 0.7962 (ttp-170) cc_final: 0.7636 (ttp-170) REVERT: P 449 ARG cc_start: 0.7372 (mtm180) cc_final: 0.6229 (pmt-80) REVERT: P 539 ASN cc_start: 0.7454 (m-40) cc_final: 0.7035 (p0) REVERT: P 602 ASN cc_start: 0.6307 (t0) cc_final: 0.5826 (t0) REVERT: R 98 ARG cc_start: 0.7952 (ttp-170) cc_final: 0.7530 (ttp-170) REVERT: R 103 TYR cc_start: 0.8424 (m-10) cc_final: 0.8215 (m-10) REVERT: S 449 ARG cc_start: 0.7359 (mtm180) cc_final: 0.6293 (pmt-80) REVERT: S 602 ASN cc_start: 0.6565 (t0) cc_final: 0.6249 (t0) outliers start: 63 outliers final: 48 residues processed: 378 average time/residue: 0.1873 time to fit residues: 108.7615 Evaluate side-chains 364 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 314 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 570 ASN Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 213 LYS Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain M residue 587 MET Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 374 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 367 VAL Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 58 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 81 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 230 optimal weight: 0.4980 chunk 241 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 326 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 12 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 597 HIS D 299 HIS J 408 ASN J 541 GLN J 570 ASN M 553 ASN S 553 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.191380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.144274 restraints weight = 35940.546| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.31 r_work: 0.3490 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29085 Z= 0.130 Angle : 0.503 6.643 39620 Z= 0.264 Chirality : 0.044 0.171 4501 Planarity : 0.004 0.056 5180 Dihedral : 3.891 19.477 4102 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.16 % Allowed : 10.97 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3745 helix: -0.02 (0.25), residues: 504 sheet: 0.37 (0.17), residues: 924 loop : -0.79 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 297 TYR 0.021 0.001 TYR U 52 PHE 0.009 0.001 PHE D 493 TRP 0.009 0.001 TRP B 35 HIS 0.007 0.001 HIS P 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 (29078) covalent geometry : angle 0.50258 / 0.26 (39606) SS BOND : bond 0.00108 / 0.06 ( 7) SS BOND : angle 0.85759 / 0.51 ( 14) hydrogen bonds : bond 0.02785 / 1.85 ( 707) hydrogen bonds : angle 4.77410 / 3.34 ( 1743) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 340 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7515 (mtm180) cc_final: 0.6355 (pmt-80) REVERT: A 539 ASN cc_start: 0.7423 (m-40) cc_final: 0.7175 (p0) REVERT: A 541 GLN cc_start: 0.8963 (mt0) cc_final: 0.8479 (mt0) REVERT: B 52 SER cc_start: 0.7931 (t) cc_final: 0.7535 (t) REVERT: C 98 ARG cc_start: 0.7927 (ttp-170) cc_final: 0.7654 (ttp-170) REVERT: D 539 ASN cc_start: 0.7488 (m-40) cc_final: 0.7011 (p0) REVERT: D 541 GLN cc_start: 0.8988 (mt0) cc_final: 0.8725 (mt0) REVERT: G 298 THR cc_start: 0.6898 (t) cc_final: 0.6444 (t) REVERT: G 472 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7090 (m-30) REVERT: G 539 ASN cc_start: 0.7360 (m-40) cc_final: 0.7012 (p0) REVERT: G 541 GLN cc_start: 0.8748 (mt0) cc_final: 0.8153 (mt0) REVERT: G 601 ASN cc_start: 0.6845 (OUTLIER) cc_final: 0.6528 (t0) REVERT: J 214 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8024 (mtpt) REVERT: J 451 ASP cc_start: 0.7726 (p0) cc_final: 0.7339 (m-30) REVERT: J 472 ASP cc_start: 0.7511 (m-30) cc_final: 0.6996 (m-30) REVERT: J 539 ASN cc_start: 0.7453 (m-40) cc_final: 0.6960 (p0) REVERT: O 98 ARG cc_start: 0.7947 (ttp-170) cc_final: 0.7699 (ttp-170) REVERT: P 449 ARG cc_start: 0.7418 (mtm180) cc_final: 0.6263 (pmt-80) REVERT: P 539 ASN cc_start: 0.7470 (m-40) cc_final: 0.7053 (p0) REVERT: P 541 GLN cc_start: 0.8898 (mt0) cc_final: 0.8574 (mt0) REVERT: R 98 ARG cc_start: 0.8001 (ttp-170) cc_final: 0.7545 (ttp-170) REVERT: R 103 TYR cc_start: 0.8483 (m-10) cc_final: 