Starting phenix.real_space_refine on Sat Mar 7 09:47:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bp0_30138/03_2026/7bp0_30138.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bp0_30138/03_2026/7bp0_30138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bp0_30138/03_2026/7bp0_30138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bp0_30138/03_2026/7bp0_30138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bp0_30138/03_2026/7bp0_30138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bp0_30138/03_2026/7bp0_30138.map" } resolution = 4.6 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= 0.038 sd= 1.852 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 216 5.16 5 C 26160 2.51 5 N 6960 2.21 5 O 8052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.04s 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: 41388 Number of models: 1 Model: "" Number of chains: 12 Chain: "a" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3449 Classifications: {'peptide': 437} Link IDs: {'CIS': 11, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 405} Chain breaks: 5 Chain: "b" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3449 Classifications: {'peptide': 437} Link IDs: {'CIS': 11, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 405} Chain breaks: 5 Chain: "c" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3449 Classifications: {'peptide': 437} Link IDs: {'CIS': 11, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 405} Chain breaks: 5 Chain: "d" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3449 Classifications: {'peptide': 437} Link IDs: {'CIS': 11, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 405} Chain breaks: 5 Chain: "e" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3449 Classifications: {'peptide': 437} Link IDs: {'CIS': 11, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 405} Chain breaks: 5 Chain: "f" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3449 Classifications: {'peptide': 437} Link IDs: {'CIS': 11, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 405} Chain breaks: 5 Chain: "g" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3449 Classifications: {'peptide': 437} Link IDs: {'CIS': 11, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 405} Chain breaks: 5 Chain: "h" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3449 Classifications: {'peptide': 437} Link IDs: {'CIS': 11, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 405} Chain breaks: 5 Chain: "i" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3449 Classifications: {'peptide': 437} Link IDs: {'CIS': 11, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 405} Chain breaks: 5 Chain: "j" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3449 Classifications: {'peptide': 437} Link IDs: {'CIS': 11, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 405} Chain breaks: 5 Chain: "k" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3449 Classifications: {'peptide': 437} Link IDs: {'CIS': 11, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 405} Chain breaks: 5 Chain: "l" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3449 Classifications: {'peptide': 437} Link IDs: {'CIS': 11, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 405} Chain breaks: 5 Time building chain proxies: 10.28, per 1000 atoms: 0.25 Number of scatterers: 41388 At special positions: 0 Unit cell: (179.07, 179.07, 125.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 216 16.00 O 8052 8.00 N 6960 7.00 C 26160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=48, symmetry=0 Number of additional bonds: simple=48, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.12 Conformation dependent library (CDL) restraints added in 1.8 seconds 10200 Ramachandran restraints generated. 5100 Oldfield, 0 Emsley, 5100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9888 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 36 sheets defined 49.7% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'a' and resid 16 through 24 Processing helix chain 'a' and resid 24 through 37 Processing helix chain 'a' and resid 59 through 78 removed outlier: 3.789A pdb=" N LEU a 66 " --> pdb=" O GLY a 62 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN a 67 " --> pdb=" O ALA a 63 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER a 71 " --> pdb=" O ASN a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 122 removed outlier: 4.042A pdb=" N GLU a 122 " --> pdb=" O MET a 118 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 138 removed outlier: 4.085A pdb=" N THR a 129 " --> pdb=" O SER a 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN a 136 " --> pdb=" O GLU a 132 " (cutoff:3.500A) Processing helix chain 'a' and resid 268 through 272 Processing helix chain 'a' and resid 274 through 295 removed outlier: 3.523A pdb=" N SER a 278 " --> pdb=" O GLY a 274 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE a 292 " --> pdb=" O LYS a 288 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER a 293 " --> pdb=" O MET a 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER a 294 " --> pdb=" O SER a 290 " (cutoff:3.500A) Processing helix chain 'a' and resid 307 through 314 removed outlier: 3.560A pdb=" N THR a 312 " --> pdb=" O PRO a 308 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS a 313 " --> pdb=" O ARG a 309 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA a 314 " --> pdb=" O ARG a 310 " (cutoff:3.500A) Processing helix chain 'a' and resid 337 through 354 removed outlier: 3.571A pdb=" N ALA a 341 " --> pdb=" O ASP a 337 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE a 354 " --> pdb=" O ALA a 350 " (cutoff:3.500A) Processing helix chain 'a' and resid 370 through 385 removed outlier: 3.582A pdb=" N ASP a 383 " --> pdb=" O SER a 379 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR a 384 " --> pdb=" O GLU a 380 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU a 385 " --> pdb=" O LEU a 381 " (cutoff:3.500A) Processing helix chain 'a' and resid 385 through 396 removed outlier: 4.013A pdb=" N SER a 390 " --> pdb=" O GLY a 386 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE a 391 " --> pdb=" O GLY a 387 " (cutoff:3.500A) Processing helix chain 'a' and resid 396 through 408 Processing helix chain 'a' and resid 435 through 452 removed outlier: 3.574A pdb=" N ARG a 444 " --> pdb=" O ASP a 440 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N CYS a 445 " --> pdb=" O LYS a 441 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL a 446 " --> pdb=" O LEU a 442 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA a 451 " --> pdb=" O THR a 447 " (cutoff:3.500A) Processing helix chain 'a' and resid 453 through 457 removed outlier: 4.572A pdb=" N ASP a 457 " --> pdb=" O PRO a 454 " (cutoff:3.500A) Processing helix chain 'a' and resid 462 through 474 Processing helix chain 'a' and resid 484 through 486 No H-bonds generated for 'chain 'a' and resid 484 through 486' Processing helix chain 'a' and resid 487 through 492 removed outlier: 4.312A pdb=" N LYS a 491 " --> pdb=" O GLN a 487 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 24 Processing helix chain 'b' and resid 24 through 37 Processing helix chain 'b' and resid 59 through 78 removed outlier: 3.789A pdb=" N LEU b 66 " --> pdb=" O GLY b 62 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN b 67 " --> pdb=" O ALA b 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER b 71 " --> pdb=" O ASN b 67 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 4.041A pdb=" N GLU b 122 " --> pdb=" O MET b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 138 removed outlier: 4.086A pdb=" N THR b 129 " --> pdb=" O SER b 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN b 136 " --> pdb=" O GLU b 132 " (cutoff:3.500A) Processing helix chain 'b' and resid 268 through 272 Processing helix chain 'b' and resid 274 through 295 removed outlier: 3.522A pdb=" N SER b 278 " --> pdb=" O GLY b 274 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE b 292 " --> pdb=" O LYS b 288 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER b 293 " --> pdb=" O MET b 289 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER b 294 " --> pdb=" O SER b 290 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 314 removed outlier: 3.559A pdb=" N THR b 312 " --> pdb=" O PRO b 308 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS b 313 " --> pdb=" O ARG b 309 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA b 314 " --> pdb=" O ARG b 310 " (cutoff:3.500A) Processing helix chain 'b' and resid 337 through 354 removed outlier: 3.569A pdb=" N ALA b 341 " --> pdb=" O ASP b 337 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE b 354 " --> pdb=" O ALA b 350 " (cutoff:3.500A) Processing helix chain 'b' and resid 370 through 385 removed outlier: 3.585A pdb=" N ASP b 383 " --> pdb=" O SER b 379 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR b 384 " --> pdb=" O GLU b 380 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU b 385 " --> pdb=" O LEU b 381 " (cutoff:3.500A) Processing helix chain 'b' and resid 385 through 396 removed outlier: 4.013A pdb=" N SER b 390 " --> pdb=" O GLY b 386 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE b 391 " --> pdb=" O GLY b 387 " (cutoff:3.500A) Processing helix chain 'b' and resid 396 through 408 Processing helix chain 'b' and resid 435 through 452 removed outlier: 3.573A pdb=" N ARG b 444 " --> pdb=" O ASP b 440 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N CYS b 445 " --> pdb=" O LYS b 441 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL b 446 " --> pdb=" O LEU b 442 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA b 451 " --> pdb=" O THR b 447 " (cutoff:3.500A) Processing helix chain 'b' and resid 453 through 457 removed outlier: 4.574A pdb=" N ASP b 457 " --> pdb=" O PRO b 454 " (cutoff:3.500A) Processing helix chain 'b' and resid 462 through 474 Processing helix chain 'b' and resid 484 through 486 No H-bonds generated for 'chain 'b' and resid 484 through 486' Processing helix