Starting phenix.real_space_refine on Tue Sep 15 15:29:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bp0_30138/09_2026/7bp0_30138.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bp0_30138/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7bp0_30138/09_2026/7bp0_30138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bp0_30138/09_2026/7bp0_30138.map" model { file = "/net/cci-nas-00/data/ceres_data/7bp0_30138/09_2026/7bp0_30138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bp0_30138/09_2026/7bp0_30138.cif" } 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-2.2.1-6174/lib/python3.11/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: 9.23, per 1000 atoms: 0.22 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: 4.08 Conformation dependent library (CDL) restraints added in 1.7 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: 1.01 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: 7.86 Time building geometry restraints manager: 5.24 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: 0.02 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 37.090 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.120 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 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/Z covalent geometry : bond 0.01376 / 0.97 (42012) covalent geometry : angle 2.51116 / 1.60 (56820) hydrogen bonds : bond 0.31566 / 20.54 ( 1630) hydrogen bonds : angle 9.46587 / 6.56 ( 4638) Misc. bond : bond 0.29960 / 19.72 ( 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 : 0.172 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: 0.0887 time to fit residues: 18.2017 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 : 0.137 ------------------------------------------------------------------------------- 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... ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 81 GLN a 156 ASN a 169 GLN a 281 ASN ** a 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.092393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.082381 restraints weight = 13325.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083956 restraints weight = 8382.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.085058 restraints weight = 5830.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.085758 restraints weight = 4421.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.086370 restraints weight = 3623.780| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.6454 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 : 25.57 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/Z covalent geometry : bond 0.00578 / 0.26 (42012) covalent geometry : angle 1.17629 / 0.61 (56820) hydrogen bonds : bond 0.07892 / 5.16 ( 1630) hydrogen bonds : angle 6.20196 / 4.34 ( 4638) Misc. bond : bond 0.00779 / 0.54 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 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 100 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 95 GLN cc_start: 0.6454 (tt0) cc_final: 0.6038 (tp40) REVERT: f 112 MET cc_start: 0.7452 (mtp) cc_final: 0.7226 (mtp) REVERT: f 122 GLU cc_start: 0.7414 (tt0) cc_final: 0.6912 (tp30) REVERT: f 257 VAL cc_start: 0.8585 (t) cc_final: 0.8351 (t) REVERT: f 271 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7090 (tp30) REVERT: f 331 GLN cc_start: 0.7445 (pm20) cc_final: 0.7180 (mm110) REVERT: f 375 ARG cc_start: 0.8272 (tmt170) cc_final: 0.8053 (mtt-85) REVERT: f 406 LYS cc_start: 0.8029 (mmpt) cc_final: 0.7729 (tmtt) outliers start: 4 outliers final: 1 residues processed: 99 average time/residue: 0.0666 time to fit residues: 8.1094 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 : 0.129 ------------------------------------------------------------------------------- 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: 0.9990 chunk 326 optimal weight: 0.2980 chunk 225 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 467 optimal weight: 10.0000 chunk 324 optimal weight: 3.9990 chunk 453 optimal weight: 5.9990 chunk 236 optimal weight: 0.0270 chunk 281 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 102 optimal weight: 0.0040 overall best weight: 0.4252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** f 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 156 ASN ** f 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 = 0.3563 r_free = 0.3563 target = 0.098238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.088261 restraints weight = 12692.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.089864 restraints weight = 8267.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.090866 restraints weight = 5883.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.091783 restraints weight = 4568.