Starting phenix.real_space_refine on Sun Mar 24 12:05:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp0_30138/03_2024/7bp0_30138.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp0_30138/03_2024/7bp0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp0_30138/03_2024/7bp0_30138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp0_30138/03_2024/7bp0_30138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp0_30138/03_2024/7bp0_30138.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp0_30138/03_2024/7bp0_30138.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "a GLU 18": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 114": "OE1" <-> "OE2" Residue "a ARG 170": "NH1" <-> "NH2" Residue "a ARG 266": "NH1" <-> "NH2" Residue "a ARG 456": "NH1" <-> "NH2" Residue "b GLU 18": "OE1" <-> "OE2" Residue "b GLU 108": "OE1" <-> "OE2" Residue "b GLU 114": "OE1" <-> "OE2" Residue "b ARG 170": "NH1" <-> "NH2" Residue "b ARG 266": "NH1" <-> "NH2" Residue "b ARG 456": "NH1" <-> "NH2" Residue "c GLU 18": "OE1" <-> "OE2" Residue "c GLU 108": "OE1" <-> "OE2" Residue "c GLU 114": "OE1" <-> "OE2" Residue "c ARG 170": "NH1" <-> "NH2" Residue "c ARG 266": "NH1" <-> "NH2" Residue "c ARG 456": "NH1" <-> "NH2" Residue "d GLU 18": "OE1" <-> "OE2" Residue "d GLU 108": "OE1" <-> "OE2" Residue "d GLU 114": "OE1" <-> "OE2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ARG 266": "NH1" <-> "NH2" Residue "d ARG 456": "NH1" <-> "NH2" Residue "e GLU 18": "OE1" <-> "OE2" Residue "e GLU 108": "OE1" <-> "OE2" Residue "e GLU 114": "OE1" <-> "OE2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e ARG 266": "NH1" <-> "NH2" Residue "e ARG 456": "NH1" <-> "NH2" Residue "f GLU 18": "OE1" <-> "OE2" Residue "f GLU 108": "OE1" <-> "OE2" Residue "f GLU 114": "OE1" <-> "OE2" Residue "f ARG 170": "NH1" <-> "NH2" Residue "f ARG 266": "NH1" <-> "NH2" Residue "f ARG 456": "NH1" <-> "NH2" Residue "g GLU 18": "OE1" <-> "OE2" Residue "g GLU 108": "OE1" <-> "OE2" Residue "g GLU 114": "OE1" <-> "OE2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g ARG 266": "NH1" <-> "NH2" Residue "g ARG 456": "NH1" <-> "NH2" Residue "h GLU 18": "OE1" <-> "OE2" Residue "h GLU 108": "OE1" <-> "OE2" Residue "h GLU 114": "OE1" <-> "OE2" Residue "h ARG 170": "NH1" <-> "NH2" Residue "h ARG 266": "NH1" <-> "NH2" Residue "h ARG 456": "NH1" <-> "NH2" Residue "i GLU 18": "OE1" <-> "OE2" Residue "i GLU 108": "OE1" <-> "OE2" Residue "i GLU 114": "OE1" <-> "OE2" Residue "i ARG 170": "NH1" <-> "NH2" Residue "i ARG 266": "NH1" <-> "NH2" Residue "i ARG 456": "NH1" <-> "NH2" Residue "j GLU 18": "OE1" <-> "OE2" Residue "j GLU 108": "OE1" <-> "OE2" Residue "j GLU 114": "OE1" <-> "OE2" Residue "j ARG 170": "NH1" <-> "NH2" Residue "j ARG 266": "NH1" <-> "NH2" Residue "j ARG 456": "NH1" <-> "NH2" Residue "k GLU 18": "OE1" <-> "OE2" Residue "k GLU 108": "OE1" <-> "OE2" Residue "k GLU 114": "OE1" <-> "OE2" Residue "k ARG 170": "NH1" <-> "NH2" Residue "k ARG 266": "NH1" <-> "NH2" Residue "k ARG 456": "NH1" <-> "NH2" Residue "l GLU 18": "OE1" <-> "OE2" Residue "l GLU 108": "OE1" <-> "OE2" Residue "l GLU 114": "OE1" <-> "OE2" Residue "l ARG 170": "NH1" <-> "NH2" Residue "l ARG 266": "NH1" <-> "NH2" Residue "l ARG 456": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 20.81, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.36 Conformation dependent library (CDL) restraints added in 7.1 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: 3.88 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: 15.60 Time building geometry restraints manager: 18.57 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: 89.47 - 99.56: 96 99.56 - 109.65: 7867 109.65 - 119.74: 