chain 'b' and resid 487 through 492 removed outlier: 4.310A pdb=" N LYS b 491 " --> pdb=" O GLN b 487 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 24 Processing helix chain 'c' and resid 24 through 37 Processing helix chain 'c' and resid 59 through 78 removed outlier: 3.786A pdb=" N LEU c 66 " --> pdb=" O GLY c 62 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN c 67 " --> pdb=" O ALA c 63 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER c 71 " --> pdb=" O ASN c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 102 through 122 removed outlier: 4.040A pdb=" N GLU c 122 " --> pdb=" O MET c 118 " (cutoff:3.500A) Processing helix chain 'c' and resid 125 through 138 removed outlier: 4.087A pdb=" N THR c 129 " --> pdb=" O SER c 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN c 136 " --> pdb=" O GLU c 132 " (cutoff:3.500A) Processing helix chain 'c' and resid 268 through 272 Processing helix chain 'c' and resid 274 through 295 removed outlier: 3.521A pdb=" N SER c 278 " --> pdb=" O GLY c 274 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE c 292 " --> pdb=" O LYS c 288 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER c 293 " --> pdb=" O MET c 289 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER c 294 " --> pdb=" O SER c 290 " (cutoff:3.500A) Processing helix chain 'c' and resid 307 through 314 removed outlier: 3.558A pdb=" N THR c 312 " --> pdb=" O PRO c 308 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS c 313 " --> pdb=" O ARG c 309 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA c 314 " --> pdb=" O ARG c 310 " (cutoff:3.500A) Processing helix chain 'c' and resid 337 through 354 removed outlier: 3.568A pdb=" N ALA c 341 " --> pdb=" O ASP c 337 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE c 354 " --> pdb=" O ALA c 350 " (cutoff:3.500A) Processing helix chain 'c' and resid 370 through 385 removed outlier: 3.582A pdb=" N ASP c 383 " --> pdb=" O SER c 379 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR c 384 " --> pdb=" O GLU c 380 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU c 385 " --> pdb=" O LEU c 381 " (cutoff:3.500A) Processing helix chain 'c' and resid 385 through 396 removed outlier: 4.011A pdb=" N SER c 390 " --> pdb=" O GLY c 386 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE c 391 " --> pdb=" O GLY c 387 " (cutoff:3.500A) Processing helix chain 'c' and resid 396 through 408 Processing helix chain 'c' and resid 435 through 452 removed outlier: 3.575A pdb=" N ARG c 444 " --> pdb=" O ASP c 440 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N CYS c 445 " --> pdb=" O LYS c 441 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL c 446 " --> pdb=" O LEU c 442 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA c 451 " --> pdb=" O THR c 447 " (cutoff:3.500A) Processing helix chain 'c' and resid 453 through 457 removed outlier: 4.573A pdb=" N ASP c 457 " --> pdb=" O PRO c 454 " (cutoff:3.500A) Processing helix chain 'c' and resid 462 through 474 Processing helix chain 'c' and resid 484 through 486 No H-bonds generated for 'chain 'c' and resid 484 through 486' Processing helix chain 'c' and resid 487 through 492 removed outlier: 4.308A pdb=" N LYS c 491 " --> pdb=" O GLN c 487 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 24 Processing helix chain 'd' and resid 24 through 37 Processing helix chain 'd' and resid 59 through 78 removed outlier: 3.789A pdb=" N LEU d 66 " --> pdb=" O GLY d 62 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN d 67 " --> pdb=" O ALA d 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER d 71 " --> pdb=" O ASN d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 102 through 122 removed outlier: 4.041A pdb=" N GLU d 122 " --> pdb=" O MET d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 125 through 138 removed outlier: 4.085A pdb=" N THR d 129 " --> pdb=" O SER d 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN d 136 " --> pdb=" O GLU d 132 " (cutoff:3.500A) Processing helix chain 'd' and resid 268 through 272 Processing helix chain 'd' and resid 274 through 295 removed outlier: 3.521A pdb=" N SER d 278 " --> pdb=" O GLY d 274 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE d 292 " --> pdb=" O LYS d 288 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER d 293 " --> pdb=" O MET d 289 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER d 294 " --> pdb=" O SER d 290 " (cutoff:3.500A) Processing helix chain 'd' and resid 307 through 314 removed outlier: 3.558A pdb=" N THR d 312 " --> pdb=" O PRO d 308 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS d 313 " --> pdb=" O ARG d 309 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA d 314 " --> pdb=" O ARG d 310 " (cutoff:3.500A) Processing helix chain 'd' and resid 337 through 354 removed outlier: 3.569A pdb=" N ALA d 341 " --> pdb=" O ASP d 337 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE d 354 " --> pdb=" O ALA d 350 " (cutoff:3.500A) Processing helix chain 'd' and resid 370 through 385 removed outlier: 3.582A pdb=" N ASP d 383 " --> pdb=" O SER d 379 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR d 384 " --> pdb=" O GLU d 380 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU d 385 " --> pdb=" O LEU d 381 " (cutoff:3.500A) Processing helix chain 'd' and resid 385 through 396 removed outlier: 4.012A pdb=" N SER d 390 " --> pdb=" O GLY d 386 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE d 391 " --> pdb=" O GLY d 387 " (cutoff:3.500A) Processing helix chain 'd' and resid 396 through 408 Processing helix chain 'd' and resid 435 through 452 removed outlier: 3.574A pdb=" N ARG d 444 " --> pdb=" O ASP d 440 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N CYS d 445 " --> pdb=" O LYS d 441 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL d 446 " --> pdb=" O LEU d 442 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA d 451 " --> pdb=" O THR d 447 " (cutoff:3.500A) Processing helix chain 'd' and resid 453 through 457 removed outlier: 4.574A pdb=" N ASP d 457 " --> pdb=" O PRO d 454 " (cutoff:3.500A) Processing helix chain 'd' and resid 462 through 474 Processing helix chain 'd' and resid 484 through 486 No H-bonds generated for 'chain 'd' and resid 484 through 486' Processing helix chain 'd' and resid 487 through 492 removed outlier: 4.312A pdb=" N LYS d 491 " --> pdb=" O GLN d 487 " (cutoff:3.500A) Processing helix chain 'e' and resid 16 through 24 Processing helix chain 'e' and resid 24 through 37 Processing helix chain 'e' and resid 59 through 78 removed outlier: 3.789A pdb=" N LEU e 66 " --> pdb=" O GLY e 62 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN e 67 " --> pdb=" O ALA e 63 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER e 71 " --> pdb=" O ASN e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 102 through 122 removed outlier: 4.042A pdb=" N GLU e 122 " --> pdb=" O MET e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 125 through 138 removed outlier: 4.086A pdb=" N THR e 129 " --> pdb=" O SER e 125 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN e 136 " --> pdb=" O GLU e 132 " (cutoff:3.500A) Processing helix chain 'e' and resid 268 through 272 Processing helix chain 'e' and resid 274 through 295 removed outlier: 3.523A pdb=" N SER e 278 " --> pdb=" O GLY e 274 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE e 292 " --> pdb=" O LYS e 288 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER e 293 " --> pdb=" O MET e 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER e 294 " --> pdb=" O SER e 290 " (cutoff:3.500A) Processing helix chain 'e' and resid 307 through 314 removed outlier: 3.558A pdb=" N THR e 312 " --> pdb=" O PRO e 308 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS e 313 " --> pdb=" O ARG e 309 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA e 314 " --> pdb=" O ARG e 310 " (cutoff:3.500A) Processing helix chain 'e' and resid 337 through 354 removed outlier: 3.568A pdb=" N ALA e 341 " --> pdb=" O ASP e 337 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE e 354 " --> pdb=" O ALA e 350 " (cutoff:3.500A) Processing helix chain 'e' and resid 370 through 385 removed outlier: 3.583A pdb=" N ASP e 383 " --> pdb=" O SER e 379 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR e 384 " --> pdb=" O GLU e 380 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU e 385 " --> pdb=" O LEU e 381 " (cutoff:3.500A) Processing helix chain 'e' and resid 385 through 396 removed outlier: 4.014A pdb=" N SER e 390 " --> pdb=" O GLY e 386 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE e 391 " --> pdb=" O GLY e 387 " (cutoff:3.500A) Processing helix chain 'e' and resid 396 through 408 Processing helix chain 'e' and resid 435 through 452 removed outlier: 3.574A pdb=" N ARG e 444 " --> pdb=" O ASP e 440 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N CYS e 445 " --> pdb=" O LYS e 441 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL e 446 " --> pdb=" O LEU e 442 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA e 451 " --> pdb=" O THR e 447 " (cutoff:3.500A) Processing helix chain 'e' and resid 453 through 457 removed outlier: 4.573A pdb=" N ASP e 457 " --> pdb=" O PRO e 454 " (cutoff:3.500A) Processing helix chain 'e' and resid 462 through 474 Processing helix chain 'e' and resid 484 through 486 No H-bonds generated for 'chain 'e' and resid 484 through 486' Processing helix chain 'e' and resid 487 through 492 removed outlier: 4.312A pdb=" N LYS e 491 " --> pdb=" O GLN e 487 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 24 Processing helix chain 'f' and resid 24 through 37 Processing helix chain 'f' and resid 59 through 78 removed outlier: 3.789A pdb=" N LEU f 66 " --> pdb=" O GLY f 62 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN f 67 " --> pdb=" O ALA f 63 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER f 71 " --> pdb=" O ASN f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 102 through 122 removed outlier: 4.042A pdb=" N GLU f 122 " --> pdb=" O MET f 118 " (cutoff:3.500A) Processing