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092311 restraints weight = 3710.914| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.7736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 42060 Z= 0.196 Angle : 1.010 9.909 56820 Z= 0.516 Chirality : 0.053 0.253 6504 Planarity : 0.006 0.057 7344 Dihedral : 8.746 45.749 5748 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.71 % Allowed : 12.47 % Favored : 86.82 % Rotamer: Outliers : 0.53 % Allowed : 6.90 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.68 % 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: -2.33 (0.11), residues: 5100 helix: -0.05 (0.10), residues: 2388 sheet: -2.72 (0.25), residues: 312 loop : -3.05 (0.11), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG l 368 TYR 0.038 0.002 TYR k 251 PHE 0.020 0.002 PHE l 78 TRP 0.013 0.002 TRP k 58 HIS 0.004 0.002 HIS i 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (42012) covalent geometry : angle 1.01003 / 0.52 (56820) hydrogen bonds : bond 0.05800 / 3.79 ( 1630) hydrogen bonds : angle 5.56281 / 3.90 ( 4638) Misc. bond : bond 0.00893 / 0.59 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 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 92 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: a 42 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8271 (mt) REVERT: a 112 MET cc_start: 0.7257 (mtp) cc_final: 0.6287 (mtp) REVERT: a 122 GLU cc_start: 0.6829 (tt0) cc_final: 0.5918 (tp30) REVERT: a 257 VAL cc_start: 0.8846 (t) cc_final: 0.8564 (p) REVERT: a 271 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7405 (tp30) REVERT: a 292 ILE cc_start: 0.8905 (pt) cc_final: 0.8554 (mp) REVERT: a 401 VAL cc_start: 0.8724 (t) cc_final: 0.8275 (t) outliers start: 2 outliers final: 0 residues processed: 92 average time/residue: 0.0602 time to fit residues: 6.9461 Evaluate side-chains 52 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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: 0.0060 chunk 216 optimal weight: 6.9990 chunk 306 optimal weight: 7.9990 chunk 253 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 189 optimal weight: 7.9990 chunk 362 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 292 optimal weight: 0.0170 chunk 424 optimal weight: 10.0000 overall best weight: 0.7236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3596 r_free = 0.3596 target = 0.099427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.089212 restraints weight = 12636.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.090854 restraints weight = 8070.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.091973 restraints weight = 5676.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.092701 restraints weight = 4332.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.093324 restraints weight = 3556.024| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.8600 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= 0.182 Angle : 0.949 9.960 56820 Z= 0.487 Chirality : 0.051 0.240 6504 Planarity : 0.005 0.051 7344 Dihedral : 8.341 42.766 5748 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.71 % Allowed : 12.71 % Favored : 86.59 % Rotamer: Outliers : 0.53 % Allowed : 6.90 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.43 % 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: -2.24 (0.11), residues: 5100 helix: -0.03 (0.11), residues: 2304 sheet: -2.93 (0.24), residues: 312 loop : -2.80 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG i 162 TYR 0.037 0.002 TYR f 251 PHE 0.023 0.002 PHE b 338 TRP 0.034 0.004 TRP k 449 HIS 0.003 0.002 HIS b 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 (42012) covalent geometry : angle 0.94921 / 0.49 (56820) hydrogen bonds : bond 0.05195 / 3.38 ( 1630) hydrogen bonds : angle 5.17292 / 3.62 ( 4638) Misc. bond : bond 0.00802 / 0.55 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 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 87 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 80 MET cc_start: 0.8160 (tpt) cc_final: 0.7866 (tpt) REVERT: c 95 GLN cc_start: 0.6771 (tt0) cc_final: 0.6109 (tp40) REVERT: c 112 MET cc_start: 0.7712 (mtp) cc_final: 0.7025 (mtp) REVERT: c 132 GLU cc_start: 0.6080 (tt0) cc_final: 0.5728 (tm-30) REVERT: c 160 LEU cc_start: 0.7240 (tp) cc_final: 0.6750 (mp) REVERT: c 173 PHE cc_start: 0.7394 (m-80) cc_final: 0.5576 (t80) REVERT: c 271 GLU cc_start: 0.8004 (mt-10) cc_final: 0.6696 (tp30) REVERT: c 356 PHE cc_start: 0.8942 (m-10) cc_final: 0.8700 (m-80) REVERT: c 358 LEU cc_start: 0.7937 (mm) cc_final: 0.7512 (tp) REVERT: c 375 ARG cc_start: 0.8492 (tmm160) cc_final: 0.7992 (tmm160) outliers start: 2 outliers final: 0 residues processed: 86 average time/residue: 0.0612 time to fit residues: 6.5783 Evaluate side-chains 59 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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: 0.9990 chunk 324 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 0.0000 chunk 328 optimal weight: 30.0000 chunk 511 optimal weight: 0.2980 chunk 399 optimal weight: 6.9990 chunk 413 optimal weight: 9.9990 chunk 509 optimal weight: 8.