30187 119.74 - 129.83: 18418 129.83 - 139.91: 252 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: 588 1.87 - 2.63: 4265 2.63 - 3.39: 66316 3.39 - 4.14: 94159 4.14 - 4.90: 158790 Nonbonded interactions: 324118 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 324113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 10.350 Check model and map are aligned: 0.640 Set scattering table: 0.380 Process input model: 104.840 Find NCS groups from input model: 2.940 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.119 42012 Z= 0.895 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 : 151.43 Ramachandran Plot: Outliers : 5.12 % Allowed : 10.08 % Favored : 84.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.004 TRP d 449 HIS 0.002 0.001 HIS d 216 PHE 0.023 0.003 PHE f 173 TYR 0.020 0.004 TYR d 376 ARG 0.006 0.001 ARG k 24 *********************** 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 fitting. rotamer outliers: 106 poor density : 85 time to evaluate : 0.395 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: 0.7635 (mm110) REVERT: a 51 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7734 (t) REVERT: a 110 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7049 (mt) REVERT: a 118 MET cc_start: 0.6945 (mmt) cc_final: 0.6412 (mmt) REVERT: a 160 LEU cc_start: 0.8325 (mt) cc_final: 0.7739 (tt) REVERT: a 231 GLU cc_start: 0.7821 (pt0) cc_final: 0.7524 (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: 0.8229 (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: 0.6530 (OUTLIER) cc_final: 0.6297 (mp10) REVERT: a 326 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.6334 (t0) REVERT: a 333 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: a 375 ARG cc_start: 0.8408 (tmt170) cc_final: 0.7920 (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: 0.4603 (mm-30) REVERT: a 439 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6507 (mm) REVERT: a 457 ASP cc_start: 0.6454 (OUTLIER) cc_final: 0.5972 (p0) REVERT: a 461 ILE cc_start: 0.7322 (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: 0.1884 time to fit residues: 38.4232 Evaluate side-chains 126 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 61 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 435 optimal weight: 2.9990 chunk 391 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 208 optimal weight: 0.6980 chunk 404 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 245 optimal weight: 3.9990 chunk 301 optimal weight: 10.0000 chunk 468 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN ** f 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 169 GLN f 281 ASN ** f 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.6708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 42012 Z= 0.398 Angle : 1.153 12.464 56820 Z= 0.600 Chirality : 0.059 0.328 6504 Planarity : 0.008 0.072 7344 Dihedral : 10.330 54.214 5748 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 29.63 Ramachandran Plot: Outliers : 1.88 % Allowed : 11.29 % Favored : 86.82 % Rotamer: Outliers : 0.80 % Allowed : 9.55 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.43 % Twisted Proline : 10.00 % Twisted General : 1.70 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.11), residues: 5100 helix: -0.15 (0.10), residues: 2268 sheet: -2.28 (0.27), residues: 192 loop : -3.05 (0.11), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP c 449 HIS 0.007 0.004 HIS j 216 PHE 0.015 0.002 PHE k 338 TYR 0.053 0.003 TYR a 251 ARG 0.006 0.001 ARG a 469 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 42 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8296 (mt) REVERT: f 78 PHE cc_start: 0.6781 (p90) cc_final: 