helix chain 'f' and resid 125 through 138 removed outlier: 4.086A pdb=" N THR f 129 " --> pdb=" O SER f 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN f 136 " --> pdb=" O GLU f 132 " (cutoff:3.500A) Processing helix chain 'f' and resid 268 through 272 Processing helix chain 'f' and resid 274 through 295 removed outlier: 3.522A pdb=" N SER f 278 " --> pdb=" O GLY f 274 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE f 292 " --> pdb=" O LYS f 288 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER f 293 " --> pdb=" O MET f 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER f 294 " --> pdb=" O SER f 290 " (cutoff:3.500A) Processing helix chain 'f' and resid 307 through 314 removed outlier: 3.557A pdb=" N THR f 312 " --> pdb=" O PRO f 308 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS f 313 " --> pdb=" O ARG f 309 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA f 314 " --> pdb=" O ARG f 310 " (cutoff:3.500A) Processing helix chain 'f' and resid 337 through 354 removed outlier: 3.569A pdb=" N ALA f 341 " --> pdb=" O ASP f 337 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE f 354 " --> pdb=" O ALA f 350 " (cutoff:3.500A) Processing helix chain 'f' and resid 370 through 385 removed outlier: 3.583A pdb=" N ASP f 383 " --> pdb=" O SER f 379 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR f 384 " --> pdb=" O GLU f 380 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU f 385 " --> pdb=" O LEU f 381 " (cutoff:3.500A) Processing helix chain 'f' and resid 385 through 396 removed outlier: 4.014A pdb=" N SER f 390 " --> pdb=" O GLY f 386 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE f 391 " --> pdb=" O GLY f 387 " (cutoff:3.500A) Processing helix chain 'f' and resid 396 through 408 Processing helix chain 'f' and resid 435 through 452 removed outlier: 3.574A pdb=" N ARG f 444 " --> pdb=" O ASP f 440 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N CYS f 445 " --> pdb=" O LYS f 441 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL f 446 " --> pdb=" O LEU f 442 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA f 451 " --> pdb=" O THR f 447 " (cutoff:3.500A) Processing helix chain 'f' and resid 453 through 457 removed outlier: 4.573A pdb=" N ASP f 457 " --> pdb=" O PRO f 454 " (cutoff:3.500A) Processing helix chain 'f' and resid 462 through 474 Processing helix chain 'f' and resid 484 through 486 No H-bonds generated for 'chain 'f' and resid 484 through 486' Processing helix chain 'f' and resid 487 through 492 removed outlier: 4.311A pdb=" N LYS f 491 " --> pdb=" O GLN f 487 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 24 Processing helix chain 'g' and resid 24 through 37 Processing helix chain 'g' and resid 59 through 78 removed outlier: 3.790A pdb=" N LEU g 66 " --> pdb=" O GLY g 62 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN g 67 " --> pdb=" O ALA g 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER g 71 " --> pdb=" O ASN g 67 " (cutoff:3.500A) Processing helix chain 'g' and resid 102 through 122 removed outlier: 4.041A pdb=" N GLU g 122 " --> pdb=" O MET g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 125 through 138 removed outlier: 4.087A pdb=" N THR g 129 " --> pdb=" O SER g 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN g 136 " --> pdb=" O GLU g 132 " (cutoff:3.500A) Processing helix chain 'g' and resid 268 through 272 Processing helix chain 'g' and resid 274 through 295 removed outlier: 3.523A pdb=" N SER g 278 " --> pdb=" O GLY g 274 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE g 292 " --> pdb=" O LYS g 288 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER g 293 " --> pdb=" O MET g 289 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER g 294 " --> pdb=" O SER g 290 " (cutoff:3.500A) Processing helix chain 'g' and resid 307 through 314 removed outlier: 3.559A pdb=" N THR g 312 " --> pdb=" O PRO g 308 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS g 313 " --> pdb=" O ARG g 309 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA g 314 " --> pdb=" O ARG g 310 " (cutoff:3.500A) Processing helix chain 'g' and resid 337 through 354 removed outlier: 3.569A pdb=" N ALA g 341 " --> pdb=" O ASP g 337 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE g 354 " --> pdb=" O ALA g 350 " (cutoff:3.500A) Processing helix chain 'g' and resid 370 through 385 removed outlier: 3.583A pdb=" N ASP g 383 " --> pdb=" O SER g 379 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR g 384 " --> pdb=" O GLU g 380 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU g 385 " --> pdb=" O LEU g 381 " (cutoff:3.500A) Processing helix chain 'g' and resid 385 through 396 removed outlier: 4.012A pdb=" N SER g 390 " --> pdb=" O GLY g 386 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE g 391 " --> pdb=" O GLY g 387 " (cutoff:3.500A) Processing helix chain 'g' and resid 396 through 408 Processing helix chain 'g' and resid 435 through 452 removed outlier: 3.573A pdb=" N ARG g 444 " --> pdb=" O ASP g 440 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N CYS g 445 " --> pdb=" O LYS g 441 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL g 446 " --> pdb=" O LEU g 442 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA g 451 " --> pdb=" O THR g 447 " (cutoff:3.500A) Processing helix chain 'g' and resid 453 through 457 removed outlier: 4.572A pdb=" N ASP g 457 " --> pdb=" O PRO g 454 " (cutoff:3.500A) Processing helix chain 'g' and resid 462 through 474 Processing helix chain 'g' and resid 484 through 486 No H-bonds generated for 'chain 'g' and resid 484 through 486' Processing helix chain 'g' and resid 487 through 492 removed outlier: 4.310A pdb=" N LYS g 491 " --> pdb=" O GLN g 487 " (cutoff:3.500A) Processing helix chain 'h' and resid 16 through 24 Processing helix chain 'h' and resid 24 through 37 Processing helix chain 'h' and resid 59 through 78 removed outlier: 3.787A pdb=" N LEU h 66 " --> pdb=" O GLY h 62 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN h 67 " --> pdb=" O ALA h 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER h 71 " --> pdb=" O ASN h 67 " (cutoff:3.500A) Processing helix chain 'h' and resid 102 through 122 removed outlier: 4.040A pdb=" N GLU h 122 " --> pdb=" O MET h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 125 through 138 removed outlier: 4.086A pdb=" N THR h 129 " --> pdb=" O SER h 125 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN h 136 " --> pdb=" O GLU h 132 " (cutoff:3.500A) Processing helix chain 'h' and resid 268 through 272 Processing helix chain 'h' and resid 274 through 295 removed outlier: 3.521A pdb=" N SER h 278 " --> pdb=" O GLY h 274 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE h 292 " --> pdb=" O LYS h 288 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER h 293 " --> pdb=" O MET h 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER h 294 " --> pdb=" O SER h 290 " (cutoff:3.500A) Processing helix chain 'h' and resid 307 through 314 removed outlier: 3.558A pdb=" N THR h 312 " --> pdb=" O PRO h 308 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS h 313 " --> pdb=" O ARG h 309 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA h 314 " --> pdb=" O ARG h 310 " (cutoff:3.500A) Processing helix chain 'h' and resid 337 through 354 removed outlier: 3.568A pdb=" N ALA h 341 " --> pdb=" O ASP h 337 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE h 354 " --> pdb=" O ALA h 350 " (cutoff:3.500A) Processing helix chain 'h' and resid 370 through 385 removed outlier: 3.582A pdb=" N ASP h 383 " --> pdb=" O SER h 379 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR h 384 " --> pdb=" O GLU h 380 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU h 385 " --> pdb=" O LEU h 381 " (cutoff:3.500A) Processing helix chain 'h' and resid 385 through 396 removed outlier: 4.013A pdb=" N SER h 390 " --> pdb=" O GLY h 386 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE h 391 " --> pdb=" O GLY h 387 " (cutoff:3.500A) Processing helix chain 'h' and resid 396 through 408 Processing helix chain 'h' and resid 435 through 452 removed outlier: 3.573A pdb=" N ARG h 444 " --> pdb=" O ASP h 440 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N CYS h 445 " --> pdb=" O LYS h 441 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL h 446 " --> pdb=" O LEU h 442 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA h 451 " --> pdb=" O THR h 447 " (cutoff:3.500A) Processing helix chain 'h' and resid 453 through 457 removed outlier: 4.572A pdb=" N ASP h 457 " --> pdb=" O PRO h 454 " (cutoff:3.500A) Processing helix chain 'h' and resid 462 through 474 Processing helix chain 'h' and resid 484 through 486 No H-bonds generated for 'chain 'h' and resid 484 through 486' Processing helix chain 'h' and resid 487 through 492 removed outlier: 4.311A pdb=" N LYS h 491 " --> pdb=" O GLN h 487 " (cutoff:3.500A) Processing helix chain 'i' and resid 16 through 24 Processing helix chain 'i' and resid 24 through 37 Processing helix chain 'i' and resid 59 through 78 removed outlier: 3.789A pdb=" N LEU i 66 " --> pdb=" O GLY i 62 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN i 67 " --> pdb=" O ALA i 63 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER i 71 " --> pdb=" O ASN i 67 " (cutoff:3.500A) Processing helix chain 'i' and resid 102 through 122 removed outlier: 4.041A pdb=" N GLU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 125 through 138 removed outlier: 4.086A pdb=" N THR i 129 " --> pdb=" O SER i 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN i 136 " --> pdb=" O GLU i 132 " (cutoff:3.500A) Processing helix chain 'i' and resid 268 through 272 Processing helix chain 'i' and resid 274 through 295 removed outlier: 3.522A pdb=" N SER i 278 " --> pdb=" O GLY i 274 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE i 292 " --> pdb=" O LYS i 288 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER i 293 " --> pdb=" O MET i 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER i 294 " --> pdb=" O SER i 290 " (cutoff:3.500A) Processing