0.8281 (m-10) REVERT: S 449 ARG cc_start: 0.7326 (mtm180) cc_final: 0.6291 (pmt-80) REVERT: S 602 ASN cc_start: 0.6620 (t0) cc_final: 0.6362 (t0) outliers start: 60 outliers final: 56 residues processed: 379 average time/residue: 0.1802 time to fit residues: 105.2737 Evaluate side-chains 385 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 327 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 570 ASN Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 213 LYS Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain M residue 587 MET Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 374 ILE Chi-restraints excluded: chain P residue 404 ILE Chi-restraints excluded: chain P residue 587 MET Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 367 VAL Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain U residue 58 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 126 optimal weight: 0.7980 chunk 253 optimal weight: 2.9990 chunk 162 optimal weight: 0.2980 chunk 290 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 276 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 223 optimal weight: 0.0980 chunk 307 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 597 HIS J 570 ASN S 299 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.192281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140030 restraints weight = 36258.965| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.75 r_work: 0.3514 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29085 Z= 0.118 Angle : 0.494 6.440 39620 Z= 0.259 Chirality : 0.044 0.180 4501 Planarity : 0.004 0.056 5180 Dihedral : 3.850 19.828 4102 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.38 % Allowed : 11.94 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3745 helix: -0.00 (0.25), residues: 504 sheet: 0.34 (0.17), residues: 924 loop : -0.79 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 297 TYR 0.018 0.001 TYR C 52 PHE 0.009 0.001 PHE D 493 TRP 0.008 0.001 TRP B 35 HIS 0.009 0.001 HIS G 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 (29078) covalent geometry : angle 0.49365 / 0.26 (39606) SS BOND : bond 0.00148 / 0.08 ( 7) SS BOND : angle 0.85163 / 0.51 ( 14) hydrogen bonds : bond 0.02656 / 1.77 ( 707) hydrogen bonds : angle 4.70730 / 3.29 ( 1743) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 342 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7526 (mtm180) cc_final: 0.6347 (pmt-80) REVERT: A 539 ASN cc_start: 0.7450 (m-40) cc_final: 0.7164 (p0) REVERT: A 541 GLN cc_start: 0.8952 (mt0) cc_final: 0.8473 (mt0) REVERT: B 52 SER cc_start: 0.7880 (t) cc_final: 0.7452 (t) REVERT: C 98 ARG cc_start: 0.7977 (ttp-170) cc_final: 0.7656 (ttp-170) REVERT: D 403 GLN cc_start: 0.5193 (OUTLIER) cc_final: 0.4960 (pt0) REVERT: D 539 ASN cc_start: 0.7492 (m-40) cc_final: 0.7033 (p0) REVERT: D 541 GLN cc_start: 0.8991 (mt0) cc_final: 0.8740 (mt0) REVERT: G 298 THR cc_start: 0.6828 (t) cc_final: 0.6558 (t) REVERT: G 472 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7077 (m-30) REVERT: G 539 ASN cc_start: 0.7387 (m-40) cc_final: 0.7059 (p0) REVERT: G 541 GLN cc_start: 0.8801 (mt0) cc_final: 0.8225 (mt0) REVERT: G 601 ASN cc_start: 0.6771 (OUTLIER) cc_final: 0.6438 (t0) REVERT: J 214 LYS cc_start: 0.8431 (mtpt) cc_final: 0.7975 (mtpt) REVERT: J 451 ASP cc_start: 0.7711 (p0) cc_final: 0.7313 (m-30) REVERT: J 472 ASP cc_start: 0.7436 (m-30) cc_final: 0.6903 (m-30) REVERT: J 539 ASN cc_start: 0.7461 (m-40) cc_final: 0.6978 (p0) REVERT: M 297 ARG cc_start: 0.7403 (mtp180) cc_final: 0.7105 (mtp180) REVERT: O 98 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.7667 (ttp-170) REVERT: P 449 ARG cc_start: 0.7492 (mtm180) cc_final: 0.6374 (pmt-80) REVERT: P 539 ASN cc_start: 0.7456 (m-40) cc_final: 0.7052 (p0) REVERT: P 541 GLN cc_start: 0.8810 (mt0) cc_final: 0.8566 (mt0) REVERT: R 98 ARG cc_start: 0.7956 (ttp-170) cc_final: 0.7498 (ttp-170) REVERT: S 449 ARG cc_start: 0.7274 (mtm180) cc_final: 0.6244 (pmt-80) REVERT: S 602 ASN cc_start: 0.6611 (t0) cc_final: 0.6354 (t0) outliers start: 66 outliers final: 