Starting phenix.real_space_refine on Tue Aug 26 06:08:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nvo_12608/08_2025/7nvo_12608.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nvo_12608/08_2025/7nvo_12608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nvo_12608/08_2025/7nvo_12608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nvo_12608/08_2025/7nvo_12608.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nvo_12608/08_2025/7nvo_12608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nvo_12608/08_2025/7nvo_12608.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 8 Type Number sf(0) Gaussians Al 12 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 188 5.16 5 C 21290 2.51 5 N 5946 2.21 5 O 6726 1.98 5 F 36 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34246 Number of models: 1 Model: "" Number of chains: 42 Chain: "E" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1873 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain breaks: 1 Chain: "H" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1900 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 9, 'TRANS': 242} Chain breaks: 1 Chain: "Q" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2685 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 9, 'TRANS': 342} Chain breaks: 1 Chain: "Z" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2417 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 8, 'TRANS': 314} Chain breaks: 1 Chain: "G" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1880 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 238} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1879 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 1 Chain: "D" Number of atoms: 1840 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1829 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 247, 1829 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain breaks: 1 bond proxies already assigned to first conformer: 1831 Chain: "B" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2073 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 323 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain breaks: 2 Chain: "e" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1873 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain breaks: 1 Chain: "h" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1900 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 9, 'TRANS': 242} Chain breaks: 1 Chain: "q" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2685 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 9, 'TRANS': 342} Chain breaks: 1 Chain: "z" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2417 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 8, 'TRANS': 314} Chain breaks: 1 Chain: "g" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1880 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 238} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1879 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 1 Chain: "d" Number of atoms: 1840 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1829 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 247, 1829 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain breaks: 1 bond proxies already assigned to first conformer: 1831 Chain: "b" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2073 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 323 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain breaks: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE D 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 35 " occ=0.50 residue: pdb=" N APHE d 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE d 35 " occ=0.50 Time building chain proxies: 8.41, per 1000 atoms: 0.25 Number of scatterers: 34246 At special positions: 0 Unit cell: (181.26, 114.48, 174.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 188 16.00 P 32 15.00 Al 12 13.00 Mg 16 11.99 F 36 9.00 O 6726 8.00 N 5946 7.00 C 21290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM34226 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM33978 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 715.3 nanoseconds 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8324 Finding SS restraints... Secondary structure from input PDB file: 223 helices and 44 sheets defined 60.4% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'E' and resid 35 through 42 Processing helix chain 'E' and resid 42 through 49 removed outlier: 3.622A pdb=" N MET E 48 " --> pdb=" O VAL E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 78 Processing helix chain 'E' and resid 79 through 81 No H-bonds generated for 'chain 'E' and resid 79 through 81' Processing helix chain 'E' and resid 87 through 96 removed outlier: 3.811A pdb=" N LYS E 96 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 127 removed outlier: 4.106A pdb=" N VAL E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 149 removed outlier: 3.505A pdb=" N ASP E 149 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 424 through 438 removed outlier: 