helix chain 'i' and resid 307 through 314 removed outlier: 3.559A pdb=" N THR i 312 " --> pdb=" O PRO i 308 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS i 313 " --> pdb=" O ARG i 309 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA i 314 " --> pdb=" O ARG i 310 " (cutoff:3.500A) Processing helix chain 'i' and resid 337 through 354 removed outlier: 3.567A pdb=" N ALA i 341 " --> pdb=" O ASP i 337 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE i 354 " --> pdb=" O ALA i 350 " (cutoff:3.500A) Processing helix chain 'i' and resid 370 through 385 removed outlier: 3.583A pdb=" N ASP i 383 " --> pdb=" O SER i 379 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR i 384 " --> pdb=" O GLU i 380 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU i 385 " --> pdb=" O LEU i 381 " (cutoff:3.500A) Processing helix chain 'i' and resid 385 through 396 removed outlier: 4.012A pdb=" N SER i 390 " --> pdb=" O GLY i 386 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE i 391 " --> pdb=" O GLY i 387 " (cutoff:3.500A) Processing helix chain 'i' and resid 396 through 408 Processing helix chain 'i' and resid 435 through 452 removed outlier: 3.573A pdb=" N ARG i 444 " --> pdb=" O ASP i 440 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS i 445 " --> pdb=" O LYS i 441 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL i 446 " --> pdb=" O LEU i 442 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA i 451 " --> pdb=" O THR i 447 " (cutoff:3.500A) Processing helix chain 'i' and resid 453 through 457 removed outlier: 4.573A pdb=" N ASP i 457 " --> pdb=" O PRO i 454 " (cutoff:3.500A) Processing helix chain 'i' and resid 462 through 474 Processing helix chain 'i' and resid 484 through 486 No H-bonds generated for 'chain 'i' and resid 484 through 486' Processing helix chain 'i' and resid 487 through 492 removed outlier: 4.310A pdb=" N LYS i 491 " --> pdb=" O GLN i 487 " (cutoff:3.500A) Processing helix chain 'j' and resid 16 through 24 Processing helix chain 'j' and resid 24 through 37 Processing helix chain 'j' and resid 59 through 78 removed outlier: 3.789A pdb=" N LEU j 66 " --> pdb=" O GLY j 62 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN j 67 " --> pdb=" O ALA j 63 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER j 71 " --> pdb=" O ASN j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 102 through 122 removed outlier: 4.041A pdb=" N GLU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 125 through 138 removed outlier: 4.086A pdb=" N THR j 129 " --> pdb=" O SER j 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN j 136 " --> pdb=" O GLU j 132 " (cutoff:3.500A) Processing helix chain 'j' and resid 268 through 272 Processing helix chain 'j' and resid 274 through 295 removed outlier: 3.522A pdb=" N SER j 278 " --> pdb=" O GLY j 274 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE j 292 " --> pdb=" O LYS j 288 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER j 293 " --> pdb=" O MET j 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER j 294 " --> pdb=" O SER j 290 " (cutoff:3.500A) Processing helix chain 'j' and resid 307 through 314 removed outlier: 3.557A pdb=" N THR j 312 " --> pdb=" O PRO j 308 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS j 313 " --> pdb=" O ARG j 309 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA j 314 " --> pdb=" O ARG j 310 " (cutoff:3.500A) Processing helix chain 'j' and resid 337 through 354 removed outlier: 3.567A pdb=" N ALA j 341 " --> pdb=" O ASP j 337 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE j 354 " --> pdb=" O ALA j 350 " (cutoff:3.500A) Processing helix chain 'j' and resid 370 through 385 removed outlier: 3.580A pdb=" N ASP j 383 " --> pdb=" O SER j 379 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR j 384 " --> pdb=" O GLU j 380 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU j 385 " --> pdb=" O LEU j 381 " (cutoff:3.500A) Processing helix chain 'j' and resid 385 through 396 removed outlier: 4.013A pdb=" N SER j 390 " --> pdb=" O GLY j 386 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE j 391 " --> pdb=" O GLY j 387 " (cutoff:3.500A) Processing helix chain 'j' and resid 396 through 408 Processing helix chain 'j' and resid 435 through 452 removed outlier: 3.574A pdb=" N ARG j 444 " --> pdb=" O ASP j 440 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N CYS j 445 " --> pdb=" O LYS j 441 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL j 446 " --> pdb=" O LEU j 442 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA j 451 " --> pdb=" O THR j 447 " (cutoff:3.500A) Processing helix chain 'j' and resid 453 through 457 removed outlier: 4.572A pdb=" N ASP j 457 " --> pdb=" O PRO j 454 " (cutoff:3.500A) Processing helix chain 'j' and resid 462 through 474 Processing helix chain 'j' and resid 484 through 486 No H-bonds generated for 'chain 'j' and resid 484 through 486' Processing helix chain 'j' and resid 487 through 492 removed outlier: 4.312A pdb=" N LYS j 491 " --> pdb=" O GLN j 487 " (cutoff:3.500A) Processing helix chain 'k' and resid 16 through 24 Processing helix chain 'k' and resid 24 through 37 Processing helix chain 'k' and resid 59 through 78 removed outlier: 3.789A pdb=" N LEU k 66 " --> pdb=" O GLY k 62 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN k 67 " --> pdb=" O ALA k 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER k 71 " --> pdb=" O ASN k 67 " (cutoff:3.500A) Processing helix chain 'k' and resid 102 through 122 removed outlier: 4.042A pdb=" N GLU k 122 " --> pdb=" O MET k 118 " (cutoff:3.500A) Processing helix chain 'k' and resid 125 through 138 removed outlier: 4.086A pdb=" N THR k 129 " --> pdb=" O SER k 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN k 136 " --> pdb=" O GLU k 132 " (cutoff:3.500A) Processing helix chain 'k' and resid 268 through 272 Processing helix chain 'k' and resid 274 through 295 removed outlier: 3.522A pdb=" N SER k 278 " --> pdb=" O GLY k 274 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE k 292 " --> pdb=" O LYS k 288 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER k 293 " --> pdb=" O MET k 289 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER k 294 " --> pdb=" O SER k 290 " (cutoff:3.500A) Processing helix chain 'k' and resid 307 through 314 removed outlier: 3.558A pdb=" N THR k 312 " --> pdb=" O PRO k 308 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS k 313 " --> pdb=" O ARG k 309 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA k 314 " --> pdb=" O ARG k 310 " (cutoff:3.500A) Processing helix chain 'k' and resid 337 through 354 removed outlier: 3.568A pdb=" N ALA k 341 " --> pdb=" O ASP k 337 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE k 354 " --> pdb=" O ALA k 350 " (cutoff:3.500A) Processing helix chain 'k' and resid 370 through 385 removed outlier: 3.584A pdb=" N ASP k 383 " --> pdb=" O SER k 379 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR k 384 " --> pdb=" O GLU k 380 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU k 385 " --> pdb=" O LEU k 381 " (cutoff:3.500A) Processing helix chain 'k' and resid 385 through 396 removed outlier: 4.013A pdb=" N SER k 390 " --> pdb=" O GLY k 386 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE k 391 " --> pdb=" O GLY k 387 " (cutoff:3.500A) Processing helix chain 'k' and resid 396 through 408 Processing helix chain 'k' and resid 435 through 452 removed outlier: 3.573A pdb=" N ARG k 444 " --> pdb=" O ASP k 440 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N CYS k 445 " --> pdb=" O LYS k 441 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL k 446 " --> pdb=" O LEU k 442 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA k 451 " --> pdb=" O THR k 447 " (cutoff:3.500A) Processing helix chain 'k' and resid 453 through 457 removed outlier: 4.574A pdb=" N ASP k 457 " --> pdb=" O PRO k 454 " (cutoff:3.500A) Processing helix chain 'k' and resid 462 through 474 Processing helix chain 'k' and resid 484 through 486 No H-bonds generated for 'chain 'k' and resid 484 through 486' Processing helix chain 'k' and resid 487 through 492 removed outlier: 4.312A pdb=" N LYS k 491 " --> pdb=" O GLN k 487 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 24 Processing helix chain 'l' and resid 24 through 37 Processing helix chain 'l' and resid 59 through 78 removed outlier: 3.791A pdb=" N LEU l 66 " --> pdb=" O GLY l 62 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN l 67 " --> pdb=" O ALA l 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER l 71 " --> pdb=" O ASN l 67 " (cutoff:3.500A) Processing helix chain 'l' and resid 102 through 122 removed outlier: 4.041A pdb=" N GLU l 122 " --> pdb=" O MET l 118 " (cutoff:3.500A) Processing helix chain 'l' and resid 125 through 138 removed outlier: 4.085A pdb=" N THR l 129 " --> pdb=" O SER l 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN l 136 " --> pdb=" O GLU l 132 " (cutoff:3.500A) Processing helix chain 'l' and resid 268 through 272 Processing helix chain 'l' and resid 274 through 295 removed outlier: 3.522A pdb=" N SER l 278 " --> pdb=" O GLY l 274 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE l 292 " --> pdb=" O LYS l 288 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER l 293 " --> pdb=" O MET l 289 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER l 294 " --> pdb=" O SER l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 307 through 314 removed outlier: 3.558A pdb=" N THR l 312 " --> pdb=" O PRO l 308 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS l 313 " --> pdb=" O ARG l 309 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA l 314 " --> pdb=" O ARG l 310 " (cutoff:3.500A) Processing helix chain 'l' and resid 337 through 354 removed outlier: 3.569A pdb=" N ALA l 341 " --> pdb=" O ASP l 337 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE l 354 " --> pdb=" O ALA l 350 " (cutoff:3.500A) Processing helix chain 'l' and resid 370 through 385 removed outlier: 3.583A pdb=" N ASP l 383 " --> pdb=" O SER l 379 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR l 384 " --> pdb=" O GLU l 380 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU l 385 " --> pdb=" O LEU l 381 " (cutoff:3.500A) Processing helix chain 'l' and resid 385 through 396 removed outlier: 4.012A pdb=" N SER l 390 " --> pdb=" O GLY l 386 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE l 391 " --> pdb=" O GLY l 387 " (cutoff:3.500A) Processing helix chain 'l' and resid 396 through 408 Processing helix chain 'l' and resid 435 through 452 removed outlier: 3.574A pdb=" N ARG l 444 " --> pdb=" O ASP l 440 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N CYS l 445 " --> pdb=" O LYS l 441 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL l 446 " --> pdb=" O LEU l 442 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA l 451 " --> pdb=" O THR l 447 " (cutoff:3.500A) Processing helix chain 'l' and resid 453 through 457 removed outlier: 4.573A pdb=" N ASP l 457 " --> pdb=" O PRO l 454 " (cutoff:3.500A) Processing helix chain 'l' and resid 462 through 474 Processing helix chain 'l' and resid 484 through 486 No H-bonds generated for 'chain 'l' and resid 484 through 486' Processing helix chain 'l' and resid 487 through 492 removed outlier: 4.312A pdb=" N LYS l 491 " --> pdb=" O GLN l 487 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 167 through 169 removed outlier: 3.860A pdb=" N GLN a 169 " --> pdb=" O GLN a 178 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLN a 178 " --> pdb=" O GLN a 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 214 through 216 Processing sheet with id=AA3, first strand: chain 'a' and resid 328 through 329 removed outlier: 5.357A pdb=" N GLY a 298 " --> pdb=" O VAL l 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 319 through 321 Processing sheet with id=AA5, first strand: chain 'b' and resid 167 through 169 removed outlier: 3.860A pdb=" N GLN b 169 " --> pdb=" O GLN b 178 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN b 178 " --> pdb=" O GLN b 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 214 through 216 Processing sheet with id=AA7, first strand: chain 'b' and resid 319 through 321 Processing sheet with id=AA8, first strand: chain 'c' and resid 167 through 169 removed outlier: 3.859A pdb=" N GLN c 169 " --> pdb=" O GLN c 178 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN c 178 " --> pdb=" O GLN c 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 214 through 216 Processing sheet with id=AB1, first strand: chain 'c' and resid 319 through 321 Processing sheet with id=AB2, first strand: chain 'd' and resid 167 through 169 removed outlier: 3.861A pdb=" N GLN d 169 " --> pdb=" O GLN d 178 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN d 178 " --> pdb=" O GLN d 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'd' and resid 214 through 216 Processing sheet with id=AB4, first strand: chain 'd' and resid 319 through 321 Processing sheet with id=AB5, first strand: chain 'e' and resid 167 through 169 removed outlier: 3.858A pdb=" N GLN e 169 " --> pdb=" O GLN e 178 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN e 178 " --> pdb=" O GLN e 169 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'e' and resid 214 through 216 Processing sheet with id=AB7, first strand: chain 'e' and resid 319 through 321 Processing sheet with id=AB8, first strand: chain 'f' and resid 167 through 169 removed outlier: 3.861A pdb=" N GLN f 169 " --> pdb=" O GLN f 178 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN f 178 " --> pdb=" O GLN f 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'f' and resid 214 through 216 Processing sheet with id=AC1, first strand: chain 'f' and resid 319 through 321 Processing sheet with id=AC2, first strand: chain 'g' and resid 167 through 169 removed outlier: 3.859A pdb=" N GLN g 169 " --> pdb=" O GLN g 178 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN g 178 " --> pdb=" O GLN g 169 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'g' and resid 214 through 216 Processing sheet with id=AC4, first strand: chain 'g' and resid 319 through 321 Processing sheet with id=AC5, first strand: chain 'h' and resid 167 through 169 removed outlier: 3.858A pdb=" N GLN h 169 " --> pdb=" O GLN h 178 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN h 178 " --> pdb=" O GLN h 169 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'h' and resid 214 through 216 Processing sheet with id=AC7, first strand: chain 'h' and resid 319 through 321 Processing sheet with id=AC8, first strand: chain 'i' and resid 167 through 169 removed outlier: 3.860A pdb=" N GLN i 169 " --> pdb=" O GLN i 178 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLN i 178 " --> pdb=" O GLN i 169 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'i' and resid 214 through 216 Processing sheet with id=AD1, first strand: chain 'i' and resid 319 through 321 Processing sheet with id=AD2, first strand: chain 'j' and resid 167 through 169 removed outlier: 3.859A pdb=" N GLN j 169 " --> pdb=" O GLN j 178 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN j 178 " --> pdb=" O GLN j 169 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'j' and resid 214 through 216 Processing sheet with id=AD4, first strand: chain 'j' and resid 319 through 321 Processing sheet with id=AD5, first strand: chain 'k' and resid 167 through 169 removed outlier: 3.861A pdb=" N GLN k 169 " --> pdb=" O GLN k 178 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN k 178 " --> pdb=" O GLN k 169 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'k' and resid 214 through 216 Processing sheet with id=AD7, first strand: chain 'k' and resid 319 through 321 Processing sheet with id=AD8, first strand: chain 'l' and resid 167 through 169 removed outlier: 3.861A pdb=" N GLN l 169 " --> pdb=" O GLN l 178 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN l 178 " --> pdb=" O GLN l 169 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'l' and resid 214 through 216 1630 hydrogen bonds defined for protein. 4638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.14 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8221 1.32 - 1.45: 10765 1.45 - 1.58: 22582 1.58 - 1.71: 48 1.71 - 1.84: 396 Bond restraints: 42012 Sorted by residual: bond pdb=" CA VAL h 16 " pdb=" C VAL h 16 " ideal model delta sigma weight residual 1.522 1.641 -0.119 1.20e-02 6.94e+03 9.78e+01 bond pdb=" CA VAL c 16 " pdb=" C VAL c 16 " ideal model delta sigma weight residual 1.522 1.641 -0.118 1.20e-02 6.94e+03 9.69e+01 bond pdb=" CA VAL e 16 " pdb=" C VAL e 16 " ideal model delta sigma weight residual 1.522 1.641 -0.118 1.20e-02 6.94e+03 9.67e+01 bond pdb=" CA VAL f 16 " pdb=" C VAL f 16 " ideal model delta sigma weight residual 1.522 1.640 -0.118 1.20e-02 6.94e+03 9.59e+01 bond pdb=" CA VAL i 16 " pdb=" C VAL i 16 " ideal model delta sigma weight residual 1.522 1.640 -0.117 1.20e-02 6.94e+03 9.56e+01 ... (remaining 42007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.74: 53680 4.74 - 9.48: 2439 9.48 - 14.23: 488 14.23 - 18.97: 165 18.97 - 23.71: 48 Bond angle restraints: 56820 Sorted by residual: angle pdb=" O LEU c 86 " pdb=" C LEU c 86 " pdb=" N THR c 87 " ideal model delta sigma weight residual 122.82 103.67 19.15 1.30e+00 5.92e-01 2.17e+02 angle pdb=" O LEU j 86 " pdb=" C LEU j 86 " pdb=" N THR j 87 " ideal model delta sigma weight residual 122.82 103.68 19.14 1.30e+00 5.92e-01 2.17e+02 angle pdb=" O LEU g 86 " pdb=" C LEU g 86 " pdb=" N THR g 87 " ideal model delta sigma weight residual 122.82 103.71 19.11 1.30e+00 5.92e-01 2.16e+02 angle pdb=" O LEU d 86 " pdb=" C LEU d 86 " pdb=" N THR d 87 " ideal model delta sigma weight residual 122.82 103.73 19.09 1.30e+00 5.92e-01 2.16e+02 angle pdb=" O LEU e 86 " pdb=" C LEU e 86 " pdb=" N THR e 87 " ideal model delta sigma weight residual 122.82 103.73 19.09 1.30e+00 5.92e-01 2.16e+02 ... (remaining 56815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.60: 22816 24.60 - 49.21: 2472 49.21 - 73.81: 548 73.81 - 98.41: 60 98.41 - 123.01: 24 Dihedral angle restraints: 25920 sinusoidal: 10596 harmonic: 15324 Sorted by residual: dihedral pdb=" CA LYS k 14 " pdb=" C LYS k 14 " pdb=" N SER k 15 " pdb=" CA SER k 15 " ideal model delta harmonic sigma weight residual -180.00 -56.99 -123.01 0 5.00e+00 4.00e-02 6.05e+02 dihedral pdb=" CA LYS j 14 " pdb=" C LYS j 14 " pdb=" N SER j 15 " pdb=" CA SER j 15 " ideal model delta harmonic sigma weight residual -180.00 -57.08 -122.92 0 5.00e+00 4.00e-02 6.04e+02 dihedral pdb=" CA LYS b 14 " pdb=" C LYS b 14 " pdb=" N SER b 15 " pdb=" CA SER b 15 " ideal model delta harmonic sigma weight residual -180.00 -57.10 -122.90 0 5.00e+00 4.00e-02 6.04e+02 ... (remaining 25917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 5328 0.186 - 0.371: 921 0.371 - 0.557: 143 0.557 - 0.742: 64 0.742 - 0.928: 48 Chirality restraints: 6504 Sorted by residual: chirality pdb=" CA TYR l 251 " pdb=" N TYR l 251 " pdb=" C TYR l 251 " pdb=" CB TYR l 251 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" CA TYR g 251 " pdb=" N TYR g 251 " pdb=" C TYR g 251 " pdb=" CB TYR g 251 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" CA TYR k 251 " pdb=" N TYR k 251 " pdb=" C TYR k 251 " pdb=" CB TYR k 251 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.15e+01 ... (remaining 6501 not shown) Planarity restraints: 7344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU i 86 " 0.062 2.00e-02 2.50e+03 1.06e-01 1.12e+02 pdb=" C LEU i 86 " -0.183 2.00e-02 2.50e+03 pdb=" O LEU i 86 " 0.062 2.00e-02 2.50e+03 pdb=" N THR i 87 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU c 86 " -0.062 2.00e-02 2.50e+03 1.06e-01 1.12e+02 pdb=" C LEU c 86 " 0.183 2.00e-02 2.50e+03 pdb=" O LEU c 86 " -0.062 2.00e-02 2.50e+03 pdb=" N THR c 87 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU g 86 " 0.062 2.00e-02 2.50e+03 1.06e-01 1.12e+02 pdb=" C LEU g 86 " -0.183 2.00e-02 2.50e+03 pdb=" O LEU g 86 " 0.062 2.00e-02 2.50e+03 pdb=" N THR g 87 " 0.059 2.00e-02 2.50e+03 ... (remaining 7341 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.87: 528 1.87 - 2.63: 4169 2.63 - 3.39: 66280 3.39 - 4.14: 94159 4.14 - 4.90: 158790 Nonbonded interactions: 323926 Sorted by model distance: nonbonded pdb=" O TYR a 226 " pdb=" O THR a 243 " model vdw 1.115 3.040 nonbonded pdb=" O TYR h 226 " pdb=" O THR h 243 " model vdw 1.115 3.040 nonbonded pdb=" O TYR d 226 " pdb=" O THR d 243 " model vdw 1.115 3.040 nonbonded pdb=" O TYR b 226 " pdb=" O THR b 243 " model vdw 1.115 3.040 nonbonded pdb=" O TYR k 226 " pdb=" O THR k 243 " model vdw 1.115 3.040 ... (remaining 323921 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: 0.01 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 38.900 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 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 : 0.017 0.444 42060 Z= 1.405 Angle : 2.511 23.712 56820 Z= 1.601 Chirality : 0.170 0.928 6504 Planarity : 0.016 0.144 7344 Dihedral : 20.409 123.015 16032 Min Nonbonded Distance : 1.115 Molprobity Statistics. All-atom Clashscore : 151.45 Ramachandran Plot: Outliers : 5.12 % Allowed : 10.31 % Favored : 84.57 % Rotamer: Outliers : 28.18 % Allowed : 15.19 % Favored : 56.63 % Cbeta Deviations : 4.63 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.17 % Twisted Proline : 10.00 % Twisted General : 3.