Starting phenix.real_space_refine on Fri Mar 6 04:34:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o85_12761/03_2026/7o85_12761.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o85_12761/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7o85_12761/03_2026/7o85_12761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o85_12761/03_2026/7o85_12761.map" model { file = "/net/cci-nas-00/data/ceres_data/7o85_12761/03_2026/7o85_12761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o85_12761/03_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-5986/lib/python3.9/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: 3.10, per 1000 atoms: 0.11 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: 2.16 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: 1.34 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: 5.93 Time building geometry restraints manager: 2.99 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: 0.09 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: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 23.180 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 covalent geometry : bond 0.00194 (29078) covalent geometry : angle 0.48011 (39606) SS BOND : bond 0.00037 ( 7) SS BOND : angle 0.39170 ( 14) hydrogen bonds : bond 0.24094 ( 707) hydrogen bonds : angle 8.54255 ( 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 : 0.670 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: 0.1847 time to fit residues: 128.2699 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 : 0.929 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4308 r_free = 0.4308 target = 0.194289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.156249 restraints weight = 36342.339| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.82 r_work: 0.3508 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29085 Z= 0.143 Angle : 0.533 6.158 39620 Z= 0.282 Chirality : 0.045 0.152 4501 Planarity : 0.005 0.050 5180 Dihedral : 3.946 17.189 4102 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.15 % Allowed : 7.36 % Favored : 91.49 % 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: -0.45 (0.14), residues: 3745 helix: 0.10 (0.25), residues: 497 sheet: 0.44 (0.18), residues: 917 loop : -0.69 (0.13), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 24 TYR 0.014 0.001 TYR A 233 PHE 0.010 0.001 PHE A 531 TRP 0.020 0.001 TRP B 35 HIS 0.004 0.001 HIS D 263 Details of bonding type rmsd covalent geometry : bond 0.00357 (29078) covalent geometry : angle 0.53304 (39606) SS BOND : bond 0.00030 ( 7) SS BOND : angle 1.05297 ( 14) hydrogen bonds : bond 0.03340 ( 707) hydrogen bonds : angle 5.59359 ( 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 387 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 355 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7416 (mtm180) cc_final: 0.6293 (pmt-80) REVERT: A 539 ASN cc_start: 0.7633 (m-40) cc_final: 0.7307 (p0) REVERT: A 541 GLN cc_start: 0.8826 (mt0) cc_final: 0.8438 (mt0) REVERT: C 98 ARG cc_start: 0.8029 (ttp-170) cc_final: 0.7805 (ttp-170) REVERT: D 539 ASN cc_start: 0.7396 (m-40) cc_final: 0.6897 (p0) REVERT: D 541 GLN cc_start: 0.8888 (mt0) cc_final: 0.8582 (mt0) REVERT: G 539 ASN cc_start: 0.7439 (m-40) cc_final: 0.7024 (p0) REVERT: G 541 GLN cc_start: 0.8682 (mt0) cc_final: 0.7899 (mt0) REVERT: G 601 ASN cc_start: 0.6883 (OUTLIER) cc_final: 0.6615 (t0) REVERT: G 602 ASN cc_start: 0.6247 (t0) cc_final: 0.5629 (t0) REVERT: J 214 LYS cc_start: 0.8526 (mtpt) cc_final: 0.8193 (mtpt) REVERT: J 539 ASN cc_start: 0.7367 (m-40) cc_final: 0.7070 (p0) REVERT: O 98 ARG cc_start: 0.7937 (ttp-170) cc_final: 0.7661 (ttp-170) REVERT: P 449 ARG cc_start: 0.7443 (mtm180) cc_final: 0.6299 (pmt-80) REVERT: P 539 ASN cc_start: 0.7387 (m-40) cc_final: 0.6985 (p0) REVERT: P 602 ASN cc_start: 0.6464 (t0) cc_final: 0.6259 (t0) REVERT: R 98 ARG cc_start: 0.7966 (ttp-170) cc_final: 0.7580 (ttp-170) REVERT: S 449 ARG cc_start: 0.7322 (mtm180) cc_final: 0.6411 (pmt-80) REVERT: S 602 ASN cc_start: 0.6681 (t0) cc_final: 0.6386 (t0) outliers start: 32 outliers final: 23 residues processed: 374 average time/residue: 0.2104 time to fit residues: 119.2682 Evaluate side-chains 338 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 314 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 274 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 197 optimal weight: 0.0980 chunk 342 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 330 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN D 485 GLN D 553 ASN G 299 HIS G 553 ASN G 561 ASN G 573 ASN J 299 HIS J 408 ASN J 570 ASN J 597 HIS M 408 ASN ** M 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 597 HIS P 299 HIS ** P 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN S 454 GLN ** S 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.191670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.140320 restraints weight = 36375.397| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.67 r_work: 0.3532 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29085 Z= 0.152 Angle : 0.527 6.877 39620 Z= 0.276 Chirality : 0.044 0.153 4501 Planarity : 0.005 0.054 5180 Dihedral : 4.020 18.887 4102 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.20 % Allowed : 8.51 % Favored : 89.29 % 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: -0.11 (0.25), residues: 504 sheet: 0.41 (0.18), residues: 917 loop : -0.79 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 365 TYR 0.015 0.002 TYR O 52 PHE 0.010 0.001 PHE G 531 TRP 0.011 0.001 TRP N 35 HIS 0.007 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00379 (29078) covalent geometry : angle 0.52685 (39606) SS BOND : bond 0.00072 ( 7) SS BOND : angle 0.79947 ( 14) hydrogen bonds : bond 0.03341 ( 707) hydrogen bonds : angle 5.10932 ( 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 408 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 347 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7644 (mtm180) cc_final: 0.6301 (pmt-80) REVERT: A 539 ASN cc_start: 0.7690 (m-40) cc_final: 0.7264 (p0) REVERT: A 541 GLN cc_start: 0.8968 (mt0) cc_final: 0.8580 (mt0) REVERT: B 52 SER cc_start: 0.7816 (OUTLIER) cc_final: 0.7426 (t) REVERT: C 98 ARG cc_start: 0.7964 (ttp-170) cc_final: 0.7722 (ttp-170) REVERT: D 539 ASN cc_start: 0.7572 (m-40) cc_final: 0.6979 (p0) REVERT: D 541 GLN cc_start: 0.9034 (mt0) cc_final: 0.8755 (mt0) REVERT: G 472 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: G 539 ASN cc_start: 0.7599 (m-40) cc_final: 0.7134 (p0) REVERT: G 570 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7556 (t0) REVERT: G 601 ASN cc_start: 0.6716 (OUTLIER) cc_final: 0.6431 (t0) REVERT: J 214 LYS cc_start: 0.8471 (mtpt) cc_final: 0.8007 (mtpt) REVERT: J 451 ASP cc_start: 0.7861 (p0) cc_final: 0.7416 (m-30) REVERT: J 472 ASP cc_start: 0.7630 (m-30) cc_final: 0.6944 (m-30) REVERT: J 539 ASN cc_start: 0.7573 (m-40) cc_final: 0.7024 (p0) REVERT: O 98 ARG cc_start: 0.7997 (ttp-170) cc_final: 0.7678 (ttp-170) REVERT: P 449 ARG cc_start: 0.7560 (mtm180) cc_final: 0.6273 (pmt-80) REVERT: P 539 ASN cc_start: 0.7504 (m-40) cc_final: 0.7010 (p0) REVERT: Q 52 SER cc_start: 0.8000 (t) cc_final: 0.7800 (t) REVERT: Q 65 SER cc_start: 0.8277 (t) cc_final: 0.8074 (t) REVERT: R 98 ARG cc_start: 0.8000 (ttp-170) cc_final: 0.7587 (ttp-170) REVERT: R 103 TYR cc_start: 0.8433 (m-10) cc_final: 0.8191 (m-10) REVERT: S 449 ARG cc_start: 0.7512 (mtm180) cc_final: 0.6334 (pmt-80) REVERT: S 539 ASN cc_start: 0.7377 (m-40) cc_final: 0.6880 (p0) REVERT: S 602 ASN cc_start: 0.6606 (t0) cc_final: 0.6336 (t0) outliers start: 61 outliers final: 44 residues processed: 384 average time/residue: 0.2055 time to fit residues: 120.4266 Evaluate side-chains 366 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 318 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 52 SER 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 570 ASN Chi-restraints excluded: chain G residue 601 ASN 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 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 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 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 590 LEU 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 374 ILE Chi-restraints excluded: chain S residue 472 ASP Chi-restraints excluded: chain U residue 30 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 19 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 0.0570 chunk 374 optimal weight: 0.0980 chunk 260 optimal weight: 50.0000 chunk 321 optimal weight: 0.9990 chunk 213 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 200 optimal weight: 0.0570 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 ASN ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN ** G 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 454 GLN J 553 ASN J 570 ASN M 299 HIS M 553 ASN P 553 ASN ** S 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.194190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143191 restraints weight = 36187.104| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.65 r_work: 0.3563 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29085 Z= 0.099 Angle : 0.479 5.839 39620 Z= 0.253 Chirality : 0.043 0.160 4501 Planarity : 0.004 0.053 5180 Dihedral : 3.786 18.787 4102 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.80 % Allowed : 9.99 % Favored : 88.20 % 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: 0.11 (0.26), residues: 497 sheet: 0.33 (0.17), residues: 931 loop : -0.71 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 449 TYR 0.020 0.001 TYR U 52 PHE 0.009 0.001 PHE D 493 TRP 0.009 0.001 TRP B 35 HIS 0.004 0.001 HIS G 263 Details of bonding type rmsd covalent geometry : bond 0.00247 (29078) covalent geometry : angle 0.47873 (39606) SS BOND : bond 0.00112 ( 7) SS BOND : angle 0.88286 ( 14) hydrogen bonds : bond 0.02627 ( 707) hydrogen bonds : angle 4.93122 ( 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 399 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 349 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7601 (mtm180) cc_final: 0.6356 (pmt-80) REVERT: A 539 ASN cc_start: 0.7587 (m-40) cc_final: 0.7178 (p0) REVERT: A 541 GLN cc_start: 0.8900 (mt0) cc_final: 0.8477 (mt0) REVERT: B 52 SER cc_start: 0.7776 (t) cc_final: 0.7364 (t) REVERT: C 98 ARG cc_start: 0.7952 (ttp-170) cc_final: 0.7705 (ttp-170) REVERT: D 539 ASN cc_start: 0.7519 (m-40) cc_final: 0.6935 (p0) REVERT: D 541 GLN