0.6421 (p90) REVERT: f 112 MET cc_start: 0.7611 (mtp) cc_final: 0.7255 (mtp) REVERT: f 122 GLU cc_start: 0.7447 (tt0) cc_final: 0.6891 (tp30) REVERT: f 257 VAL cc_start: 0.8632 (t) cc_final: 0.8197 (p) REVERT: f 262 GLU cc_start: 0.5398 (mt-10) cc_final: 0.5186 (tt0) REVERT: f 271 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7044 (mm-30) REVERT: f 395 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7343 (mt-10) REVERT: f 481 ILE cc_start: 0.7421 (tp) cc_final: 0.6618 (tp) outliers start: 3 outliers final: 0 residues processed: 93 average time/residue: 0.1505 time to fit residues: 17.1060 Evaluate side-chains 60 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 260 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 389 optimal weight: 0.7980 chunk 319 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 469 optimal weight: 0.0070 chunk 507 optimal weight: 0.6980 chunk 418 optimal weight: 0.1980 chunk 465 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 376 optimal weight: 5.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 59 GLN i 81 GLN ** i 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 487 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.8034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 42012 Z= 0.258 Angle : 0.982 9.966 56820 Z= 0.496 Chirality : 0.052 0.239 6504 Planarity : 0.006 0.059 7344 Dihedral : 8.554 44.231 5748 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 26.00 Ramachandran Plot: Outliers : 0.94 % Allowed : 13.18 % Favored : 85.88 % Rotamer: Outliers : 0.53 % Allowed : 9.02 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.68 % Twisted Proline : 5.00 % Twisted General : 0.97 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.11), residues: 5100 helix: -0.08 (0.10), residues: 2316 sheet: -2.06 (0.29), residues: 240 loop : -2.86 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP k 449 HIS 0.007 0.004 HIS l 216 PHE 0.015 0.002 PHE a 131 TYR 0.042 0.003 TYR k 251 ARG 0.006 0.001 ARG b 368 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: i 78 PHE cc_start: 0.6514 (p90) cc_final: 0.5714 (p90) REVERT: i 84 MET cc_start: 0.7999 (ttm) cc_final: 0.7783 (ttm) REVERT: i 112 MET cc_start: 0.7623 (mtp) cc_final: 0.7057 (mtp) REVERT: i 238 GLN cc_start: 0.7704 (mp10) cc_final: 0.7473 (mp10) REVERT: i 257 VAL cc_start: 0.8568 (t) cc_final: 0.8348 (p) REVERT: i 271 GLU cc_start: 0.7951 (mt-10) cc_final: 0.6824 (mm-30) REVERT: i 289 MET cc_start: 0.6728 (tpt) cc_final: 0.6514 (mmm) REVERT: i 306 THR cc_start: 0.6656 (p) cc_final: 0.6424 (p) REVERT: i 352 LEU cc_start: 0.9129 (tp) cc_final: 0.8910 (tp) REVERT: i 375 ARG cc_start: 0.8796 (mtt180) cc_final: 0.8036 (tmm160) REVERT: i 383 ASP cc_start: 0.8640 (m-30) cc_final: 0.8396 (m-30) REVERT: i 407 GLN cc_start: 0.7965 (mt0) cc_final: 0.7451 (pt0) outliers start: 2 outliers final: 1 residues processed: 96 average time/residue: 0.1563 time to fit residues: 18.5669 Evaluate side-chains 60 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 463 optimal weight: 6.9990 chunk 352 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 chunk 315 optimal weight: 5.9990 chunk 471 optimal weight: 1.9990 chunk 498 optimal weight: 10.0000 chunk 246 optimal weight: 0.8980 chunk 446 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 22 ASN ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 216 HIS ** d 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.8547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 42012 Z= 0.259 Angle : 0.939 10.615 56820 Z= 0.479 Chirality : 0.052 0.294 6504 Planarity : 0.006 0.053 7344 Dihedral : 8.242 39.588 5748 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 