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.11), residues: 5100 helix: 1.49 (0.11), residues: 2028 sheet: -2.30 (0.34), residues: 240 loop : -3.16 (0.10), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG k 24 TYR 0.020 0.004 TYR d 376 PHE 0.023 0.003 PHE f 173 TRP 0.023 0.004 TRP d 449 HIS 0.002 0.001 HIS d 216 Details of bonding type rmsd covalent geometry : bond 0.01376 (42012) covalent geometry : angle 2.51116 (56820) hydrogen bonds : bond 0.31566 ( 1630) hydrogen bonds : angle 9.46587 ( 4638) Misc. bond : bond 0.29960 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10200 Ramachandran restraints generated. 5100 Oldfield, 0 Emsley, 5100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10200 Ramachandran restraints generated. 5100 Oldfield, 0 Emsley, 5100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 85 time to evaluate : 0.147 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 32 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7636 (mm110) REVERT: a 51 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7735 (t) REVERT: a 110 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7050 (mt) REVERT: a 118 MET cc_start: 0.6945 (mmt) cc_final: 0.6408 (mmt) REVERT: a 160 LEU cc_start: 0.8325 (mt) cc_final: 0.7743 (tt) REVERT: a 231 GLU cc_start: 0.7820 (pt0) cc_final: 0.7523 (pt0) REVERT: a 257 VAL cc_start: 0.8583 (t) cc_final: 0.8298 (t) REVERT: a 262 GLU cc_start: 0.5991 (mt-10) cc_final: 0.5613 (mt-10) REVERT: a 268 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.6739 (t80) REVERT: a 271 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7415 (tp30) REVERT: a 289 MET cc_start: 0.6378 (ttm) cc_final: 0.5092 (tpt) REVERT: a 315 GLN cc_start: 0.6529 (OUTLIER) cc_final: 0.6297 (mp10) REVERT: a 326 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.6335 (t0) REVERT: a 333 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: a 375 ARG cc_start: 0.8409 (tmt170) cc_final: 0.7921 (tmm-80) REVERT: a 391 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8558 (mm) REVERT: a 416 GLU cc_start: 0.4880 (mt-10) cc_final: 0.4588 (mm-30) REVERT: a 439 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6506 (mm) REVERT: a 457 ASP cc_start: 0.6454 (OUTLIER) cc_final: 0.5973 (p0) REVERT: a 461 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.6796 (pt) REVERT: a 465 MET cc_start: 0.7978 (tpt) cc_final: 0.7525 (tpp) outliers start: 106 outliers final: 54 residues processed: 176 average time/residue: 0.0914 time to fit residues: 18.6561 Evaluate side-chains 126 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 61 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 0.7980 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 10.0000 chunk 488 optimal weight: 0.0070 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 overall best weight: 2.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN f 156 ASN f 169 GLN ** f 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.092398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.082390 restraints weight = 13333.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083968 restraints weight = 8354.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.085071 restraints weight = 5812.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085846 restraints weight = 4409.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.086428 restraints weight = 3583.628| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 42060 Z= 0.264 Angle : 1.176 13.912 56820 Z= 0.609 Chirality : 0.061 0.338 6504 Planarity : 0.008 0.074 7344 Dihedral : 10.369 55.475 5748 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 1.65 % Allowed : 12.71 % Favored : 85.65 % Rotamer: Outliers : 1.06 % Allowed : 9.55 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.43 % Twisted Proline : 10.00 % Twisted General : 1.95 % 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: -2.12 (0.11), residues: 5100 helix: 0.16 (0.10), residues: 2268 sheet: -2.48 (0.33), residues: 192 loop : -2.89 (0.11), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG k 162 TYR 0.054 0.003 TYR j 251 PHE 0.016 0.002 PHE j 338 TRP 0.018 0.004 TRP h 58 HIS 0.004 0.003 HIS g 216 Details of bonding type rmsd covalent geometry : bond 0.00578 (42012) covalent geometry : angle 1.17629 (56820) hydrogen bonds : bond 0.07892 ( 1630) hydrogen bonds : angle 6.20196 ( 4638) Misc. bond : bond 0.00779 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 95 GLN cc_start: 0.6447 (tt0) cc_final: 0.6022 (tp40) REVERT: f 112 MET cc_start: 0.7453 (mtp) cc_final: 0.7206 (mtp) REVERT: f 122 GLU cc_start: 0.7412 (tt0) cc_final: 0.6792 (tp30) REVERT: f 257 VAL cc_start: 0.8583 (t) cc_final: 0.8347 (t) REVERT: f 271 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7087 (tp30) REVERT: f 331 GLN cc_start: 0.7442 (pm20) cc_final: 0.7178 (mm110) REVERT: f 375 ARG cc_start: 0.8267 (tmt170) cc_final: 0.8052 (mtt-85) REVERT: f 406 LYS cc_start: 0.8029 (mmpt) cc_final: 0.7725 (tmtt) outliers start: 4 outliers final: 1 residues processed: 100 average time/residue: 0.0711 time to fit residues: 8.7315 Evaluate side-chains 60 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 515 optimal weight: 0.7980 chunk 326 optimal weight: 0.2980 chunk 225 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 467 optimal weight: 10.0000 chunk 324 optimal weight: 3.9990 chunk 453 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 281 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 102 optimal weight: 0.0040 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 156 ASN ** a 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.096521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.086516 restraints weight = 12525.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.088059 restraints weight = 8216.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.089166 restraints weight = 5893.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.089942 restraints weight = 4553.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.090519 restraints weight = 3743.155| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.7657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 42060 Z= 0.194 Angle : 1.004 9.971 56820 Z= 0.514 Chirality : 0.053 0.251 6504 Planarity : 0.006 0.061 7344 Dihedral : 8.798 45.459 5748 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.71 % Allowed : 12.94 % Favored : 86.35 % Rotamer: Outliers : 0.53 % Allowed : 7.16 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.68 % Twisted Proline : 5.00 % Twisted General : 1.22 % 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: -2.42 (0.11), residues: 5100 helix: -0.17 (0.10), residues: 2388 sheet: -2.67 (0.28), residues: 240 loop : -3.07 (0.11), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 368 TYR 0.040 0.002 TYR l 251 PHE 0.019 0.002 PHE j 78 TRP 0.013 0.002 TRP k 58 HIS 0.004 0.002 HIS a 216 Details of bonding type rmsd covalent geometry : bond 0.00396 (42012) covalent geometry : angle 1.00409 (56820) hydrogen bonds : bond 0.05805 ( 1630) hydrogen bonds : angle 5.60175 ( 4638) Misc. bond : bond 0.00855 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8402 (mt) REVERT: a 112 MET cc_start: 0.7256 (mtp) cc_final: 0.6294 (mtp) REVERT: a 257 VAL cc_start: 0.8945 (t) cc_final: 0.8667 (p) REVERT: a 271 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7380 (mm-30) REVERT: a 292 ILE cc_start: 0.8935 (pt) cc_final: 0.8610 (mp) REVERT: a 306 THR cc_start: 0.6689 (p) cc_final: 0.6393 (p) outliers start: 2 outliers final: 0 residues processed: 89 average time/residue: 0.0616 time to fit residues: 6.8537 Evaluate side-chains 58 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 205 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 306 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 189 optimal weight: 7.9990 chunk 362 optimal weight: 4.9990 chunk 68 optimal weight: 0.0060 chunk 103 optimal weight: 8.9990 chunk 292 optimal weight: 1.9990 chunk 424 optimal weight: 4.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 81 GLN c 156 ASN ** c 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.094742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.084268 restraints weight = 13133.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085876 restraints weight = 8349.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.086959 restraints weight = 5896.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.087663 restraints weight = 4532.