cc_start: 0.9016 (mt0) cc_final: 0.8741 (mt0) REVERT: F 99 ASP cc_start: 0.6016 (t0) cc_final: 0.5546 (t70) REVERT: G 472 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7314 (m-30) REVERT: G 539 ASN cc_start: 0.7563 (m-40) cc_final: 0.7061 (p0) REVERT: G 541 GLN cc_start: 0.8732 (mt0) cc_final: 0.8123 (mt0) REVERT: G 570 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7589 (t0) REVERT: G 601 ASN cc_start: 0.6576 (OUTLIER) cc_final: 0.6245 (t0) REVERT: J 214 LYS cc_start: 0.8419 (mtpt) cc_final: 0.7934 (mtpt) REVERT: J 451 ASP cc_start: 0.7817 (p0) cc_final: 0.7348 (m-30) REVERT: J 472 ASP cc_start: 0.7654 (m-30) cc_final: 0.6962 (m-30) REVERT: J 539 ASN cc_start: 0.7568 (m-40) cc_final: 0.6987 (p0) REVERT: O 98 ARG cc_start: 0.7945 (ttp-170) cc_final: 0.7639 (ttp-170) REVERT: P 449 ARG cc_start: 0.7572 (mtm180) cc_final: 0.6313 (pmt-80) REVERT: P 539 ASN cc_start: 0.7387 (m-40) cc_final: 0.6900 (p0) REVERT: P 541 GLN cc_start: 0.8893 (mt0) cc_final: 0.8653 (mt0) REVERT: P 602 ASN cc_start: 0.6190 (t0) cc_final: 0.5721 (t0) REVERT: Q 52 SER cc_start: 0.7948 (t) cc_final: 0.7737 (t) REVERT: R 98 ARG cc_start: 0.8013 (ttp-170) cc_final: 0.7574 (ttp-170) REVERT: R 103 TYR cc_start: 0.8423 (m-10) cc_final: 0.8157 (m-10) REVERT: S 204 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8482 (m) REVERT: S 297 ARG cc_start: 0.6835 (mtp180) cc_final: 0.6609 (tpt-90) REVERT: S 449 ARG cc_start: 0.7480 (mtm180) cc_final: 0.6332 (pmt-80) REVERT: S 539 ASN cc_start: 0.7351 (m-40) cc_final: 0.6765 (p0) REVERT: S 590 LEU cc_start: 0.8750 (tp) cc_final: 0.8541 (tp) REVERT: S 602 ASN cc_start: 0.6548 (t0) cc_final: 0.6313 (t0) outliers start: 50 outliers final: 34 residues processed: 376 average time/residue: 0.1880 time to fit residues: 109.1538 Evaluate side-chains 354 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 316 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain D residue 185 ASP 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 469 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 570 ASN Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 58 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 570 ASN 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 194 VAL Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain M residue 587 MET Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 404 ILE Chi-restraints excluded: chain P residue 587 MET Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 204 SER 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 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: 0.9990 chunk 147 optimal weight: 0.6980 chunk 230 optimal weight: 0.0770 chunk 241 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 326 optimal weight: 0.9980 chunk 98 optimal weight: 50.0000 chunk 70 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 561 ASN A 597 HIS D 299 HIS G 408 ASN ** G 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 597 HIS M 541 GLN P 485 GLN P 597 HIS S 299 HIS ** S 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 597 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.190118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.142303 restraints weight = 36026.449| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.39 r_work: 0.3478 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29085 Z= 0.146 Angle : 0.519 7.281 39620 Z= 0.271 Chirality : 0.044 0.189 4501 Planarity : 0.005 0.057 5180 Dihedral : 4.011 20.149 4102 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.27 % Allowed : 11.54 % Favored : 86.18 % 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: -0.67 (0.14), residues: 3745 helix: -0.12 (0.25), residues: 504 sheet: 0.32 (0.17), residues: 917 loop : -0.84 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 297 TYR 0.012 0.001 TYR A 233 PHE 0.011 0.001 PHE D 531 TRP 0.010 0.001 TRP B 35 HIS 0.006 0.001 HIS G 597 Details of bonding type rmsd covalent geometry : bond 0.00367 (29078) covalent geometry : angle 0.51915 (39606) SS BOND : bond 0.00103 ( 7) SS BOND : angle 0.84104 ( 14) hydrogen bonds : bond 0.02950 ( 707) hydrogen bonds : angle 4.74575 ( 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 411 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 348 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7582 (mtm180) cc_final: 0.6345 (pmt-80) REVERT: A 539 ASN cc_start: 0.7520 (m-40) cc_final: 0.7259 (p0) REVERT: A 541 GLN cc_start: 0.8983 (mt0) cc_final: 0.8514 (mt0) REVERT: B 52 SER cc_start: 0.7835 (t) cc_final: 0.7448 (t) REVERT: C 98 ARG cc_start: 0.7987 (ttp-170) cc_final: 0.7673 (ttp-170) REVERT: D 539 ASN cc_start: 0.7533 (m-40) cc_final: 0.7019 (p0) REVERT: D 541 GLN cc_start: 0.8993 (mt0) cc_final: 0.8641 (mt0) REVERT: G 472 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7094 (m-30) REVERT: G 539 ASN cc_start: 0.7450 (m-40) cc_final: 0.7124 (p0) REVERT: J 214 LYS cc_start: 0.8406 (mtpt) cc_final: 0.7998 (mtpt) REVERT: J 451 ASP cc_start: 0.7739 (p0) cc_final: 0.7350 (m-30) REVERT: J 472 ASP cc_start: 0.7465 (m-30) cc_final: 0.6925 (m-30) REVERT: J 539 ASN cc_start: 0.7555 (m-40) cc_final: 0.7069 (p0) REVERT: O 98 ARG cc_start: 0.7906 (ttp-170) cc_final: 0.7660 (ttp-170) REVERT: P 449 ARG cc_start: 0.7460 (mtm180) cc_final: 