26.46 Ramachandran Plot: Outliers : 0.94 % Allowed : 13.88 % Favored : 85.18 % Rotamer: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.68 % Twisted Proline : 5.00 % Twisted General : 0.97 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.11), residues: 5100 helix: -0.42 (0.10), residues: 2280 sheet: -2.23 (0.26), residues: 240 loop : -2.82 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP j 58 HIS 0.004 0.003 HIS f 216 PHE 0.013 0.002 PHE b 78 TYR 0.034 0.003 TYR b 251 ARG 0.006 0.001 ARG b 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 95 GLN cc_start: 0.6982 (tt0) cc_final: 0.6576 (pt0) REVERT: d 112 MET cc_start: 0.7357 (mtp) cc_final: 0.6449 (mtp) REVERT: d 225 GLU cc_start: 0.6564 (mm-30) cc_final: 0.6222 (pm20) REVERT: d 271 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7298 (mm-30) REVERT: d 292 ILE cc_start: 0.8941 (pt) cc_final: 0.8717 (pt) REVERT: d 358 LEU cc_start: 0.8046 (mm) cc_final: 0.7717 (tp) REVERT: d 407 GLN cc_start: 0.8396 (mt0) cc_final: 0.7459 (tm-30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1381 time to fit residues: 13.3446 Evaluate side-chains 55 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 415 optimal weight: 6.9990 chunk 283 optimal weight: 0.0870 chunk 7 optimal weight: 7.9990 chunk 371 optimal weight: 20.0000 chunk 205 optimal weight: 0.5980 chunk 425 optimal weight: 5.9990 chunk 344 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 254 optimal weight: 0.0270 chunk 447 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 22 ASN j 59 GLN ** j 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.8894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 42012 Z= 0.239 Angle : 0.915 10.010 56820 Z= 0.465 Chirality : 0.051 0.221 6504 Planarity : 0.005 0.058 7344 Dihedral : 7.807 35.969 5748 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 0.94 % Allowed : 14.12 % Favored : 84.94 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.68 % Twisted Proline : 5.00 % Twisted General : 0.73 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.11), residues: 5100 helix: -0.60 (0.10), residues: 2376 sheet: -2.06 (0.27), residues: 240 loop : -2.87 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP b 449 HIS 0.000 0.000 HIS a 216 PHE 0.018 0.002 PHE j 78 TYR 0.037 0.002 TYR a 251 ARG 0.003 0.001 ARG l 351 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: j 95 GLN cc_start: 0.7083 (tt0) cc_final: 0.6677 (pt0) REVERT: j 112 MET cc_start: 0.7349 (mtp) cc_final: 0.6409 (mtp) REVERT: j 160 LEU cc_start: 0.7580 (tp) cc_final: 0.7290 (tp) REVERT: j 173 PHE cc_start: 0.6774 (m-10) cc_final: 0.6047 (t80) REVERT: j 256 MET cc_start: 0.8312 (tpt) cc_final: 0.8108 (tpt) REVERT: j 271 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7869 (mt-10) REVERT: j 358 LEU cc_start: 0.8282 (mm) cc_final: 0.7852 (tp) REVERT: j 401 VAL cc_start: 0.8545 (t) cc_final: 0.8344 (t) REVERT: j 407 GLN cc_start: 0.8333 (mt0) cc_final: 0.7469 (tm-30) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1299 time to fit residues: 12.8819 Evaluate side-chains 55 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 167 optimal weight: 0.0050 chunk 449 optimal weight: 0.0370 chunk 98 optimal weight: 0.0070 chunk 292 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 499 optimal weight: 0.0010 chunk 414 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 262 optimal weight: 8.