58 residues processed: 384 average time/residue: 0.1847 time to fit residues: 109.8963 Evaluate side-chains 388 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 327 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 570 ASN Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 213 LYS Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 404 ILE Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain M residue 587 MET Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 374 ILE Chi-restraints excluded: chain P residue 404 ILE Chi-restraints excluded: chain P residue 587 MET Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 367 VAL Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 58 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 347 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 374 optimal weight: 3.9990 chunk 96 optimal weight: 0.0980 chunk 72 optimal weight: 0.0170 chunk 323 optimal weight: 3.9990 chunk 110 optimal weight: 0.0980 chunk 237 optimal weight: 0.9990 chunk 230 optimal weight: 0.0370 chunk 346 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 overall best weight: 0.1696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 597 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.195991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.159029 restraints weight = 36029.616| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.56 r_work: 0.3561 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29085 Z= 0.085 Angle : 0.469 6.721 39620 Z= 0.247 Chirality : 0.043 0.223 4501 Planarity : 0.004 0.056 5180 Dihedral : 3.611 19.099 4102 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.84 % Allowed : 13.31 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3745 helix: 0.22 (0.26), residues: 497 sheet: 0.26 (0.17), residues: 938 loop : -0.71 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 297 TYR 0.016 0.001 TYR B 32 PHE 0.011 0.001 PHE R 64 TRP 0.010 0.001 TRP N 35 HIS 0.006 0.001 HIS S 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.08 (29078) covalent geometry : angle 0.46869 / 0.25 (39606) SS BOND : bond 0.00205 / 0.12 ( 7) SS BOND : angle 0.80724 / 0.47 ( 14) hydrogen bonds : bond 0.02250 / 1.53 ( 707) hydrogen bonds : angle 4.69956 / 3.28 ( 1743) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 361 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7538 (mtm180) cc_final: 0.6463 (pmt-80) REVERT: A 539 ASN cc_start: 0.7302 (m-40) cc_final: 0.7005 (p0) REVERT: A 541 GLN cc_start: 0.8890 (mt0) cc_final: 0.8306 (mt0) REVERT: C 64 PHE cc_start: 0.7064 (m-80) cc_final: 0.6769 (m-10) REVERT: C 98 ARG cc_start: 0.7970 (ttp-170) cc_final: 0.7705 (ttp-170) REVERT: D 539 ASN cc_start: 0.7423 (m-40) cc_final: 0.6962 (p0) REVERT: D 541 GLN cc_start: 0.8967 (mt0) cc_final: 0.8728 (mt0) REVERT: G 185 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: G 472 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7112 (m-30) REVERT: G 535 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7275 (pp20) REVERT: G 539 ASN cc_start: 0.7358 (m-40) cc_final: 0.7046 (p0) REVERT: G 541 GLN cc_start: 0.8859 (mt0) cc_final: 0.8080 (mt0) REVERT: J 185 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: J 214 LYS cc_start: 0.8417 (mtpt) cc_final: 0.7979 (mtpt) REVERT: J 259 TYR cc_start: 0.8954 (p90) cc_final: 0.8630 (p90) REVERT: J 451 ASP cc_start: 0.7573 (p0) cc_final: 0.7339 (m-30) REVERT: J 472 ASP cc_start: 0.7594 (m-30) cc_final: 0.6861 (m-30) REVERT: J 539 ASN cc_start: 0.7412 (m-40) cc_final: 0.6892 (p0) REVERT: M 535 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7430 (pp20) REVERT: O 98 ARG cc_start: 0.7888 (ttp-170) cc_final: 0.7679 (ttp-170) REVERT: O 103 TYR cc_start: 0.8558 (m-10) cc_final: 0.8354 (m-10) REVERT: P 449 ARG cc_start: 0.7450 (mtm180) cc_final: 0.6373 (pmt-80) REVERT: P 535 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7553 (pp20) REVERT: P 539 ASN cc_start: 0.7258 (m-40) cc_final: 0.6832 (p0) REVERT: P 541 GLN cc_start: 0.8764 (mt0) cc_final: 0.8533 (mt0) REVERT: P 602 ASN cc_start: 0.6405 (t0) cc_final: 