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088152 restraints weight = 3759.342| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.8165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 42060 Z= 0.218 Angle : 0.992 10.405 56820 Z= 0.511 Chirality : 0.052 0.238 6504 Planarity : 0.005 0.054 7344 Dihedral : 8.652 44.928 5748 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.71 % Allowed : 13.65 % Favored : 85.65 % Rotamer: Outliers : 0.27 % Allowed : 5.84 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.43 % Twisted Proline : 5.00 % Twisted General : 0.97 % 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: -2.48 (0.11), residues: 5100 helix: -0.39 (0.10), residues: 2376 sheet: -2.94 (0.25), residues: 312 loop : -2.84 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG i 162 TYR 0.045 0.003 TYR j 251 PHE 0.018 0.002 PHE d 338 TRP 0.009 0.003 TRP l 83 HIS 0.002 0.002 HIS l 216 Details of bonding type rmsd covalent geometry : bond 0.00468 (42012) covalent geometry : angle 0.99234 (56820) hydrogen bonds : bond 0.05884 ( 1630) hydrogen bonds : angle 5.66384 ( 4638) Misc. bond : bond 0.01113 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 95 GLN cc_start: 0.6700 (tt0) cc_final: 0.6065 (tp40) REVERT: c 112 MET cc_start: 0.7706 (mtp) cc_final: 0.7002 (mtp) REVERT: c 132 GLU cc_start: 0.6529 (tt0) cc_final: 0.6190 (tm-30) REVERT: c 173 PHE cc_start: 0.7593 (m-80) cc_final: 0.5946 (t80) REVERT: c 271 GLU cc_start: 0.7905 (mt-10) cc_final: 0.6973 (mm-30) REVERT: c 358 LEU cc_start: 0.8319 (mm) cc_final: 0.7781 (tp) REVERT: c 375 ARG cc_start: 0.8512 (tmm160) cc_final: 0.8289 (tmm160) REVERT: c 406 LYS cc_start: 0.7772 (mmpt) cc_final: 0.7466 (tptt) outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.0651 time to fit residues: 6.1332 Evaluate side-chains 54 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 229 optimal weight: 0.8980 chunk 324 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 328 optimal weight: 20.0000 chunk 511 optimal weight: 0.9990 chunk 399 optimal weight: 0.0870 chunk 413 optimal weight: 0.7980 chunk 509 optimal weight: 7.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.098346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.088079 restraints weight = 12930.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.089678 restraints weight = 8143.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.090771 restraints weight = 5655.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.091553 restraints weight = 4301.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.091966 restraints weight = 3520.621| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.8709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 42060 Z= 0.182 Angle : 0.944 9.915 56820 Z= 0.486 Chirality : 0.052 0.248 6504 Planarity : 0.005 0.051 7344 Dihedral : 8.066 40.152 5748 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.71 % Allowed : 14.12 % Favored : 85.18 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.43 % Twisted Proline : 5.00 % Twisted General : 1.46 % 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: -2.55 (0.11), residues: 5100 helix: -0.41 (0.11), residues: 2328 sheet: -2.79 (0.24), residues: 312 loop : -2.90 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG d 127 TYR 0.033 0.002 TYR h 251 PHE 0.028 0.002 PHE h 338 TRP 0.034 0.003 TRP h 449 HIS 0.003 0.002 HIS h 216 Details of bonding type rmsd covalent geometry : bond 0.00378 (42012) covalent geometry : angle 0.94394 (56820) hydrogen bonds : bond 0.05467 ( 1630) hydrogen bonds : angle 5.37339 ( 4638) Misc. bond : bond 0.01078 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: l 14 LYS cc_start: 0.6057 (tmmt) cc_final: 0.5712 (mmtm) REVERT: l 78 PHE cc_start: 0.7845 (p90) cc_final: 0.6982 (p90) REVERT: l 80 MET cc_start: 0.6392 (tpt) cc_final: 0.5501 (ttt) REVERT: l 95 GLN cc_start: 0.6560 (tt0) cc_final: 0.5962 (tp40) REVERT: l 112 MET cc_start: 0.7800 (mtp) cc_final: 0.7154 (mtp) REVERT: l 132 GLU cc_start: 0.6155 (tt0) cc_final: 0.5827 (tm-30) REVERT: l 160 LEU cc_start: 0.7717 (tp) cc_final: 0.7355 (tp) REVERT: l 173 PHE cc_start: 0.7465 (m-80) cc_final: 0.5597 (t80) REVERT: l 271 GLU cc_start: 0.7921 (mt-10) cc_final: 0.6721 (mm-30) REVERT: l 358 LEU cc_start: 0.8083 (mm) cc_final: 0.7541 (tp) REVERT: l 375 ARG cc_start: 0.8282 (tmm160) cc_final: 0.7774 (tmm160) REVERT: l 376 TYR cc_start: 0.7728 (t80) cc_final: 0.7270 (t80) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0693 time to fit residues: 6.0695 Evaluate side-chains 55 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 190 optimal weight: 0.9980 chunk 264 optimal weight: 0.7980 chunk 484 optimal weight: 4.9990 chunk 274 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 360 optimal weight: 10.0000 chunk 426 optimal weight: 0.0870 chunk 73 optimal weight: 0.0670 chunk 91 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 436 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.099494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.089962 restraints weight = 12806.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.091610 restraints weight = 7899.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.092779 restraints weight = 5395.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.093564 restraints weight = 4017.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.094136 restraints weight = 3210.823| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.9229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 42060 Z= 0.173 Angle : 0.933 9.627 56820 Z= 0.480 Chirality : 0.049 0.221 6504 Planarity : 0.005 0.049 7344 Dihedral : 7.769 47.458 5748 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.71 % Allowed : 14.82 % Favored : 84.47 % Rotamer: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.68 % Twisted Proline : 5.00 % Twisted General : 0.73 % 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: -2.66 (0.11), residues: 5100 helix: -0.64 (0.10), residues: 2388 sheet: -2.66 (0.24), residues: 312 loop : -2.88 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG k 127 TYR 0.035 0.002 TYR k 54 PHE 0.023 0.002 PHE h 338 TRP 0.022 0.002 TRP g 449 HIS 0.002 0.001 HIS c 216 Details of bonding type rmsd covalent geometry : bond 0.00360 (42012) covalent geometry : angle 0.93279 (56820) hydrogen bonds : bond 0.04970 ( 1630) hydrogen bonds : angle 5.15606 ( 4638) Misc. bond : bond 0.00813 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: l 14 LYS cc_start: 0.6536 (tmmt) cc_final: 0.6226 (mmtm) REVERT: l 80 MET cc_start: 0.6578 (tpt) cc_final: 0.5422 (ttt) REVERT: l 84 MET cc_start: 0.7865 (mmm) cc_final: 0.7603 (mmt) REVERT: l 95 GLN cc_start: 0.6622 (tt0) cc_final: 0.5999 (tp40) REVERT: l 101 ASP cc_start: 0.5023 (t70) cc_final: 0.4743 (p0) REVERT: l 112 MET cc_start: 0.7841 (mtp) cc_final: 0.7111 (mtp) REVERT: l 132 GLU cc_start: 0.6079 (tt0) cc_final: 0.5796 (tm-30) REVERT: l 160 LEU cc_start: 0.7875 (tp) cc_final: 0.7398 (tp) REVERT: l 173 PHE cc_start: 0.7634 (m-80) cc_final: 0.6023 (t80) REVERT: l 358 LEU cc_start: 0.8075 (mm) cc_final: 0.7495 (tp) REVERT: l 375 ARG cc_start: 0.8083 (tmm160) cc_final: 0.7734 (tmm160) REVERT: l 376 TYR cc_start: 0.7610 (t80) cc_final: 0.7079 (t80) REVERT: l 449 TRP cc_start: 0.7932 (m-10) cc_final: 0.7661 (m-90) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0669 time to fit residues: 6.0387 Evaluate side-chains 60 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 288 optimal weight: 5.9990 chunk 126 optimal weight: 0.0470 chunk 332 optimal weight: 0.0060 chunk 364 optimal weight: 8.9990 chunk 95 optimal weight: 0.2980 chunk 204 optimal weight: 0.9990 chunk 333 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 chunk 259 optimal weight: 8.9990 chunk 281 optimal weight: 0.0770 chunk 320 optimal weight: 6.9990 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 68 ASN ** i 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.102102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.092381 restraints weight = 12920.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.094122 restraints weight = 8070.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.095293 restraints weight = 5533.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.096136 restraints weight = 4126.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.096702 restraints weight = 3286.143| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.9689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 42060 Z= 0.172 Angle : 0.944 9.566 56820 Z= 0.482 Chirality : 0.049 0.270 6504 Planarity : 0.005 0.047 7344 Dihedral : 7.364 41.960 5748 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.94 % Allowed : 12.94 % Favored : 86.12 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 2.68 % Twisted Proline : 0.00 % Twisted General : 0.73 % 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: -2.58 (0.11), residues: 5100 helix: -0.53 (0.11), residues: 2340 sheet: -2.72 (0.25), residues: 312 loop : -2.83 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG j 170 TYR 0.030 0.002 TYR k 251 PHE 0.019 0.002 PHE c 78 TRP 0.017 0.002 TRP g 449 HIS 0.002 0.001 HIS b 216 Details of bonding type rmsd covalent geometry : bond 0.00346 (42012) covalent geometry : angle 0.94441 (56820) hydrogen bonds : bond 0.04862 ( 1630) hydrogen bonds : angle 5.15178 ( 4638) Misc. bond : bond 0.00781 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 14 LYS cc_start: 0.6781 (tmmt) cc_final: 0.6344 (mmtm) REVERT: i 80 MET cc_start: 0.6587 (tpt) cc_final: 0.5547 (mtp) REVERT: i 81 GLN cc_start: 0.7906 (pm20) cc_final: 0.7253 (mm-40) REVERT: i 84 MET cc_start: 0.7837 (mmm) cc_final: 0.7568 (mmt) REVERT: i 112 MET cc_start: 0.7747 (mtp) cc_final: 0.6975 (mtp) REVERT: i 132 GLU cc_start: 0.6090 (tt0) cc_final: 0.5791 (tm-30) REVERT: i 160 LEU cc_start: 0.7624 (tp) cc_final: 0.6667 (mp) REVERT: i 381 LEU cc_start: 0.8321 (tp) cc_final: 0.8022 (tp) REVERT: i 395 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7012 (tp30) REVERT: i 449 TRP cc_start: 0.7832 (m-10) cc_final: 0.7607 (m-90) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0728 time to fit residues: 6.9167 Evaluate side-chains 62 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 405 optimal weight: 0.6980 chunk 229 optimal weight: 0.9990 chunk 320 optimal weight: 3.9990 chunk 132 optimal weight: 0.0370 chunk 3 optimal weight: 0.5980 chunk 163 optimal weight: 4.9990 chunk 351 optimal weight: 0.2980 chunk 50 optimal weight: 0.0070 chunk 275 optimal weight: 8.9990 chunk 392 optimal weight: 5.9990 chunk 408 optimal weight: 0.9980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 283 GLN ** i 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.103211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.093649 restraints weight = 12892.