0.6275 (pmt-80) REVERT: P 539 ASN cc_start: 0.7466 (m-40) cc_final: 0.7047 (p0) REVERT: P 541 GLN cc_start: 0.8841 (mt0) cc_final: 0.8531 (mt0) REVERT: R 98 ARG cc_start: 0.8017 (ttp-170) cc_final: 0.7562 (ttp-170) REVERT: R 103 TYR cc_start: 0.8463 (m-10) cc_final: 0.8255 (m-10) REVERT: S 449 ARG cc_start: 0.7325 (mtm180) cc_final: 0.6259 (pmt-80) REVERT: S 539 ASN cc_start: 0.7196 (m-40) cc_final: 0.6628 (p0) REVERT: S 602 ASN cc_start: 0.6662 (t0) cc_final: 0.6427 (t0) outliers start: 63 outliers final: 53 residues processed: 385 average time/residue: 0.1981 time to fit residues: 116.3719 Evaluate side-chains 381 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 327 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 374 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 53 ARG 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 51 THR 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 587 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 58 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 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 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 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 587 MET 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 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 472 ASP Chi-restraints excluded: chain S residue 587 MET Chi-restraints excluded: chain T residue 33 LEU 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: 0.4980 chunk 253 optimal weight: 0.3980 chunk 162 optimal weight: 0.7980 chunk 290 optimal weight: 1.9990 chunk 207 optimal weight: 0.2980 chunk 99 optimal weight: 0.0020 chunk 79 optimal weight: 0.0370 chunk 276 optimal weight: 0.6980 chunk 38 optimal weight: 0.0040 chunk 223 optimal weight: 0.4980 chunk 307 optimal weight: 2.9990 overall best weight: 0.1478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 HIS G 573 ASN M 561 ASN P 485 GLN P 597 HIS S 553 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.195091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.147777 restraints weight = 36194.746| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.45 r_work: 0.3549 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2702 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 : 0.468 5.741 39620 Z= 0.248 Chirality : 0.043 0.188 4501 Planarity : 0.004 0.056 5180 Dihedral : 3.680 19.387 4102 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.95 % Allowed : 13.13 % Favored : 84.92 % 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: -0.56 (0.14), residues: 3745 helix: 0.18 (0.26), residues: 497 sheet: 0.37 (0.17), residues: 896 loop : -0.79 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 297 TYR 0.013 0.001 TYR L 32 PHE 0.009 0.001 PHE P 493 TRP 0.007 0.001 TRP B 35 HIS 0.009 0.001 HIS G 263 Details of bonding type rmsd covalent geometry : bond 0.00212 (29078) covalent geometry : angle 0.46822 (39606) SS BOND : bond 0.00147 ( 7) SS BOND : angle 0.88092 ( 14) hydrogen bonds : bond 0.02345 ( 707) hydrogen bonds : angle 4.72211 ( 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 400 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 346 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7475 (mtm180) cc_final: 0.6356 (pmt-80) REVERT: A 539 ASN cc_start: 0.7437 (m-40) cc_final: 0.7178 (p0) REVERT: A 541 GLN cc_start: 0.8894 (mt0) cc_final: 0.8333 (mt0) REVERT: A 601 ASN cc_start: 0.6701 (OUTLIER) cc_final: 0.6215 (t0) REVERT: C 64 PHE cc_start: 0.7134 (m-80) cc_final: 0.6795 (m-10) REVERT: C 98 ARG cc_start: 0.7938 (ttp-170) cc_final: 0.7670 (ttp-170) REVERT: D 539 ASN cc_start: 0.7440 (m-40) cc_final: 0.6953 (p0) REVERT: D 541 GLN cc_start: 0.8960 (mt0) cc_final: 0.8703 (mt0) REVERT: G 472 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7075 (m-30) REVERT: G 539 ASN cc_start: 0.7396 (m-40) cc_final: 0.6976 (p0) REVERT: G 541 GLN cc_start: 0.8791 (mt0) cc_final: 0.8055 (mt0) REVERT: J 185 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7544 (m-30) REVERT: J 214 LYS cc_start: 0.8405 (mtpt) cc_final: 0.7952 (mtpt) REVERT: J 259 TYR cc_start: 0.8948 (p90) cc_final: 0.8611 (p90) REVERT: J 451 ASP cc_start: 0.7547 (p0) cc_final: 0.7333 (m-30) REVERT: J 472 ASP cc_start: 0.7521 (m-30) cc_final: 0.6772 (m-30) REVERT: J 539 ASN cc_start: 0.7417 (m-40) cc_final: 0.6903 (p0) REVERT: L 99 ASP cc_start: 0.5785 (t0) cc_final: 0.5576 (t0) REVERT: O 98 ARG cc_start: 0.7868 (ttp-170) cc_final: 0.7667 (ttp-170) REVERT: P 449 ARG cc_start: 0.7360 (mtm180) cc_final: 0.6290 (pmt-80) REVERT: P 539 ASN cc_start: 0.7430 (m-40) cc_final: 0.7006 (p0) REVERT: P 541 GLN cc_start: 0.8759 (mt0) cc_final: 0.8497 (mt0) REVERT: R 98 ARG cc_start: 0.7890 (ttp-170) cc_final: 0.7458 (ttp-170) REVERT: R 103 TYR cc_start: 0.8402 (m-10) cc_final: 0.8187 (m-10) REVERT: S 449 ARG cc_start: 0.7253 (mtm180) cc_final: 0.6298 (pmt-80) REVERT: S 602 ASN cc_start: 0.6625 (t0) cc_final: 0.6377 (t0) outliers start: 54 outliers final: 40 residues processed: 370 average time/residue: 0.1922 time to fit residues: 109.4569 Evaluate side-chains 369 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 326 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 A residue 601 ASN Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain D residue 194 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 587 MET 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 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 213 LYS Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain P residue 210 ILE 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 Q residue 53 ARG 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 194 VAL Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 367 VAL 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: 0.8980 chunk 0 optimal weight: 4.9990 chunk 374 optimal weight: 2.9990 chunk 96 optimal weight: 0.0870 chunk 72 optimal weight: 0.9990 chunk 323 optimal weight: 3.9990 chunk 110 optimal weight: 0.0970 chunk 237 optimal weight: 0.9980 chunk 230 optimal weight: 0.1980 chunk 346 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 597 HIS J 597 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.194556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143597 restraints weight = 36107.116| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.63 r_work: 0.3565 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29085 Z= 0.096 Angle : 0.476 6.099 39620 Z= 0.250 Chirality : 0.043 0.206 4501 Planarity : 0.004 0.057 5180 Dihedral : 3.656 19.192 4102 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.09 % Allowed : 13.38 % Favored : 84.52 % 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: 0.10 (0.26), residues: 504 sheet: 0.36 (0.17), residues: 924 loop : -0.74 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 297 TYR 0.015 0.001 TYR F 32 PHE 0.008 0.001 PHE M 202 TRP 0.007 0.001 TRP B 35 HIS 0.006 0.001 HIS J 597 Details of bonding type rmsd covalent geometry : bond 0.00244 (29078) covalent geometry : angle 0.47546 (39606) SS BOND : bond 0.00145 ( 7) SS BOND : angle 0.80644 ( 14) hydrogen bonds : bond 0.02407 ( 707) hydrogen bonds : angle 4.61882 ( 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 390 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 332 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7728 (mtm180) cc_final: 0.6461 (pmt-80) REVERT: A 535 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7699 (pp20) REVERT: A 539 ASN cc_start: 0.7589 (m-40) cc_final: 0.7160 (p0) REVERT: A 541 GLN cc_start: 0.8913 (mt0) cc_final: 0.8417 (mt0) REVERT: A 601 ASN cc_start: 0.6705 (OUTLIER) cc_final: 0.6215 (t0) REVERT: C 64 PHE cc_start: 0.7150 (m-80) cc_final: 0.6794 (m-10) REVERT: C 98 ARG cc_start: 0.8020 (ttp-170) cc_final: 0.7696 (ttp-170) REVERT: D 539 ASN cc_start: 0.7509 (m-40) cc_final: 0.6942 (p0) REVERT: D 541 GLN cc_start: 0.9010 (mt0) cc_final: 0.8756 (mt0) REVERT: G 472 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7228 (m-30) REVERT: G 535 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7330 (pp20) REVERT: G 539 ASN cc_start: 0.7505 (m-40) cc_final: 0.7043 (p0) REVERT: G 541 GLN cc_start: 0.8907 (mt0) cc_final: 0.8195 (mt0) REVERT: J 185 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7553 (m-30) REVERT: J 214 LYS cc_start: 0.8386 (mtpt) cc_final: 0.7948 (mtpt) REVERT: J 259 TYR cc_start: 0.8986 (p90) cc_final: 0.8709 (p90) REVERT: J 451 ASP cc_start: 0.7822 (p0) cc_final: 0.7352 (m-30) REVERT: J 472 ASP cc_start: 0.7678 (m-30) cc_final: 0.6946 (m-30) REVERT: J 535 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7849 (pp20) REVERT: J 539 ASN cc_start: 0.7535 (m-40) cc_final: 0.6919 (p0) REVERT: L 99 ASP cc_start: 0.6022 (t0) cc_final: 0.5760 (t0) REVERT: M 535 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7391 (pp20) REVERT: O 98 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7691 (ttp-170) REVERT: P 449 ARG cc_start: 0.7557 (mtm180) cc_final: 0.6359 (pmt-80) REVERT: P 535 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7641 (pp20) REVERT: P 539 ASN cc_start: 0.7555 (m-40) cc_final: 0.7092 (p0) REVERT: R 98 ARG cc_start: 0.7964 (ttp-170) cc_final: 0.7514 (ttp-170) REVERT: R 103 TYR cc_start: 0.8481 (m-10) cc_final: 0.8239 (m-10) REVERT: S 449 ARG cc_start: 0.7472 (mtm180) cc_final: 0.6388 (pmt-80) REVERT: S 535 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7562 (pp20) REVERT: S 539 ASN cc_start: 0.7279 (m-40) cc_final: 0.6706 (p0) REVERT: S 590 LEU cc_start: 0.8738 (tp) cc_final: 0.8538 (tp) REVERT: S 602 ASN cc_start: 0.6679 (t0) cc_final: 0.6453 (t0) outliers start: 58 outliers final: 47 residues processed: 364 average time/residue: 0.1946 time to fit residues: 109.3511 Evaluate side-chains 378 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 322 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 535 GLU Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain C residue 30 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 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 472 ASP Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 587 MET Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 58 THR 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 J residue 535 GLU Chi-restraints excluded: chain J residue 587 MET 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 213 LYS Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 404 ILE Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain N residue 53 ARG 