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 156 ASN ** c 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 = 0.3602 r_free = 0.3602 target = 0.100215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090732 restraints weight = 13021.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092245 restraints weight = 8349.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.093301 restraints weight = 5940.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.094064 restraints weight = 4564.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.094550 restraints weight = 3733.459| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.9105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 42060 Z= 0.174 Angle : 0.954 9.848 56820 Z= 0.489 Chirality : 0.051 0.214 6504 Planarity : 0.006 0.072 7344 Dihedral : 7.942 38.150 5748 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.71 % Allowed : 13.65 % Favored : 85.65 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: -2.24 (0.11), residues: 5100 helix: -0.19 (0.11), residues: 2388 sheet: -2.86 (0.23), residues: 312 loop : -2.71 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG g 127 TYR 0.034 0.002 TYR d 251 PHE 0.018 0.002 PHE k 78 TRP 0.063 0.006 TRP k 449 HIS 0.002 0.001 HIS b 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (42012) covalent geometry : angle 0.95447 / 0.49 (56820) hydrogen bonds : bond 0.04874 / 3.18 ( 1630) hydrogen bonds : angle 5.07991 / 3.57 ( 4638) Misc. bond : bond 0.00905 / 0.60 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 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 78 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 14 LYS cc_start: 0.6195 (tmmt) cc_final: 0.5746 (mmtm) REVERT: i 80 MET cc_start: 0.7227 (tpt) cc_final: 0.5718 (ttt) REVERT: i 101 ASP cc_start: 0.5015 (t70) cc_final: 0.4588 (p0) REVERT: i 112 MET cc_start: 0.7782 (mtp) cc_final: 0.7031 (mtp) REVERT: i 160 LEU cc_start: 0.7257 (tp) cc_final: 0.6916 (mp) REVERT: i 173 PHE cc_start: 0.7351 (m-80) cc_final: 0.5824 (t80) REVERT: i 271 GLU cc_start: 0.8050 (mt-10) cc_final: 0.6706 (mm-30) REVERT: i 289 MET cc_start: 0.4407 (ttm) cc_final: 0.4138 (tpp) REVERT: i 292 ILE cc_start: 0.8508 (pt) cc_final: 0.8278 (mp) REVERT: i 305 ILE cc_start: 0.7909 (pt) cc_final: 0.7611 (pt) REVERT: i 356 PHE cc_start: 0.8651 (m-10) cc_final: 0.8373 (m-80) REVERT: i 357 MET cc_start: 0.8087 (mmm) cc_final: 0.7884 (tpt) REVERT: i 358 LEU cc_start: 0.8195 (mm) cc_final: 0.7687 (tp) REVERT: i 375 ARG cc_start: 0.8339 (tmm160) cc_final: 0.8135 (tmm160) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0619 time to fit residues: 6.0635 Evaluate side-chains 58 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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: 0.9990 chunk 264 optimal weight: 0.9980 chunk 484 optimal weight: 0.4980 chunk 274 optimal weight: 8.9990 chunk 216 optimal weight: 2.9990 chunk 360 optimal weight: 10.0000 chunk 426 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 436 optimal weight: 0.0980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... i 68 ASN i 156 ASN ** i 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 = 0.3631 r_free = 0.3631 target = 0.101912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.092259 restraints weight = 12631.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.093698 restraints weight = 8264.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.094833 restraints weight = 5938.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.095589 restraints weight = 4579.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.096135 restraints weight = 3757.885| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.9542 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= 0.170 Angle : 0.939 9.773 56820 Z= 0.478 Chirality : 0.049 0.193 6504 Planarity : 0.005 0.049 7344 Dihedral : 7.638 36.202 5748 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.71 % Allowed : 12.47 % Favored : 86.82 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: -2.23 (0.12), residues: 5100 helix: -0.07 (0.11), residues: 2352 sheet: -2.77 (0.24), residues: 312 loop : -2.82 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG h 127 TYR 0.035 0.002 TYR h 251 PHE 0.020 0.001 PHE k 78 TRP 0.043 0.004 TRP e 449 HIS 0.002 0.001 HIS i 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (42012) covalent geometry : angle 0.93873 / 0.48 (56820) hydrogen bonds : bond 0.04715 / 3.07 ( 1630) hydrogen bonds : angle 4.86436 / 3.41 ( 4638) Misc. bond : bond 0.00909 / 0.60 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 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 75 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: a 14 LYS cc_start: 0.6604 (tmmt) cc_final: 0.6195 (mmtt) REVERT: a 80 MET cc_start: 0.6949 (tpt) cc_final: 0.5694 (ttt) REVERT: a 101 ASP cc_start: 0.4915 (t70) cc_final: 0.4436 (p0) REVERT: a 112 MET cc_start: 0.7483 (mtp) cc_final: 0.6476 (mtp) REVERT: a 137 LEU cc_start: 0.8114 (tt) cc_final: 0.7838 (tt) REVERT: a 144 LEU cc_start: 0.6818 (pt) cc_final: 0.6582 (pp) REVERT: a 173 PHE cc_start: 0.7578 (m-80) cc_final: 0.5730 (t80) REVERT: a 271 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7999 (mt-10) REVERT: a 356 PHE cc_start: 0.8708 (m-10) cc_final: 0.8484 (m-80) REVERT: a 358 LEU cc_start: 0.8274 (mm) cc_final: 0.7973 (tp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0656 time to fit residues: 6.1228 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 : 0.143 ------------------------------------------------------------------------------- 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: 1.9990 chunk 126 optimal weight: 6.9990 chunk 332 optimal weight: 7.9990 chunk 364 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 204 optimal weight: 4.9990 chunk 333 optimal weight: 0.6980 chunk 250 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 281 optimal weight: 5.9990 chunk 320 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 32 GLN a 68 ASN a 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.095155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.085165 restraints weight = 13113.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086592 restraints weight = 8679.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.087597 restraints weight = 6263.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088350 restraints weight = 4920.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.088872 restraints weight = 4096.791| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.9194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 42060 Z= 0.219 Angle : 0.988 10.308 56820 Z= 0.505 Chirality : 0.051 0.243 6504 Planarity : 0.006 0.077 7344 Dihedral : 7.952 39.847 5748 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.71 % Allowed : 13.88 % Favored : 85.41 % Rotamer: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.43 % 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: -2.33 (0.11), residues: 5100 helix: -0.23 (0.11), residues: 2376 sheet: -2.62 (0.28), residues: 240 loop : -2.86 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG h 64 TYR 0.038 0.003 TYR a 251 PHE 0.011 0.002 PHE i 338 TRP 0.034 0.004 TRP g 449 HIS 0.001 0.001 HIS h 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 (42012) covalent geometry : angle 0.98799 / 0.50 (56820) hydrogen bonds : bond 0.05245 / 3.40 ( 1630) hydrogen bonds : angle 5.21614 / 3.63 ( 4638) Misc. bond : bond 0.00952 / 0.61 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 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 58 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 14 LYS cc_start: 0.6854 (tmmt) cc_final: 0.6248 (mmtm) REVERT: a 80 MET cc_start: 0.6966 (tpt) cc_final: 0.5669 (ttt) REVERT: a 95 GLN cc_start: 0.7055 (tt0) cc_final: 0.6756 (pt0) REVERT: a 112 MET cc_start: 0.7545 (mtp) cc_final: 0.6537 (mtp) REVERT: a 173 PHE cc_start: 0.7763 (m-80) cc_final: 0.6073 (t80) REVERT: a 357 MET cc_start: 0.8328 (mmm) cc_final: 0.8060 (mmm) REVERT: a 395 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7133 (mm-30) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0629 time to fit residues: 4.6082 Evaluate side-chains 45 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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: 0.2980 chunk 320 optimal weight: 6.9990 chunk 132 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 351 optimal weight: 0.0050 chunk 50 optimal weight: 7.9990 chunk 275 optimal weight: 0.0030 chunk 392 optimal weight: 5.9990 chunk 408 optimal weight: 4.9990 overall best weight: 0.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.101229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.091084 restraints weight = 12851.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.092802 restraints weight = 8273.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.093959 restraints weight = 5825.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.094804 restraints weight = 4426.