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 22 ASN i 283 GLN ** i 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.9405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 42012 Z= 0.220 Angle : 0.903 9.805 56820 Z= 0.463 Chirality : 0.049 0.229 6504 Planarity : 0.005 0.054 7344 Dihedral : 7.290 37.328 5748 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.94 % Allowed : 14.12 % Favored : 84.94 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 2.68 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.11), residues: 5100 helix: -0.81 (0.10), residues: 2472 sheet: -2.07 (0.26), residues: 312 loop : -3.11 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP g 449 HIS 0.003 0.002 HIS l 216 PHE 0.022 0.002 PHE h 78 TYR 0.030 0.002 TYR g 251 ARG 0.003 0.001 ARG b 351 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: i 80 MET cc_start: 0.7296 (tpt) cc_final: 0.6229 (ttt) REVERT: i 95 GLN cc_start: 0.6556 (tt0) cc_final: 0.6123 (pt0) REVERT: i 101 ASP cc_start: 0.5028 (t70) cc_final: 0.4730 (p0) REVERT: i 112 MET cc_start: 0.7848 (mtp) cc_final: 0.7276 (mtp) REVERT: i 257 VAL cc_start: 0.8386 (t) cc_final: 0.8178 (p) REVERT: i 356 PHE cc_start: 0.8827 (m-10) cc_final: 0.8607 (m-80) REVERT: i 358 LEU cc_start: 0.8471 (mm) cc_final: 0.7855 (tp) REVERT: i 395 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7497 (mm-30) REVERT: i 407 GLN cc_start: 0.7888 (mt0) cc_final: 0.7363 (pt0) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1438 time to fit residues: 14.6479 Evaluate side-chains 58 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 481 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 284 optimal weight: 0.0570 chunk 364 optimal weight: 2.9990 chunk 282 optimal weight: 0.4980 chunk 420 optimal weight: 0.0170 chunk 278 optimal weight: 8.9990 chunk 497 optimal weight: 8.9990 chunk 311 optimal weight: 6.9990 chunk 303 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 overall best weight: 0.9138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 22 ASN ** l 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 283 GLN ** l 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.9555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 42012 Z= 0.216 Angle : 0.895 9.624 56820 Z= 0.458 Chirality : 0.049 0.251 6504 Planarity : 0.006 0.085 7344 Dihedral : 7.033 36.013 5748 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.94 % Allowed : 14.59 % Favored : 84.47 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 2.68 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.11), residues: 5100 helix: -0.85 (0.10), residues: 2460 sheet: -1.91 (0.30), residues: 240 loop : -3.34 (0.11), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.007 TRP g 449 HIS 0.005 0.003 HIS d 216 PHE 0.033 0.002 PHE i 78 TYR 0.030 0.002 TYR b 251 ARG 0.005 0.000 ARG c 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: l 80 MET cc_start: 0.7146 (tpt) cc_final: 0.6128 (ttt) REVERT: l 95 GLN cc_start: 0.6574 (tt0) cc_final: 0.6180 (pt0) REVERT: l 112 MET cc_start: 0.7780 (mtp) cc_final: 0.7121 (mtp) REVERT: l 156 ASN cc_start: 0.8219 (m-40) cc_final: 0.7963 (m110) REVERT: l 257 VAL cc_start: 0.8367 (t) cc_final: 0.8109 (p) REVERT: l 356 PHE cc_start: 0.8885 (m-10) cc_final: 0.8640 (m-80) REVERT: l 375 ARG cc_start: 0.7925 (tmm160) cc_final: 0.7723 (tmm160) REVERT: l 395 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7429 (mm-30) REVERT: l 407 GLN cc_start: 0.7932 (mt0) cc_final: 0.7425 (pt0) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1422 time to fit residues: 13.3684 Evaluate side-chains 58 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 307 optimal weight: 0.0060 chunk 198 optimal weight: 0.8980 chunk 297 optimal weight: 4.9990 chunk 149 optimal weight: 0.0040 chunk 97 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 316 optimal weight: 0.4980 chunk 338 optimal weight: 8.9990 chunk 245 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 