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 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 S residue 535 GLU Chi-restraints excluded: chain U residue 48 ILE Chi-restraints excluded: chain U residue 58 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 359 optimal weight: 0.1980 chunk 253 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 373 optimal weight: 2.9990 chunk 294 optimal weight: 0.9990 chunk 343 optimal weight: 0.8980 chunk 279 optimal weight: 4.9990 chunk 259 optimal weight: 0.4980 chunk 41 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 561 ASN S 541 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.187349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.139238 restraints weight = 36422.029| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.31 r_work: 0.3479 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3140 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= 0.170 Angle : 0.545 7.579 39620 Z= 0.284 Chirality : 0.045 0.278 4501 Planarity : 0.005 0.062 5180 Dihedral : 4.147 21.816 4102 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.49 % Allowed : 13.38 % Favored : 84.13 % 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: -0.17 (0.25), residues: 504 sheet: 0.33 (0.17), residues: 903 loop : -0.97 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 297 TYR 0.017 0.002 TYR Q 71 PHE 0.012 0.002 PHE D 531 TRP 0.008 0.001 TRP H 35 HIS 0.009 0.001 HIS S 263 Details of bonding type rmsd covalent geometry : bond 0.00424 (29078) covalent geometry : angle 0.54523 (39606) SS BOND : bond 0.00099 ( 7) SS BOND : angle 0.85446 ( 14) hydrogen bonds : bond 0.03044 ( 707) hydrogen bonds : angle 4.66166 ( 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 421 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 352 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7509 (mtm180) cc_final: 0.6250 (pmt-80) REVERT: A 539 ASN cc_start: 0.7569 (m-40) cc_final: 0.7359 (p0) REVERT: A 541 GLN cc_start: 0.8971 (mt0) cc_final: 0.8548 (mt0) REVERT: A 601 ASN cc_start: 0.6947 (OUTLIER) cc_final: 0.6389 (t0) REVERT: B 52 SER cc_start: 0.7850 (t) cc_final: 0.7479 (t) REVERT: C 64 PHE cc_start: 0.7179 (m-80) cc_final: 0.6777 (m-10) REVERT: C 98 ARG cc_start: 0.8025 (ttp-170) cc_final: 0.7695 (ttp-170) REVERT: D 403 GLN cc_start: 0.5196 (OUTLIER) cc_final: 0.4969 (pt0) REVERT: D 535 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7470 (pp20) REVERT: D 539 ASN cc_start: 0.7492 (m-40) cc_final: 0.7063 (p0) REVERT: D 541 GLN cc_start: 0.9009 (mt0) cc_final: 0.8705 (mt0) REVERT: F 31 ASN cc_start: 0.8060 (t0) cc_final: 0.7299 (m-40) REVERT: G 472 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7060 (m-30) REVERT: G 535 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7337 (pp20) REVERT: G 539 ASN cc_start: 0.7462 (m-40) cc_final: 0.7258 (p0) REVERT: G 541 GLN cc_start: 0.8845 (mt0) cc_final: 0.8507 (mt0) REVERT: G 570 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.7392 (t0) REVERT: J 214 LYS cc_start: 0.8392 (mtpt) cc_final: 0.7935 (mtpt) REVERT: J 451 ASP cc_start: 0.7758 (p0) cc_final: 0.7379 (m-30) REVERT: J 539 ASN cc_start: 0.7507 (m-40) cc_final: 0.7072 (p0) REVERT: L 98 ARG cc_start: 0.8031 (ttp-170) cc_final: 0.7793 (ttp-170) REVERT: M 535 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7404 (pp20) REVERT: M 602 ASN cc_start: 0.6898 (t0) cc_final: 0.6629 (t0) REVERT: O 98 ARG cc_start: 0.8006 (ttp-170) cc_final: 0.7755 (ttp-170) REVERT: P 449 ARG cc_start: 0.7507 (mtm180) cc_final: 0.6279 (pmt-80) REVERT: P 535 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7602 (pp20) REVERT: P 539 ASN cc_start: 0.7407 (m-40) cc_final: 0.7074 (p0) REVERT: P 602 ASN cc_start: 0.6632 (t0) cc_final: 0.6243 (t0) REVERT: R 70 LEU cc_start: 0.8495 (mt) cc_final: 0.8161 (mt) REVERT: R 98 ARG cc_start: 0.8002 (ttp-170) cc_final: 0.7487 (ttp-170) REVERT: S 449 ARG cc_start: 0.7253 (mtm180) cc_final: 0.6191 (pmt-80) REVERT: S 539 ASN cc_start: 0.7227 (m-40) cc_final: 0.6812 (p0) REVERT: S 602 ASN cc_start: 0.6722 (t0) cc_final: 0.6517 (t0) outliers start: 69 outliers final: 58 residues processed: 394 average time/residue: 0.1996 time to fit residues: 119.3696 Evaluate side-chains 404 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 338 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 A residue 601 ASN 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 403 GLN 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 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 535 GLU Chi-restraints excluded: chain G residue 570 ASN Chi-restraints excluded: chain G residue 587 MET 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 I residue 58 THR 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 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 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 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 O residue 70 LEU 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 Q residue 53 ARG 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 U residue 30 THR Chi-restraints excluded: chain U residue 58 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 253 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 228 