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.095330 restraints weight = 3594.787| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.9760 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= 0.173 Angle : 0.941 9.779 56820 Z= 0.479 Chirality : 0.050 0.236 6504 Planarity : 0.005 0.044 7344 Dihedral : 7.580 41.499 5748 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.71 % Allowed : 12.00 % Favored : 87.29 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.43 % 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: -2.36 (0.11), residues: 5100 helix: -0.07 (0.11), residues: 2292 sheet: -3.13 (0.23), residues: 312 loop : -2.89 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG b 170 TYR 0.032 0.002 TYR h 251 PHE 0.019 0.002 PHE b 78 TRP 0.031 0.003 TRP f 449 HIS 0.002 0.001 HIS g 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (42012) covalent geometry : angle 0.94063 / 0.48 (56820) hydrogen bonds : bond 0.04780 / 3.10 ( 1630) hydrogen bonds : angle 4.88493 / 3.44 ( 4638) Misc. bond : bond 0.01018 / 0.65 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 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 69 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: d 14 LYS cc_start: 0.6716 (tmmt) cc_final: 0.6204 (mmtt) REVERT: d 80 MET cc_start: 0.6729 (tpt) cc_final: 0.5736 (ttt) REVERT: d 84 MET cc_start: 0.8036 (mmm) cc_final: 0.7758 (mmm) REVERT: d 112 MET cc_start: 0.7776 (mtp) cc_final: 0.6943 (mtp) REVERT: d 132 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7472 (tt0) REVERT: d 173 PHE cc_start: 0.7453 (m-80) cc_final: 0.5874 (t80) REVERT: d 356 PHE cc_start: 0.8714 (m-10) cc_final: 0.8439 (m-80) REVERT: d 357 MET cc_start: 0.8417 (mmm) cc_final: 0.8150 (mmm) REVERT: d 358 LEU cc_start: 0.8162 (mm) cc_final: 0.7945 (tp) REVERT: d 375 ARG cc_start: 0.8244 (tmm160) cc_final: 0.7986 (tmm160) REVERT: d 385 LEU cc_start: 0.8786 (pp) cc_final: 0.8328 (pp) REVERT: d 449 TRP cc_start: 0.7632 (m-10) cc_final: 0.7381 (m-90) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0654 time to fit residues: 5.6335 Evaluate side-chains 52 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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: 6.9990 chunk 177 optimal weight: 7.9990 chunk 280 optimal weight: 5.9990 chunk 323 optimal weight: 0.0570 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 335 optimal weight: 5.9990 chunk 431 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 224 optimal weight: 0.5980 overall best weight: 2.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.098911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088897 restraints weight = 12973.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.090360 restraints weight = 8589.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.091427 restraints weight = 6272.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.092169 restraints weight = 4904.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.092735 restraints weight = 4068.310| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.9710 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= 0.189 Angle : 0.983 10.554 56820 Z= 0.497 Chirality : 0.052 0.255 6504 Planarity : 0.005 0.051 7344 Dihedral : 7.381 37.449 5748 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.71 % Allowed : 13.88 % Favored : 85.41 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -2.45 (0.11), residues: 5100 helix: -0.18 (0.11), residues: 2304 sheet: -3.10 (0.23), residues: 312 loop : -2.94 (0.11), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG b 277 TYR 0.038 0.002 TYR e 251 PHE 0.011 0.002 PHE k 78 TRP 0.025 0.003 TRP a 449 HIS 0.001 0.001 HIS l 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (42012) covalent geometry : angle 0.98335 / 0.50 (56820) hydrogen bonds : bond 0.05083 / 3.32 ( 1630) hydrogen bonds : angle 4.76246 / 3.34 ( 4638) Misc. bond : bond 0.01038 / 0.64 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 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 64 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: j 14 LYS cc_start: 0.6722 (tmmt) cc_final: 0.6158 (mmtm) REVERT: j 80 MET cc_start: 0.6760 (tpt) cc_final: 0.5373 (ttt) REVERT: j 81 GLN cc_start: 0.7985 (pm20) cc_final: 0.7373 (mm-40) REVERT: j 95 GLN cc_start: 0.7079 (tt0) cc_final: 0.6774 (pt0) REVERT: j 112 MET cc_start: 0.7530 (mtp) cc_final: 0.6633 (mtp) REVERT: j 132 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7725 (tt0) REVERT: j 173 PHE cc_start: 0.7628 (m-80) cc_final: 0.5980 (t80) REVERT: j 292 ILE cc_start: 0.8887 (pt) cc_final: 0.8659 (mp) REVERT: j 357 MET cc_start: 0.8283 (mmm) cc_final: 0.8052 (mmm) REVERT: j 358 LEU cc_start: 0.8273 (mm) cc_final: 0.8030 (tp) REVERT: j 449 TRP cc_start: 0.7621 (m-10) cc_final: 0.7366 (m-90) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0616 time to fit residues: 4.9797 Evaluate side-chains 52 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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: 0.0470 chunk 249 optimal weight: 0.9980 chunk 345 optimal weight: 9.9990 chunk 147 optimal weight: 0.3980 chunk 342 optimal weight: 0.7980 chunk 448 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 295 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 202 optimal weight: 0.