390 optimal weight: 5.9990 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 22 ASN j 33 ASN ** j 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 68 ASN ** j 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 1.0055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 42012 Z= 0.220 Angle : 0.908 9.555 56820 Z= 0.464 Chirality : 0.050 0.251 6504 Planarity : 0.006 0.072 7344 Dihedral : 6.702 36.310 5748 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.94 % Allowed : 15.06 % Favored : 84.00 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 2.68 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.11), residues: 5100 helix: -0.75 (0.10), residues: 2424 sheet: -1.95 (0.30), residues: 240 loop : -3.54 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.008 TRP j 449 HIS 0.005 0.003 HIS g 216 PHE 0.034 0.002 PHE g 78 TYR 0.030 0.002 TYR e 251 ARG 0.005 0.001 ARG f 266 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: j 80 MET cc_start: 0.6779 (tpt) cc_final: 0.5793 (ttt) REVERT: j 82 THR cc_start: 0.7239 (m) cc_final: 0.6863 (p) REVERT: j 95 GLN cc_start: 0.6939 (tt0) cc_final: 0.6501 (pt0) REVERT: j 112 MET cc_start: 0.7649 (mtp) cc_final: 0.6955 (mtp) REVERT: j 144 LEU cc_start: 0.7115 (pt) cc_final: 0.6783 (pp) REVERT: j 256 MET cc_start: 0.8345 (tpt) cc_final: 0.7830 (tpt) REVERT: j 257 VAL cc_start: 0.8587 (t) cc_final: 0.8222 (p) REVERT: j 289 MET cc_start: 0.6275 (mmm) cc_final: 0.5691 (mmm) REVERT: j 357 MET cc_start: 0.8357 (mmm) cc_final: 0.8038 (mmm) REVERT: j 358 LEU cc_start: 0.8328 (mm) cc_final: 0.8046 (tp) REVERT: j 407 GLN cc_start: 0.8040 (mt0) cc_final: 0.7379 (pt0) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1409 time to fit residues: 12.7111 Evaluate side-chains 50 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 452 optimal weight: 4.9990 chunk 476 optimal weight: 0.0370 chunk 434 optimal weight: 7.9990 chunk 463 optimal weight: 0.0370 chunk 278 optimal weight: 0.5980 chunk 201 optimal weight: 0.5980 chunk 363 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 418 optimal weight: 0.0020 chunk 438 optimal weight: 0.0870 chunk 461 optimal weight: 0.0010 overall best weight: 0.0328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 33 ASN j 59 GLN j 68 ASN ** j 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 1.0583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 42012 Z= 0.215 Angle : 0.888 9.422 56820 Z= 0.454 Chirality : 0.049 0.225 6504 Planarity : 0.006 0.075 7344 Dihedral : 6.699 35.840 5748 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.71 % Allowed : 14.12 % Favored : 85.18 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 2.68 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.11), residues: 5100 helix: -0.75 (0.10), residues: 2388 sheet: -0.74 (0.30), residues: 300 loop : -3.79 (0.11), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.005 TRP l 449 HIS 0.002 0.001 HIS a 216 PHE 0.017 0.002 PHE g 78 TYR 0.026 0.002 TYR k 251 ARG 0.003 0.000 ARG b 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: j 80 MET cc_start: 0.6672 (tpt) cc_final: 0.5510 (ttt) REVERT: j 95 GLN cc_start: 0.6952 (tt0) cc_final: 0.6475 (pt0) REVERT: j 112 MET cc_start: 0.7699 (mtp) cc_final: 0.7014 (mtp) REVERT: j 144 LEU cc_start: 0.6769 (pt) cc_final: 0.6461 (pp) REVERT: j 256 MET cc_start: 0.8241 (tpt) cc_final: 0.8001 (tpt) REVERT: j 289 MET cc_start: 0.6300 (mmm) cc_final: 0.5998 (mtt) REVERT: j 357 MET cc_start: 0.8295 (mmm) cc_final: 0.8014 (mmm) REVERT: j 358 LEU cc_start: 0.8298 (mm) cc_final: 0.8030 (tp) REVERT: j 395 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7051 (tp30) REVERT: j 407 GLN cc_start: 