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 57 optimal weight: 0.1980 chunk 177 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.189379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.139986 restraints weight = 36131.811| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.42 r_work: 0.3505 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29085 Z= 0.141 Angle : 0.525 7.576 39620 Z= 0.274 Chirality : 0.045 0.287 4501 Planarity : 0.005 0.061 5180 Dihedral : 4.062 22.210 4102 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.49 % Allowed : 13.92 % Favored : 83.59 % 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: -0.88 (0.13), residues: 3745 helix: -0.14 (0.25), residues: 504 sheet: 0.23 (0.17), residues: 917 loop : -1.04 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 297 TYR 0.016 0.001 TYR L 32 PHE 0.018 0.001 PHE R 64 TRP 0.010 0.001 TRP N 35 HIS 0.008 0.001 HIS J 263 Details of bonding type rmsd covalent geometry : bond 0.00356 (29078) covalent geometry : angle 0.52467 (39606) SS BOND : bond 0.00144 ( 7) SS BOND : angle 0.91255 ( 14) hydrogen bonds : bond 0.02781 ( 707) hydrogen bonds : angle 4.67957 ( 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 406 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 337 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7614 (tpt90) cc_final: 0.7256 (mtp180) REVERT: A 449 ARG cc_start: 0.7646 (mtm180) cc_final: 0.6295 (pmt-80) REVERT: A 541 GLN cc_start: 0.8903 (mt0) cc_final: 0.8436 (mt0) REVERT: A 601 ASN cc_start: 0.6891 (OUTLIER) cc_final: 0.6330 (t0) REVERT: B 52 SER cc_start: 0.7925 (t) cc_final: 0.7543 (t) REVERT: C 64 PHE cc_start: 0.7280 (m-80) cc_final: 0.6863 (m-10) REVERT: C 98 ARG cc_start: 0.8106 (ttp-170) cc_final: 0.7773 (ttp-170) REVERT: D 535 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7540 (pp20) REVERT: D 539 ASN cc_start: 0.7570 (m-40) cc_final: 0.7057 (p0) REVERT: F 31 ASN cc_start: 0.8176 (t0) cc_final: 0.7394 (m-40) REVERT: G 472 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7202 (m-30) REVERT: G 535 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7443 (pp20) REVERT: G 539 ASN cc_start: 0.7603 (m-40) cc_final: 0.7208 (p0) REVERT: G 541 GLN cc_start: 0.8908 (mt0) cc_final: 0.8586 (mt0) REVERT: G 570 ASN cc_start: 0.7878 (OUTLIER) cc_final: 0.7513 (t0) REVERT: J 214 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7858 (mtpt) REVERT: J 451 ASP cc_start: 0.7877 (p0) cc_final: 0.7415 (m-30) REVERT: J 539 ASN cc_start: 0.7656 (m-40) cc_final: 0.7081 (p0) REVERT: L 31 ASN cc_start: 0.8186 (t0) cc_final: 0.7362 (m110) REVERT: L 98 ARG cc_start: 0.8016 (ttp-170) cc_final: 0.7789 (ttp-170) REVERT: M 297 ARG cc_start: 0.7294 (mtp180) cc_final: 0.7006 (mtp85) REVERT: M 535 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7470 (pp20) REVERT: O 98 ARG cc_start: 0.8056 (ttp-170) cc_final: 0.7781 (ttp-170) REVERT: P 449 ARG cc_start: 0.7586 (mtm180) cc_final: 0.6316 (pmt-80) REVERT: P 535 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7748 (pp20) REVERT: P 539 ASN cc_start: 0.7535 (m-40) cc_final: 0.7140 (p0) REVERT: P 602 ASN cc_start: 0.6748 (t0) cc_final: 0.6368 (t0) REVERT: R 70 LEU cc_start: 0.8619 (mt) cc_final: 0.8292 (mt) REVERT: R 98 ARG cc_start: 0.8005 (ttp-170) cc_final: 0.7541 (ttp-170) REVERT: S 449 ARG cc_start: 0.7293 (mtm180) cc_final: 0.6217 (pmt-80) REVERT: S 535 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7632 (pp20) REVERT: S 539 ASN cc_start: 0.7373 (m-40) cc_final: 0.6802 (p0) REVERT: S 602 ASN cc_start: 0.6720 (t0) cc_final: 0.6480 (t0) REVERT: U 31 ASN cc_start: 0.7987 (t0) cc_final: 0.7188 (m-40) outliers start: 69 outliers final: 57 residues processed: 380 average time/residue: 0.2025 time to fit residues: 117.9726 Evaluate side-chains 394 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 329 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 A residue 601 ASN 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 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 535 GLU Chi-restraints excluded: chain G residue 570 ASN Chi-restraints excluded: chain G residue 587 MET Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 58 THR 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 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 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 O residue 70 LEU 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 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 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 187 optimal weight: 0.3980 chunk 347 optimal weight: 0.6980 chunk 312 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 209 optimal weight: 0.0570 chunk 350 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 244 optimal weight: 0.5980 chunk 256 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 561 ASN S 408 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.192048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140799 restraints weight = 36324.312| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.69 r_work: 0.3529 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29085 Z= 0.108 Angle : 0.501 8.329 39620 Z= 0.262 Chirality : 0.043 0.167 4501 Planarity : 0.004 0.061 5180 Dihedral : 3.890 21.709 