Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 19 17:11:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp0_30138/10_2023/7bp0_30138.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp0_30138/10_2023/7bp0_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_30138/10_2023/7bp0_30138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp0_30138/10_2023/7bp0_30138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp0_30138/10_2023/7bp0_30138.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp0_30138/10_2023/7bp0_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-1.21rc1-5097/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: 20.93, per 1000 atoms: 0.51 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: 17.61 Conformation dependent library (CDL) restraints added in 5.9 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: 3.46 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: 12.59 Time building geometry restraints manager: 18.77 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.740 Check model and map are aligned: 0.620 Set scattering table: 0.370 Process input model: 100.110 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.650 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.454 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 outliers start: 106 outliers final: 54 residues processed: 176 average time/residue: 0.1968 time to fit residues: 40.1237 Evaluate side-chains 111 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 57 time to evaluate : 0.393 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 4 residues processed: 54 average time/residue: 0.0887 time to fit residues: 6.8348 ------------------------------------------------------------------------------- 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: 6.9990 chunk 391 optimal weight: 10.0000 chunk 217 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 263 optimal weight: 2.9990 chunk 208 optimal weight: 0.0010 chunk 404 optimal weight: 9.9990 chunk 156 optimal weight: 30.0000 chunk 245 optimal weight: 5.9990 chunk 301 optimal weight: 9.9990 chunk 468 optimal weight: 4.9990 overall best weight: 3.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 81 GLN ** f 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 169 GLN ** f 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: 0.7070 moved from start: 0.6602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 42012 Z= 0.396 Angle : 1.181 13.523 56820 Z= 0.606 Chirality : 0.058 0.298 6504 Planarity : 0.008 0.074 7344 Dihedral : 10.507 54.763 5748 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 31.39 Ramachandran Plot: Outliers : 1.88 % Allowed : 13.18 % Favored : 84.94 % Rotamer: Outliers : 1.59 % Allowed : 13.79 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.43 % Twisted Proline : 10.00 % Twisted General : 2.19 % 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: -2.53 (0.11), residues: 5100 helix: -0.24 (0.10), residues: 2268 sheet: -2.58 (0.25), residues: 192 loop : -3.05 (0.11), residues: 2640 *********************** 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 95 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 92 average time/residue: 0.1508 time to fit residues: 17.1084 Evaluate side-chains 57 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0415 time to fit residues: 0.6289 ------------------------------------------------------------------------------- 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: 0.6980 chunk 145 optimal weight: 8.9990 chunk 389 optimal weight: 0.8980 chunk 319 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 469 optimal weight: 0.4980 chunk 507 optimal weight: 0.8980 chunk 418 optimal weight: 9.9990 chunk 465 optimal weight: 1.9990 chunk 160 optimal weight: 0.0470 chunk 376 optimal weight: 0.2980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 59 GLN f 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.8108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 42012 Z= 0.254 Angle : 1.012 9.877 56820 Z= 0.516 Chirality : 0.052 0.243 6504 Planarity : 0.006 0.061 7344 Dihedral : 8.620 42.217 5748 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 25.04 Ramachandran Plot: Outliers : 1.18 % Allowed : 12.71 % Favored : 86.12 % Rotamer: Outliers : 0.27 % Allowed : 7.16 % Favored : 92.57 % 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: -2.42 (0.11), residues: 5100 helix: -0.21 (0.10), residues: 2280 sheet: -2.61 (0.25), residues: 240 loop : -2.92 (0.11), residues: 2580 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.1537 time to fit residues: 17.5831 Evaluate side-chains 57 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.418 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5664 ------------------------------------------------------------------------------- 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: 0.0070 chunk 352 optimal weight: 0.0570 chunk 243 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 315 optimal weight: 3.9990 chunk 471 optimal weight: 1.9990 chunk 498 optimal weight: 0.9980 chunk 246 optimal weight: 0.9990 chunk 446 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.8854 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= 0.248 Angle : 0.951 9.900 56820 Z= 0.489 Chirality : 0.051 0.219 6504 Planarity : 0.006 0.053 