0.5996 (t0) REVERT: R 98 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.7526 (ttp-170) REVERT: S 449 ARG cc_start: 0.7263 (mtm180) cc_final: 0.6365 (pmt-80) REVERT: S 535 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7589 (pp20) REVERT: S 602 ASN cc_start: 0.6640 (t0) cc_final: 0.6358 (t0) outliers start: 51 outliers final: 34 residues processed: 391 average time/residue: 0.1768 time to fit residues: 107.8212 Evaluate side-chains 367 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 326 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain M residue 587 MET Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 404 ILE Chi-restraints excluded: chain P residue 535 GLU Chi-restraints excluded: chain P residue 587 MET Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain S residue 535 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 359 optimal weight: 0.8980 chunk 253 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 373 optimal weight: 2.9990 chunk 294 optimal weight: 0.6980 chunk 343 optimal weight: 0.6980 chunk 279 optimal weight: 4.9990 chunk 259 optimal weight: 0.0970 chunk 41 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 485 GLN A 561 ASN D 597 HIS ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 597 HIS M 541 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.190198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138500 restraints weight = 36385.689| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.66 r_work: 0.3498 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29085 Z= 0.167 Angle : 0.548 9.365 39620 Z= 0.283 Chirality : 0.045 0.252 4501 Planarity : 0.005 0.061 5180 Dihedral : 4.036 21.128 4102 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.16 % Allowed : 13.78 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.13), residues: 3745 helix: -0.10 (0.25), residues: 504 sheet: 0.35 (0.17), residues: 917 loop : -0.90 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 297 TYR 0.013 0.002 TYR A 233 PHE 0.013 0.001 PHE D 531 TRP 0.011 0.001 TRP B 35 HIS 0.008 0.001 HIS J 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (29078) covalent geometry : angle 0.54769 / 0.28 (39606) SS BOND : bond 0.00144 / 0.07 ( 7) SS BOND : angle 0.81807 / 0.48 ( 14) hydrogen bonds : bond 0.02963 / 1.96 ( 707) hydrogen bonds : angle 4.66728 / 3.25 ( 1743) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 346 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7661 (mtm180) cc_final: 0.6268 (pmt-80) REVERT: A 541 GLN cc_start: 0.8985 (mt0) cc_final: 0.8543 (mt0) REVERT: C 64 PHE cc_start: 0.7254 (m-80) cc_final: 0.6834 (m-10) REVERT: C 98 ARG cc_start: 0.8049 (ttp-170) cc_final: 0.7705 (ttp-170) REVERT: D 535 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7578 (pp20) REVERT: D 539 ASN cc_start: 0.7551 (m-40) cc_final: 0.7078 (p0) REVERT: D 541 GLN cc_start: 0.9053 (mt0) cc_final: 0.8759 (mt0) REVERT: F 31 ASN cc_start: 0.8204 (t0) cc_final: 0.7448 (m-40) REVERT: G 472 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7228 (m-30) REVERT: G 535 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7461 (pp20) REVERT: G 539 ASN cc_start: 0.7596 (m-40) cc_final: 0.7237 (p0) REVERT: G 541 GLN cc_start: 0.8855 (mt0) cc_final: 0.8511 (mt0) REVERT: J 214 LYS cc_start: 0.8350 (mtpt) cc_final: 0.7882 (mtpt) REVERT: J 451 ASP cc_start: 0.7916 (p0) cc_final: 0.7441 (m-30) REVERT: J 472 ASP cc_start: 0.7543 (m-30) cc_final: 0.6993 (m-30) REVERT: J 539 ASN cc_start: 0.7430 (m-40) cc_final: 0.6998 (p0) REVERT: L 98 ARG cc_start: 0.8139 (ttp-170) cc_final: 0.7919 (ttp-170) REVERT: M 535 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7485 (pp20) REVERT: M 602 ASN cc_start: 0.6829 (t0) cc_final: 0.6553 (t0) REVERT: O 98 ARG cc_start: 0.8099 (ttp-170) cc_final: 0.7821 (ttp-170) REVERT: O 103 TYR cc_start: 0.8628 (m-10) cc_final: 0.8407 (m-10) REVERT: P 449 ARG cc_start: 0.7654 (mtm180) cc_final: 0.6378 (pmt-80) REVERT: P 535 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7724 (pp20) REVERT: P 539 ASN cc_start: 0.7404 (m-40) cc_final: 