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.095300 restraints weight = 8127.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.096455 restraints weight = 5689.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.097277 restraints weight = 4297.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.097768 restraints weight = 3449.416| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 1.0036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 42060 Z= 0.173 Angle : 0.929 10.619 56820 Z= 0.478 Chirality : 0.051 0.336 6504 Planarity : 0.006 0.085 7344 Dihedral : 7.210 46.231 5748 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.71 % Allowed : 14.35 % Favored : 84.94 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 2.68 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.91 (0.11), residues: 5100 helix: -0.71 (0.11), residues: 2352 sheet: -2.80 (0.24), residues: 312 loop : -3.15 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 127 TYR 0.032 0.002 TYR e 251 PHE 0.029 0.002 PHE c 338 TRP 0.013 0.002 TRP d 449 HIS 0.002 0.001 HIS j 216 Details of bonding type rmsd covalent geometry : bond 0.00358 (42012) covalent geometry : angle 0.92895 (56820) hydrogen bonds : bond 0.04684 ( 1630) hydrogen bonds : angle 5.13113 ( 4638) Misc. bond : bond 0.00900 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 14 LYS cc_start: 0.7056 (tmmt) cc_final: 0.6111 (mmtm) REVERT: i 80 MET cc_start: 0.6396 (tpt) cc_final: 0.5361 (mtp) REVERT: i 81 GLN cc_start: 0.7783 (pm20) cc_final: 0.7268 (mm-40) REVERT: i 84 MET cc_start: 0.7860 (mmm) cc_final: 0.7385 (mmt) REVERT: i 112 MET cc_start: 0.7783 (mtp) cc_final: 0.7024 (mtp) REVERT: i 126 TYR cc_start: 0.8272 (m-80) cc_final: 0.7875 (m-80) REVERT: i 132 GLU cc_start: 0.6126 (tt0) cc_final: 0.5736 (tm-30) REVERT: i 158 MET cc_start: 0.8369 (mtm) cc_final: 0.7954 (mpp) REVERT: i 160 LEU cc_start: 0.7655 (tp) cc_final: 0.6921 (tp) REVERT: i 381 LEU cc_start: 0.8384 (tp) cc_final: 0.8069 (tp) REVERT: i 449 TRP cc_start: 0.7844 (m-10) cc_final: 0.7619 (m-90) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0699 time to fit residues: 6.4675 Evaluate side-chains 60 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 223 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 280 optimal weight: 0.0020 chunk 323 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 335 optimal weight: 6.9990 chunk 431 optimal weight: 6.9990 chunk 62 optimal weight: 0.0050 chunk 21 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 overall best weight: 1.3406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 283 GLN a 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.103385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093902 restraints weight = 12888.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.095592 restraints weight = 8031.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.096743 restraints weight = 5611.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.097406 restraints weight = 4236.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.098086 restraints weight = 3492.129| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 1.0086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 42060 Z= 0.178 Angle : 0.934 9.722 56820 Z= 0.476 Chirality : 0.051 0.259 6504 Planarity : 0.006 0.071 7344 Dihedral : 7.216 42.695 5748 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.47 % Allowed : 15.29 % Favored : 84.24 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 2.68 % Twisted Proline : 0.00 % Twisted General : 0.73 % 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: -3.01 (0.11), residues: 5100 helix: -0.73 (0.10), residues: 2340 sheet: -2.85 (0.24), residues: 312 loop : -3.26 (0.11), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG j 170 TYR 0.031 0.002 TYR k 251 PHE 0.025 0.002 PHE k 338 TRP 0.019 0.002 TRP a 58 HIS 0.001 0.001 HIS i 216 Details of bonding type rmsd covalent geometry : bond 0.00382 (42012) covalent geometry : angle 0.93390 (56820) hydrogen bonds : bond 0.04730 ( 1630) hydrogen bonds : angle 4.94961 ( 4638) Misc. bond : bond 0.00780 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 14 LYS cc_start: 0.6817 (tmmt) cc_final: 0.6127 (mmtt) REVERT: a 80 MET cc_start: 0.6290 (tpt) cc_final: 0.5442 (mtt) REVERT: a 81 GLN cc_start: 0.7886 (pm20) cc_final: 0.7355 (mm-40) REVERT: a 95 GLN cc_start: 0.7061 (tt0) cc_final: 0.6816 (pt0) REVERT: a 112 MET cc_start: 0.7479 (mtp) cc_final: 0.6686 (mtp) REVERT: a 126 TYR cc_start: 0.7918 (m-80) cc_final: 0.7651 (m-80) REVERT: a 132 GLU cc_start: 0.6034 (tt0) cc_final: 0.5602 (tm-30) REVERT: a 160 LEU cc_start: 0.8043 (tp) cc_final: 0.7307 (mp) REVERT: a 173 PHE cc_start: 0.6663 (m-10) cc_final: 0.6183 (t80) REVERT: a 289 MET cc_start: 0.3391 (ttt) cc_final: 0.3144 (ttt) REVERT: a 385 LEU cc_start: 0.8847 (pp) cc_final: 0.8403 (pp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0730 time to fit residues: 6.5154 Evaluate side-chains 61 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 45 optimal weight: 8.9990 chunk 249 optimal weight: 4.9990 chunk 345 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 342 optimal weight: 0.8980 chunk 448 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 266 optimal weight: 0.0670 chunk 295 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 202 optimal weight: 0.0470 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.105396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.095353 restraints weight = 13023.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.097099 restraints weight = 8110.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.098341 restraints weight = 5666.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.099056 restraints weight = 4282.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.099659 restraints weight = 3524.811| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 1.0384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 42060 Z= 0.176 Angle : 0.998 12.013 56820 Z= 0.504 Chirality : 0.052 0.264 6504 Planarity : 0.006 0.071 7344 Dihedral : 6.998 36.275 5748 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.71 % Allowed : 15.29 % Favored : 84.00 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 2.68 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.23 (0.11), residues: 5100 helix: -0.88 (0.10), residues: 2316 sheet: -3.40 (0.25), residues: 240 loop : -3.35 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG l 127 TYR 0.030 0.002 TYR e 251 PHE 0.027 0.003 PHE e 338 TRP 0.018 0.003 TRP c 58 HIS 0.002 0.001 HIS c 216 Details of bonding type rmsd covalent geometry : bond 0.00370 (42012) covalent geometry : angle 0.99813 (56820) hydrogen bonds : bond 0.04647 ( 1630) hydrogen bonds : angle 5.05158 ( 4638) Misc. bond : bond 0.00826 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 14 LYS cc_start: 0.6869 (tmmt) cc_final: 0.6080 (mmtt) REVERT: a 80 MET cc_start: 0.5954 (tpt) cc_final: 0.5605 (ptm) REVERT: a 81 GLN cc_start: 0.7663 (pm20) cc_final: 0.7250 (mm-40) REVERT: a 95 GLN cc_start: 0.7123 (tt0) cc_final: 0.6813 (pt0) REVERT: a 112 MET cc_start: 0.7591 (mtp) cc_final: 0.6729 (mtp) REVERT: a 126 TYR cc_start: 0.7835 (m-80) cc_final: 0.7313 (m-80) REVERT: a 132 GLU cc_start: 0.6041 (tt0) cc_final: 0.5320 (tm-30) REVERT: a 144 LEU cc_start: 0.7249 (pt) cc_final: 0.6769 (pp) REVERT: a 160 LEU cc_start: 0.8054 (tp) cc_final: 0.7036 (mp) REVERT: a 173 PHE cc_start: 0.6651 (m-10) cc_final: 0.6136 (t80) REVERT: a 289 MET cc_start: 0.3675 (ttt) cc_final: 0.2688 (mtt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0697 time to fit residues: 6.3324 Evaluate side-chains 63 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 413 optimal weight: 0.2980 chunk 236 optimal weight: 0.5980 chunk 80 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 247 optimal weight: 7.9990 chunk 395 optimal weight: 0.4980 chunk 127 optimal weight: 0.5980 chunk 182 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 209 optimal weight: 10.0000 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** j 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.106849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.096460 restraints weight = 13242.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.098201 restraints weight = 8340.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.099507 restraints weight = 5833.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.100314 restraints weight = 4418.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.101007 restraints weight = 3606.207| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 1.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 42060 Z= 0.179 Angle : 0.973 10.556 56820 Z= 0.492 Chirality : 0.052 0.357 6504 Planarity : 0.008 0.153 7344 Dihedral : 7.067 42.981 5748 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.71 % Allowed : 14.35 % Favored : 84.94 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 2.68 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.42 (0.11), residues: 5100 helix: -1.04 (0.10), residues: 2424 sheet: -3.49 (0.23), residues: 240 loop : -3.53 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG i 127 TYR 0.028 0.001 TYR b 251 PHE 0.026 0.003 PHE l 131 TRP 0.015 0.002 TRP a 83 HIS 0.001 0.001 HIS d 216 Details of bonding type rmsd covalent geometry : bond 0.00385 (42012) covalent geometry : angle 0.97340 (56820) hydrogen bonds : bond 0.04819 ( 1630) hydrogen bonds : angle 5.02316 ( 4638) Misc. bond : bond 0.00818 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2311.78 seconds wall clock time: 43 minutes 8.85 seconds (2588.85 seconds total)