7344 Dihedral : 8.247 36.320 5748 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.94 % Allowed : 12.24 % Favored : 86.82 % Rotamer: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % 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: -2.23 (0.11), residues: 5100 helix: -0.24 (0.10), residues: 2376 sheet: -2.34 (0.26), residues: 312 loop : -2.72 (0.12), residues: 2412 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1824 time to fit residues: 18.1629 Evaluate side-chains 60 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6331 ------------------------------------------------------------------------------- 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: 0.0370 chunk 283 optimal weight: 0.0370 chunk 7 optimal weight: 0.5980 chunk 371 optimal weight: 20.0000 chunk 205 optimal weight: 0.0040 chunk 425 optimal weight: 0.6980 chunk 344 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 254 optimal weight: 0.2980 chunk 447 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.1948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 22 ASN ** f 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.9584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 42012 Z= 0.220 Angle : 0.910 9.488 56820 Z= 0.463 Chirality : 0.049 0.202 6504 Planarity : 0.006 0.056 7344 Dihedral : 7.491 32.514 5748 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.94 % Allowed : 13.41 % Favored : 85.65 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.68 % Twisted Proline : 5.00 % Twisted General : 0.00 % 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: -2.49 (0.11), residues: 5100 helix: -0.44 (0.10), residues: 2424 sheet: -1.77 (0.28), residues: 312 loop : -3.03 (0.12), residues: 2364 *********************** REFINEMENT MACRO_CYCLE 5 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 81 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1705 time to fit residues: 16.7162 Evaluate side-chains 56 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5829 ------------------------------------------------------------------------------- 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: 0.0670 chunk 449 optimal weight: 0.9980 chunk 98 optimal weight: 0.0870 chunk 292 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 499 optimal weight: 0.0070 chunk 414 optimal weight: 9.9990 chunk 231 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 262 optimal weight: 8.9990 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 22 ASN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 1.0008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 42012 Z= 0.214 Angle : 0.889 9.491 56820 Z= 0.448 Chirality : 0.047 0.205 6504 Planarity : 0.005 0.062 7344 Dihedral : 7.054 30.967 5748 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 24.13 Ramachandran Plot: Outliers : 0.94 % Allowed : 12.94 % Favored : 86.12 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 2.68 % Twisted Proline : 5.00 % Twisted General : 0.00 % 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: -2.37 (0.12), residues: 5100 helix: -0.23 (0.11), residues: 2412 sheet: -1.42 (0.29), residues: 312 loop : -3.14 (0.12), residues: 2376 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1387 time to fit residues: 12.9358 Evaluate side-chains 59 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.418 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.8851 > 50: distance: 0 - 1: 7.049 distance: 1 - 2: 36.094 distance: 1 - 4: 4.341 distance: 2 - 3: 43.404 distance: 4 - 5: 40.555 distance: 5 - 6: 39.273 distance: 5 - 7: 32.183 distance: 8 - 9: 4.771 distance: 9 - 10: 3.639 distance: 9 - 12: 22.595 distance: 10 - 11: 27.248 distance: 10 - 20: 36.807 distance: 12 - 13: 13.854 distance: 13 - 14: 28.841 distance: 13 - 15: 16.177 distance: 14 - 16: 30.808 distance: 15 - 17: 33.094 distance: 16 - 18: 28.727 distance: 17 - 18: 45.243 distance: 18 - 19: 12.728 distance: 20 - 21: 40.070 distance: 21 - 24: 38.855 distance: 22 - 23: 41.027 distance: 24 - 25: 39.781 distance: 28 - 29: 39.792 distance: 28 - 34: 40.004 distance: 29 - 32: 40.293 distance: 30 - 31: 39.227 distance: 32 - 33: 17.400 distance: 33 - 34: 61.244 distance: 35 - 36: 23.598 distance: 36 - 37: 59.262 distance: 36 - 39: 46.446 distance: 37 - 47: 30.595 distance: 39 - 40: 11.054 distance: 40 - 41: 46.331 distance: 40 - 42: 12.631 distance: 43 - 45: 46.794 distance: 44 - 45: 20.582 distance: 45 - 46: 39.660 distance: 47 - 48: 7.101 distance: 48 - 49: 46.453 distance: 48 - 51: 56.092 distance: 49 - 50: 47.133 distance: 49 - 55: 46.375 distance: 51 - 52: 41.630 distance: 52 - 53: 22.479 distance: 52 - 54: 3.785 distance: 55 - 61: 39.227 distance: 56 - 57: 41.525 distance: 57 - 58: 30.649 distance: 57 - 62: 40.900 distance: 60 - 61: 37.691 distance: 62 - 63: 53.581 distance: 63 - 64: 3.019 distance: 63 - 66: 4.239 distance: 64 - 65: 54.863 distance: 64 - 70: 17.403 distance: 67 - 68: 40.687 distance: 68 - 69: 38.345 distance: 70 - 71: 45.445 distance: 71 - 72: 26.175 distance: 71 - 74: 14.617 distance: 72 - 73: 40.512 distance: 74 - 75: 40.718 distance: 75 - 76: 56.838 distance: 76 - 77: 57.066 distance: 77 - 78: 69.289 distance: 79 - 80: 41.701 distance: 80 - 81: 30.545 distance: 80 - 83: 21.233 distance: 81 - 82: 55.017 distance: 83 - 84: 10.488 distance: 84 - 85: 37.761 distance: 84 - 86: 40.104