0.6882 (p0) REVERT: P 541 GLN cc_start: 0.8926 (mt0) cc_final: 0.8590 (mt0) REVERT: P 602 ASN cc_start: 0.6562 (t0) cc_final: 0.6159 (t0) REVERT: Q 71 TYR cc_start: 0.6268 (m-10) cc_final: 0.6058 (m-10) REVERT: R 70 LEU cc_start: 0.8627 (mt) cc_final: 0.8354 (mt) REVERT: R 98 ARG cc_start: 0.8098 (ttp-170) cc_final: 0.7611 (ttp-170) REVERT: S 204 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8500 (m) REVERT: S 449 ARG cc_start: 0.7371 (mtm180) cc_final: 0.6226 (pmt-80) REVERT: S 602 ASN cc_start: 0.6706 (t0) cc_final: 0.6478 (t0) outliers start: 60 outliers final: 52 residues processed: 384 average time/residue: 0.2154 time to fit residues: 126.7423 Evaluate side-chains 394 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 336 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 213 LYS Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 404 ILE Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 374 ILE Chi-restraints excluded: chain P residue 404 ILE Chi-restraints excluded: chain P residue 535 GLU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 213 LYS Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain U residue 30 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 253 optimal weight: 4.9990 chunk 285 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 185 optimal weight: 0.0030 chunk 228 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 162 optimal weight: 0.0670 chunk 57 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 overall best weight: 0.4528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 561 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.192253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.145459 restraints weight = 36271.691| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.44 r_work: 0.3506 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29085 Z= 0.111 Angle : 0.508 8.231 39620 Z= 0.265 Chirality : 0.044 0.218 4501 Planarity : 0.004 0.060 5180 Dihedral : 3.871 21.384 4102 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.13 % Allowed : 14.61 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.14), residues: 3745 helix: -0.02 (0.25), residues: 504 sheet: 0.35 (0.17), residues: 924 loop : -0.87 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 297 TYR 0.015 0.001 TYR F 32 PHE 0.019 0.001 PHE R 64 TRP 0.010 0.001 TRP B 35 HIS 0.007 0.001 HIS J 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.11 (29078) covalent geometry : angle 0.50826 / 0.27 (39606) SS BOND : bond 0.00192 / 0.11 ( 7) SS BOND : angle 0.91388 / 0.54 ( 14) hydrogen bonds : bond 0.02541 / 1.72 ( 707) hydrogen bonds : angle 4.68649 / 3.27 ( 1743) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 334 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7494 (mtm180) cc_final: 0.6269 (pmt-80) REVERT: A 601 ASN cc_start: 0.6838 (OUTLIER) cc_final: 0.6338 (t0) REVERT: C 64 PHE cc_start: 0.7213 (m-80) cc_final: 0.6857 (m-10) REVERT: C 98 ARG cc_start: 0.8000 (ttp-170) cc_final: 0.7685 (ttp-170) REVERT: D 535 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7493 (pp20) REVERT: D 539 ASN cc_start: 0.7456 (m-40) cc_final: 0.7053 (p0) REVERT: D 541 GLN cc_start: 0.8979 (mt0) cc_final: 0.8712 (mt0) REVERT: F 31 ASN cc_start: 0.8059 (t0) cc_final: 0.7290 (m-40) REVERT: G 472 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7074 (m-30) REVERT: G 535 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7293 (pp20) REVERT: G 539 ASN cc_start: 0.7436 (m-40) cc_final: 0.7159 (p0) REVERT: G 541 GLN cc_start: 0.8891 (mt0) cc_final: 0.8493 (mt0) REVERT: J 185 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: J 214 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7933 (mtpt) REVERT: J 259 TYR cc_start: 0.8946 (p90) cc_final: 0.8656 (p90) REVERT: J 451 ASP cc_start: 0.7684 (p0) cc_final: 0.7324 (m-30) REVERT: J 472 ASP cc_start: 0.7417 (m-30) cc_final: 0.6849 (m-30) REVERT: J 539 ASN cc_start: 0.7272 (m-40) cc_final: 0.6847 (p0) REVERT: L 98 ARG cc_start: 0.8045 (ttp-170) cc_final: 0.7835 (ttp-170) REVERT: M 535 