3.548A pdb=" N ALA E 430 " --> pdb=" O GLU E 426 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN E 435 " --> pdb=" O LEU E 431 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP E 438 " --> pdb=" O SER E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 456 removed outlier: 3.716A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 462 Processing helix chain 'E' and resid 469 through 482 removed outlier: 4.146A pdb=" N ARG E 480 " --> pdb=" O GLU E 476 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL E 482 " --> pdb=" O ARG E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 511 through 513 No H-bonds generated for 'chain 'E' and resid 511 through 513' Processing helix chain 'E' and resid 515 through 528 removed outlier: 3.797A pdb=" N THR E 521 " --> pdb=" O ILE E 517 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET E 526 " --> pdb=" O GLN E 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 35 Processing helix chain 'H' and resid 36 through 40 Processing helix chain 'H' and resid 62 through 67 Processing helix chain 'H' and resid 73 through 90 Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'H' and resid 108 through 113 Processing helix chain 'H' and resid 117 through 123 Processing helix chain 'H' and resid 126 through 140 Processing helix chain 'H' and resid 415 through 425 Processing helix chain 'H' and resid 431 through 441 removed outlier: 3.790A pdb=" N ALA H 437 " --> pdb=" O LEU H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 444 through 454 removed outlier: 4.334A pdb=" N CYS H 450 " --> pdb=" O PRO H 446 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA H 453 " --> pdb=" O LEU H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 471 removed outlier: 3.585A pdb=" N ILE H 460 " --> pdb=" O ASP H 456 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN H 462 " --> pdb=" O THR H 458 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN H 470 " --> pdb=" O ALA H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 28 through 45 removed outlier: 3.866A pdb=" N ASN Q 32 " --> pdb=" O ALA Q 28 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE Q 33 " --> pdb=" O VAL Q 29 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU Q 38 " --> pdb=" O GLN Q 34 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR Q 42 " --> pdb=" O GLU Q 38 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 77 removed outlier: 3.504A pdb=" N ARG Q 74 " --> pdb=" O ALA Q 70 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 97 removed outlier: 3.937A pdb=" N ILE Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 107 Processing helix chain 'Q' and resid 107 through 120 Processing helix chain 'Q' and resid 124 through 143 removed outlier: 3.605A pdb=" N VAL Q 128 " --> pdb=" O SER Q 124 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU Q 130 " --> pdb=" O SER Q 126 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY Q 131 " --> pdb=" O GLU Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 146 No H-bonds generated for 'chain 'Q' and resid 144 through 146' Processing helix chain 'Q' and resid 156 through 162 Processing helix chain 'Q' and resid 164 through 170 removed outlier: 3.983A pdb=" N ILE Q 168 " --> pdb=" O LEU Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 175 through 190 removed outlier: 3.554A pdb=" N LEU Q 179 " --> pdb=" O ASN Q 175 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA Q 186 " --> pdb=" O LEU Q 182 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE Q 190 " --> pdb=" O ALA Q 186 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 385 through 405 Processing helix chain 'Q' and resid 413 through 430 Processing helix chain 'Q' and resid 433 through 446 removed outlier: 4.103A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 455 removed outlier: 3.513A pdb=" N ASN Q 455 " --> pdb=" O ALA Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 459 through 474 removed outlier: 3.652A pdb=" N VAL Q 470 " --> pdb=" O LYS Q 466 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU Q 473 " --> pdb=" O ALA Q 469 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY Q 474 " --> pdb=" O VAL Q 470 " (cutoff:3.500A) Processing helix chain 'Q' and resid 501 through 521 removed outlier: 3.670A pdb=" N ALA Q 507 " --> pdb=" O GLY Q 503 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 35 removed outlier: 3.632A pdb=" N VAL Z 22 " --> pdb=" O ALA Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 60 through 65 Processing helix chain 'Z' and resid 71 through 83 removed outlier: 3.588A pdb=" N ALA Z 83 " --> pdb=" O LYS Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 94 through 103 Processing helix chain 'Z' and resid 104 through 112 removed outlier: 3.558A pdb=" N LEU Z 108 " --> pdb=" O LYS Z 104 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 136 removed outlier: 3.685A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU Z 121 " --> pdb=" O ARG Z 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 157 removed outlier: 3.898A pdb=" N SER Z 155 " --> pdb=" O VAL Z 151 " (cutoff:3.500A) Processing helix chain 'Z' and resid 167 through 174 removed outlier: 4.139A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 383 through 405 removed outlier: 3.656A pdb=" N ASP Z 404 " --> pdb=" O ASN Z 400 " (cutoff:3.500A) Processing helix chain 'Z' and resid 412 through 426 removed outlier: 3.535A pdb=" N LEU Z 422 " --> pdb=" O MET Z 418 " (cutoff:3.500A) Processing helix chain 'Z' and resid 427 through 429 No H-bonds generated for 'chain 'Z' and resid 427 through 429' Processing helix chain 'Z' and resid 433 through 438 removed outlier: 3.633A pdb=" N VAL Z 437 " --> pdb=" O ALA Z 433 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 455 removed outlier: 3.616A pdb=" N SER Z 455 " --> pdb=" O LEU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 460 through 474 Processing helix chain 'Z' and resid 488 through 493 Processing helix chain 'Z' and resid 500 through 517 removed outlier: 3.760A pdb=" N LEU Z 505 " --> pdb=" O LYS Z 501 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS Z 506 " --> pdb=" O LYS Z 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.613A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 70 Processing helix chain 'G' and resid 74 through 89 Processing helix chain 'G' and resid 95 through 100 removed outlier: 4.198A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 95 through 100' Processing helix chain 'G' and resid 103 through 108 Processing helix chain 'G' and resid 109 through 114 Processing helix chain 'G' and resid 118 through 137 removed outlier: 3.567A pdb=" N VAL G 122 " --> pdb=" O HIS G 118 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP G 131 " --> pdb=" O ARG G 127 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER G 135 " --> pdb=" O ASP G 131 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR G 136 " --> pdb=" O ASP G 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU G 137 " --> pdb=" O MET G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 426 Processing helix chain 'G' and resid 427 through 429 No H-bonds generated for 'chain 'G' and resid 427 through 429' Processing helix chain 'G' and resid 434 through 442 Processing helix chain 'G' and resid 445 through 454 Processing helix chain 'G' and resid 458 through 471 removed outlier: 3.909A pdb=" N SER G 465 " --> pdb=" O ARG G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 502 through 516 removed outlier: 3.587A pdb=" N TYR G 506 " --> pdb=" O LYS G 502 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL G 514 " --> pdb=" O VAL G 510 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU G 516 " --> pdb=" O THR G 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 33 Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.819A pdb=" N ILE A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 86 Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.937A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 129 removed outlier: 3.695A pdb=" N VAL A 129 " --> pdb=" O CYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 413 through 429 removed outlier: 3.864A pdb=" N ILE A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.593A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 460 through 471 removed outlier: 3.820A pdb=" N VAL A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 475 Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.783A pdb=" N LYS A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 526 removed outlier: 3.539A pdb=" N LYS A 510 " --> pdb=" O PRO A 506 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.562A pdb=" N SER D 51 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 80 removed outlier: 3.836A pdb=" N ILE D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 removed outlier: 3.514A pdb=" N LEU D 94 " --> pdb=" O MET D 90 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 96 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.611A pdb=" N ILE D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 removed outlier: 3.996A pdb=" N LYS D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 440 removed outlier: 3.973A pdb=" N LEU D 432 " --> pdb=" O PRO D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 459 removed outlier: 3.756A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ARG D 452 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA D 453 " --> pdb=" O TYR D 449 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 469 Processing helix chain 'D' and resid 472 through 486 removed outlier: 3.601A pdb=" N GLN D 486 " --> pdb=" O ASN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'B' and resid 29 through 39 removed outlier: 3.746A pdb=" N VAL B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 94 removed outlier: 3.991A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 119 removed outlier: 3.621A pdb=" N ALA B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 142 removed outlier: 3.619A pdb=" N ILE B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 165 removed outlier: 3.600A pdb=" N ARG B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 