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... j 156 ASN j 283 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 = 0.3652 r_free = 0.3652 target = 0.102580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.092234 restraints weight = 13015.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.093863 restraints weight = 8552.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.094891 restraints weight = 6162.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.095748 restraints weight = 4827.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.096349 restraints weight = 3971.376| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 1.0176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 42060 Z= 0.172 Angle : 0.947 10.490 56820 Z= 0.479 Chirality : 0.051 0.235 6504 Planarity : 0.006 0.086 7344 Dihedral : 7.189 34.415 5748 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.71 % Allowed : 12.24 % Favored : 87.06 % 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 : 0.49 % 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: -2.53 (0.11), residues: 5100 helix: -0.18 (0.11), residues: 2268 sheet: -3.35 (0.25), residues: 240 loop : -3.03 (0.11), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG j 170 TYR 0.030 0.002 TYR k 251 PHE 0.016 0.002 PHE l 78 TRP 0.043 0.006 TRP a 83 HIS 0.002 0.001 HIS l 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (42012) covalent geometry : angle 0.94702 / 0.48 (56820) hydrogen bonds : bond 0.04554 / 2.96 ( 1630) hydrogen bonds : angle 4.78699 / 3.35 ( 4638) Misc. bond : bond 0.01004 / 0.63 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 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 65 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: g 14 LYS cc_start: 0.7060 (tmmt) cc_final: 0.6105 (mmtt) REVERT: g 80 MET cc_start: 0.6374 (tpt) cc_final: 0.5583 (mtt) REVERT: g 81 GLN cc_start: 0.7702 (pm20) cc_final: 0.7173 (mm-40) REVERT: g 95 GLN cc_start: 0.7021 (tt0) cc_final: 0.6408 (tp40) REVERT: g 112 MET cc_start: 0.7675 (mtp) cc_final: 0.6821 (mtp) REVERT: g 132 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7511 (tt0) REVERT: g 356 PHE cc_start: 0.8790 (m-10) cc_final: 0.8443 (m-80) REVERT: g 395 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7421 (tp30) REVERT: g 449 TRP cc_start: 0.7554 (m-10) cc_final: 0.7303 (m-90) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0610 time to fit residues: 5.0057 Evaluate side-chains 58 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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: 5.9990 chunk 236 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 22 optimal weight: 0.0470 chunk 247 optimal weight: 4.9990 chunk 395 optimal weight: 0.3980 chunk 127 optimal weight: 0.7980 chunk 182 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 209 optimal weight: 10.0000 overall best weight: 1.2480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.100531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090402 restraints weight = 13265.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.092060 restraints weight = 8474.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.093192 restraints weight = 5967.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.093848 restraints weight = 4580.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.094500 restraints weight = 3806.112| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 1.0293 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= 0.172 Angle : 0.973 12.781 56820 Z= 0.483 Chirality : 0.050 0.222 6504 Planarity : 0.006 0.071 7344 Dihedral : 7.071 32.199 5748 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.47 % Favored : 87.06 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -2.42 (0.11), residues: 5100 helix: -0.02 (0.11), residues: 2364 sheet: -3.26 (0.25), residues: 240 loop : -3.15 (0.11), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 277 TYR 0.032 0.002 TYR g 251 PHE 0.011 0.001 PHE k 78 TRP 0.024 0.005 TRP h 449 HIS 0.002 0.001 HIS l 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (42012) covalent geometry : angle 0.97291 / 0.48 (56820) hydrogen bonds : bond 0.04459 / 2.90 ( 1630) hydrogen bonds : angle 4.67700 / 3.27 ( 4638) Misc. bond : bond 0.01013 / 0.62 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2510.49 seconds wall clock time: 46 minutes 18.21 seconds (2778.21 seconds total)