0.7669 (mt0) cc_final: 0.7248 (pt0) REVERT: j 465 MET cc_start: 0.7740 (tpt) cc_final: 0.7537 (tpp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1647 time to fit residues: 15.4560 Evaluate side-chains 54 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 304 optimal weight: 8.9990 chunk 490 optimal weight: 3.9990 chunk 299 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 340 optimal weight: 0.9990 chunk 514 optimal weight: 0.1980 chunk 473 optimal weight: 10.0000 chunk 409 optimal weight: 0.0670 chunk 42 optimal weight: 0.8980 chunk 316 optimal weight: 0.5980 chunk 251 optimal weight: 9.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 1.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 42012 Z= 0.216 Angle : 0.884 9.417 56820 Z= 0.452 Chirality : 0.049 0.221 6504 Planarity : 0.006 0.075 7344 Dihedral : 6.512 35.636 5748 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.71 % Allowed : 13.88 % Favored : 85.41 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 2.68 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.11), residues: 5100 helix: -0.79 (0.10), residues: 2388 sheet: -0.61 (0.30), residues: 300 loop : -3.81 (0.11), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP a 449 HIS 0.002 0.001 HIS a 216 PHE 0.018 0.002 PHE d 131 TYR 0.026 0.001 TYR k 251 ARG 0.002 0.000 ARG d 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: d 80 MET cc_start: 0.6231 (tpt) cc_final: 0.5764 (mtt) REVERT: d 95 GLN cc_start: 0.6824 (tt0) cc_final: 0.6579 (pt0) REVERT: d 112 MET cc_start: 0.7642 (mtp) cc_final: 0.6831 (mtp) REVERT: d 142 ASN cc_start: 0.7382 (p0) cc_final: 0.7159 (p0) REVERT: d 159 LYS cc_start: 0.6925 (mmpt) cc_final: 0.6478 (mmtp) REVERT: d 173 PHE cc_start: 0.6696 (m-10) cc_final: 0.6363 (t80) REVERT: d 271 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7091 (tp30) REVERT: d 289 MET cc_start: 0.6369 (mmm) cc_final: 0.5848 (mtt) REVERT: d 375 ARG cc_start: 0.7952 (tmm160) cc_final: 0.7631 (tmm160) REVERT: d 391 ILE cc_start: 0.8439 (mm) cc_final: 0.8188 (mt) REVERT: d 407 GLN cc_start: 0.7652 (mt0) cc_final: 0.7256 (pt0) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1395 time to fit residues: 12.4005 Evaluate side-chains 56 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 325 optimal weight: 5.9990 chunk 436 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 377 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 410 optimal weight: 0.0870 chunk 171 optimal weight: 0.9990 chunk 421 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.099751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.089955 restraints weight = 13218.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.091429 restraints weight = 8595.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.092536 restraints weight = 6192.718| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 1.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 42012 Z= 0.234 Angle : 0.913 9.811 56820 Z= 0.466 Chirality : 0.049 0.201 6504 Planarity : 0.006 0.076 7344 Dihedral : 6.669 34.706 5748 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.71 % Allowed : 15.06 % Favored : 84.24 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 2.68 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.11), residues: 5100 helix: -0.62 (0.10), residues: 2340 sheet: -1.05 (0.35), residues: 240 loop : -3.63 (0.10), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP f 449 HIS 0.001 0.000 HIS e 216 PHE 0.013 0.002 PHE a 43 TYR 0.034 0.002 TYR b 251 ARG 0.006 0.001 ARG j 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4140.09 seconds wall clock time: 78 minutes 32.57 seconds (4712.57 seconds total)