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7457 (pp20) REVERT: O 98 ARG cc_start: 0.7981 (ttp-170) cc_final: 0.7739 (ttp-170) REVERT: P 449 ARG cc_start: 0.7453 (mtm180) cc_final: 0.6421 (pmt-80) REVERT: P 535 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7582 (pp20) REVERT: P 539 ASN cc_start: 0.7340 (m-40) cc_final: 0.6866 (p0) REVERT: P 541 GLN cc_start: 0.8830 (mt0) cc_final: 0.8410 (mt0) REVERT: P 602 ASN cc_start: 0.6427 (t0) cc_final: 0.6051 (t0) REVERT: R 70 LEU cc_start: 0.8469 (mt) cc_final: 0.8199 (mt) REVERT: R 98 ARG cc_start: 0.7937 (ttp-170) cc_final: 0.7489 (ttp-170) REVERT: S 449 ARG cc_start: 0.7169 (mtm180) cc_final: 0.6203 (pmt-80) REVERT: S 535 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7411 (pp20) REVERT: S 590 LEU cc_start: 0.8745 (tp) cc_final: 0.8530 (tp) REVERT: S 602 ASN cc_start: 0.6600 (t0) cc_final: 0.6394 (t0) outliers start: 59 outliers final: 49 residues processed: 371 average time/residue: 0.2058 time to fit residues: 118.9377 Evaluate side-chains 385 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 328 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 404 ILE Chi-restraints excluded: chain M residue 481 LEU Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 374 ILE Chi-restraints excluded: chain P residue 404 ILE Chi-restraints excluded: chain P residue 535 GLU Chi-restraints excluded: chain P residue 587 MET Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 367 VAL Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain S residue 535 GLU Chi-restraints excluded: chain U residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 187 optimal weight: 0.8980 chunk 347 optimal weight: 1.9990 chunk 312 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 350 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 chunk 244 optimal weight: 0.5980 chunk 256 optimal weight: 1.9990 chunk 219 optimal weight: 0.7980 chunk 242 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4274 r_free = 0.4274 target = 0.191033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139551 restraints weight = 36313.918| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.67 r_work: 0.3512 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29085 Z= 0.132 Angle : 0.525 8.082 39620 Z= 0.273 Chirality : 0.044 0.241 4501 Planarity : 0.005 0.061 5180 Dihedral : 3.951 21.652 4102 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.16 % Allowed : 14.72 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.13), residues: 3745 helix: -0.08 (0.25), residues: 504 sheet: 0.29 (0.17), residues: 917 loop : -0.99 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 54 TYR 0.015 0.001 TYR F 32 PHE 0.020 0.001 PHE R 64 TRP 0.009 0.001 TRP B 35 HIS 0.008 0.001 HIS J 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.13 (29078) covalent geometry : angle 0.52507 / 0.27 (39606) SS BOND : bond 0.00177 / 0.10 ( 7) SS BOND : angle 0.89730 / 0.53 ( 14) hydrogen bonds : bond 0.02707 / 1.81 ( 707) hydrogen bonds : angle 4.66390 / 3.25 ( 1743) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 335 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7614 (tpt90) cc_final: 0.7259 (mtp180) REVERT: A 449 ARG cc_start: 0.7689 (mtm180) cc_final: 0.6312 (pmt-80) REVERT: A 601 ASN cc_start: 0.6881 (OUTLIER) cc_final: 0.6325 (t0) REVERT: C 64 PHE cc_start: 0.7417 (m-80) cc_final: 0.7007 (m-10) REVERT: C 98 ARG cc_start: 0.8079 (ttp-170) cc_final: 0.7730 (ttp-170) REVERT: D 535 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7501 (pp20) REVERT: D 539 ASN cc_start: 0.7577 (m-40) cc_final: 0.7115 (p0) REVERT: D 541 GLN cc_start: 0.9035 (mt0) cc_final: 0.8779 (mt0) REVERT: F 31 ASN cc_start: 0.8158 (t0) cc_final: 0.7384 (m-40) REVERT: G 472 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7246 (m-30) REVERT: G 535 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7430 (pp20) REVERT: G 539 ASN cc_start: 0.7599 (m-40) cc_final: 0.7265 (p0) REVERT: G 541 GLN cc_start: 0.8962 (mt0) cc_final: 0.8613 (mt0) REVERT: I 71 THR cc_start: 0.8915 (t) cc_final: 0.8710 (t) REVERT: J 185 