4102 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.31 % Allowed : 13.96 % Favored : 83.73 % 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: -0.75 (0.13), residues: 3745 helix: -0.01 (0.25), residues: 504 sheet: 0.38 (0.17), residues: 896 loop : -0.98 (0.12), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 297 TYR 0.020 0.001 TYR U 52 PHE 0.018 0.001 PHE R 64 TRP 0.012 0.001 TRP B 35 HIS 0.006 0.001 HIS J 263 Details of bonding type rmsd covalent geometry : bond 0.00274 (29078) covalent geometry : angle 0.50064 (39606) SS BOND : bond 0.00183 ( 7) SS BOND : angle 0.87607 ( 14) hydrogen bonds : bond 0.02489 ( 707) hydrogen bonds : angle 4.66498 ( 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 393 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 329 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7489 (tpt90) cc_final: 0.7179 (mtp180) REVERT: A 449 ARG cc_start: 0.7662 (mtm180) cc_final: 0.6287 (pmt-80) REVERT: A 601 ASN cc_start: 0.6685 (OUTLIER) cc_final: 0.6179 (t0) REVERT: B 52 SER cc_start: 0.7906 (t) cc_final: 0.7515 (t) REVERT: C 64 PHE cc_start: 0.7366 (m-80) cc_final: 0.6956 (m-10) REVERT: C 98 ARG cc_start: 0.8051 (ttp-170) cc_final: 0.7728 (ttp-170) REVERT: D 539 ASN cc_start: 0.7550 (m-40) cc_final: 0.7114 (p0) REVERT: F 31 ASN cc_start: 0.8173 (t0) cc_final: 0.7390 (m-40) REVERT: G 472 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: G 535 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7414 (pp20) REVERT: G 539 ASN cc_start: 0.7588 (m-40) cc_final: 0.7255 (p0) REVERT: G 541 GLN cc_start: 0.8939 (mt0) cc_final: 0.8586 (mt0) REVERT: J 185 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7704 (m-30) REVERT: J 214 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7868 (mtpt) REVERT: J 259 TYR cc_start: 0.8968 (p90) cc_final: 0.8734 (p90) REVERT: J 451 ASP cc_start: 0.7865 (p0) cc_final: 0.7398 (m-30) REVERT: J 539 ASN cc_start: 0.7406 (m-40) cc_final: 0.6934 (p0) REVERT: L 31 ASN cc_start: 0.8102 (t0) cc_final: 0.7363 (m110) REVERT: M 535 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7500 (pp20) REVERT: M 602 ASN cc_start: 0.6772 (t0) cc_final: 0.6564 (t0) REVERT: P 449 ARG cc_start: 0.7581 (mtm180) cc_final: 0.6316 (pmt-80) REVERT: P 535 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7689 (pp20) REVERT: P 539 ASN cc_start: 0.7564 (m-40) cc_final: 0.7133 (p0) REVERT: P 602 ASN cc_start: 0.6585 (t0) cc_final: 0.6168 (t0) REVERT: R 70 LEU cc_start: 0.8598 (mt) cc_final: 0.8234 (mt) REVERT: R 98 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7577 (ttp-170) REVERT: S 449 ARG cc_start: 0.7310 (mtm180) cc_final: 0.6236 (pmt-80) REVERT: S 535 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7469 (pp20) REVERT: S 539 ASN cc_start: 0.7335 (m-40) cc_final: 0.6761 (p0) REVERT: S 590 LEU cc_start: 0.8818 (tp) cc_final: 0.8617 (tp) REVERT: S 602 ASN cc_start: 0.6681 (t0) cc_final: 0.6476 (t0) REVERT: U 31 ASN cc_start: 0.7960 (t0) cc_final: 0.7198 (m-40) outliers start: 64 outliers final: 53 residues processed: 368 average time/residue: 0.2017 time to fit residues: 115.0042 Evaluate side-chains 381 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 321 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 30 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 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 G residue 587 MET Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 58 THR 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 K residue 53 ARG 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 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 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 S residue 535 GLU Chi-restraints excluded: chain T residue 53 ARG 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: 0.3980 chunk 308 optimal weight: 0.0770 chunk 300 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 24 optimal weight: 0.7980 chunk 240 optimal weight: 0.1980 chunk 164 optimal weight: 0.9980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.193936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143092 restraints weight = 36275.377| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.68 r_work: 0.3559 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3192 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= 0.096 Angle : 0.492 8.123 39620 Z= 0.258 Chirality : 0.043 0.182 4501 Planarity : 0.004 0.060 5180 Dihedral : 3.740 21.019 4102 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.24 % Allowed : 14.32 % Favored : 83.44 % 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: -0.72 (0.13), residues: 3745 helix: 0.07 (0.25), residues: 504 sheet: 0.24 (0.16), residues: 931 loop : -0.91 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 54 TYR 0.017 0.001 TYR U 52 PHE 0.018 0.001 PHE R 64 TRP 0.010 0.001 TRP E 35 HIS 0.005 0.001 HIS J 263 Details of bonding type rmsd covalent geometry : bond 0.00245 (29078) covalent geometry : angle 0.49134 (39606) SS BOND : bond 0.00212 ( 7) SS BOND : angle 0.85908 ( 14) hydrogen bonds : bond 0.02329 ( 707) hydrogen bonds : angle 4.61304 ( 1743) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7158.29 seconds wall clock time: 123 minutes 12.51 seconds (7392.51 seconds total)