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: J 214 LYS cc_start: 0.8361 (mtpt) cc_final: 0.7900 (mtpt) REVERT: J 259 TYR cc_start: 0.9003 (p90) cc_final: 0.8713 (p90) REVERT: J 451 ASP cc_start: 0.7882 (p0) cc_final: 0.7418 (m-30) REVERT: J 472 ASP cc_start: 0.7529 (m-30) cc_final: 0.7079 (m-30) REVERT: J 539 ASN cc_start: 0.7328 (m-40) cc_final: 0.6741 (p0) REVERT: L 31 ASN cc_start: 0.8050 (t0) cc_final: 0.7294 (m110) REVERT: L 98 ARG cc_start: 0.8089 (ttp-170) cc_final: 0.7888 (ttp-170) REVERT: M 297 ARG cc_start: 0.7427 (mtp180) cc_final: 0.7167 (mtp85) REVERT: M 535 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7457 (pp20) REVERT: M 602 ASN cc_start: 0.6765 (t0) cc_final: 0.6557 (t0) REVERT: N 71 TYR cc_start: 0.6035 (m-10) cc_final: 0.5704 (m-10) REVERT: O 98 ARG cc_start: 0.7983 (ttp-170) cc_final: 0.7740 (ttp-170) REVERT: P 449 ARG cc_start: 0.7666 (mtm180) cc_final: 0.6465 (pmt-80) REVERT: P 535 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7667 (pp20) REVERT: P 539 ASN cc_start: 0.7455 (m-40) cc_final: 0.6930 (p0) REVERT: P 541 GLN cc_start: 0.8906 (mt0) cc_final: 0.8553 (mt0) REVERT: P 602 ASN cc_start: 0.6537 (t0) cc_final: 0.6165 (t0) REVERT: R 70 LEU cc_start: 0.8579 (mt) cc_final: 0.8270 (mt) REVERT: R 98 ARG cc_start: 0.8063 (ttp-170) cc_final: 0.7587 (ttp-170) REVERT: S 449 ARG cc_start: 0.7350 (mtm180) cc_final: 0.6231 (pmt-80) REVERT: S 535 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7451 (pp20) REVERT: S 602 ASN cc_start: 0.6698 (t0) cc_final: 0.6453 (t0) REVERT: U 31 ASN cc_start: 0.8022 (t0) cc_final: 0.7283 (m-40) outliers start: 60 outliers final: 50 residues processed: 371 average time/residue: 0.2128 time to fit residues: 121.4256 Evaluate side-chains 391 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 333 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 404 ILE Chi-restraints excluded: chain M residue 481 LEU Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 374 ILE Chi-restraints excluded: chain P residue 404 ILE Chi-restraints excluded: chain P residue 535 GLU Chi-restraints excluded: chain P residue 587 MET Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 367 VAL Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain S residue 535 GLU Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 58 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 188 optimal weight: 0.0020 chunk 308 optimal weight: 0.5980 chunk 300 optimal weight: 1.9990 chunk 168 optimal weight: 0.0980 chunk 121 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 227 optimal weight: 0.5980 chunk 54 optimal weight: 0.0050 chunk 24 optimal weight: 0.9990 chunk 240 optimal weight: 0.5980 chunk 164 optimal weight: 0.9980 overall best weight: 0.2602 ------------------------------------------------------------------------------- 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 = 0.4302 r_free = 0.4302 target = 0.193925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.142967 restraints weight = 36201.906| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.69 r_work: 0.3558 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29085 Z= 0.097 Angle : 0.497 8.162 39620 Z= 0.259 Chirality : 0.043 0.138 4501 Planarity : 0.004 0.060 5180 Dihedral : 3.748 20.924 4102 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.91 % Allowed : 14.97 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.14), residues: 3745 helix: 0.06 (0.25), residues: 504 sheet: 0.17 (0.17), residues: 959 loop : -0.84 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 252 TYR 0.016 0.001 TYR U 52 PHE 0.019 0.001 PHE R 64 TRP 0.010 0.001 TRP T 35 HIS 0.005 0.001 HIS J 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 (29078) covalent geometry : angle 0.49679 / 0.26 (39606) SS BOND : bond 0.00216 / 0.12 ( 7) SS BOND : angle 0.89062 / 0.52 ( 14) hydrogen bonds : bond 0.02362 / 1.60 ( 707) hydrogen bonds : angle 4.66137 / 3.25 ( 1743) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6414.18 seconds wall clock time: 110 minutes 54.98 seconds (6654.98 seconds total)