403 Processing helix chain 'B' and resid 411 through 426 Processing helix chain 'B' and resid 432 through 444 removed outlier: 3.502A pdb=" N SER B 438 " --> pdb=" O VAL B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 453 removed outlier: 3.698A pdb=" N THR B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 469 removed outlier: 4.155A pdb=" N ALA B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'e' and resid 35 through 42 Processing helix chain 'e' and resid 42 through 49 removed outlier: 3.622A pdb=" N MET e 48 " --> pdb=" O VAL e 44 " (cutoff:3.500A) Processing helix chain 'e' and resid 73 through 78 Processing helix chain 'e' and resid 79 through 81 No H-bonds generated for 'chain 'e' and resid 79 through 81' Processing helix chain 'e' and resid 87 through 96 removed outlier: 3.813A pdb=" N LYS e 96 " --> pdb=" O VAL e 92 " (cutoff:3.500A) Processing helix chain 'e' and resid 106 through 127 removed outlier: 4.105A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP e 125 " --> pdb=" O GLU e 121 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG e 126 " --> pdb=" O GLN e 122 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY e 127 " --> pdb=" O LEU e 123 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 149 removed outlier: 3.506A pdb=" N ASP e 149 " --> pdb=" O ILE e 145 " (cutoff:3.500A) Processing helix chain 'e' and resid 150 through 152 No H-bonds generated for 'chain 'e' and resid 150 through 152' Processing helix chain 'e' and resid 424 through 436 removed outlier: 3.547A pdb=" N ALA e 430 " --> pdb=" O GLU e 426 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN e 435 " --> pdb=" O LEU e 431 " (cutoff:3.500A) Processing helix chain 'e' and resid 437 through 440 Processing helix chain 'e' and resid 443 through 456 removed outlier: 3.715A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 457 through 462 Processing helix chain 'e' and resid 469 through 482 removed outlier: 4.145A pdb=" N ARG e 480 " --> pdb=" O GLU e 476 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL e 482 " --> pdb=" O ARG e 478 " (cutoff:3.500A) Processing helix chain 'e' and resid 500 through 505 Processing helix chain 'e' and resid 511 through 513 No H-bonds generated for 'chain 'e' and resid 511 through 513' Processing helix chain 'e' and resid 515 through 528 removed outlier: 3.798A pdb=" N THR e 521 " --> pdb=" O ILE e 517 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET e 526 " --> pdb=" O GLN e 522 " (cutoff:3.500A) Processing helix chain 'h' and resid 18 through 35 Processing helix chain 'h' and resid 36 through 40 Processing helix chain 'h' and resid 62 through 67 Processing helix chain 'h' and resid 73 through 90 Processing helix chain 'h' and resid 95 through 107 Processing helix chain 'h' and resid 108 through 113 Processing helix chain 'h' and resid 117 through 123 Processing helix chain 'h' and resid 126 through 140 Processing helix chain 'h' and resid 415 through 425 Processing helix chain 'h' and resid 431 through 441 removed outlier: 3.789A pdb=" N ALA h 437 " --> pdb=" O LEU h 433 " (cutoff:3.500A) Processing helix chain 'h' and resid 444 through 454 removed outlier: 4.333A pdb=" N CYS h 450 " --> pdb=" O PRO h 446 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA h 453 " --> pdb=" O LEU h 449 " (cutoff:3.500A) Processing helix chain 'h' and resid 456 through 471 removed outlier: 3.584A pdb=" N ILE h 460 " --> pdb=" O ASP h 456 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN h 462 " --> pdb=" O THR h 458 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN h 470 " --> pdb=" O ALA h 466 " (cutoff:3.500A) Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'q' and resid 28 through 45 removed outlier: 3.865A pdb=" N ASN q 32 " --> pdb=" O ALA q 28 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE q 33 " --> pdb=" O VAL q 29 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU q 38 " --> pdb=" O GLN q 34 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR q 42 " --> pdb=" O GLU q 38 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 70 through 77 removed outlier: 3.504A pdb=" N ARG q 74 " --> pdb=" O ALA q 70 " (cutoff:3.500A) Processing helix chain 'q' and resid 80 through 97 removed outlier: 3.937A pdb=" N ILE q 86 " --> pdb=" O ALA q 82 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 107 Processing helix chain 'q' and resid 107 through 120 Processing helix chain 'q' and resid 124 through 143 removed outlier: 3.606A pdb=" N VAL q 128 " --> pdb=" O SER q 124 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU q 130 " --> pdb=" O SER q 126 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY q 131 " --> pdb=" O GLU q 127 " (cutoff:3.500A) Processing helix chain 'q' and resid 144 through 146 No H-bonds generated for 'chain 'q' and resid 144 through 146' Processing helix chain 'q' and resid 156 through 162 Processing helix chain 'q' and resid 164 through 170 removed outlier: 3.984A pdb=" N ILE q 168 " --> pdb=" O LEU q 164 " (cutoff:3.500A) Processing helix chain 'q' and resid 175 through 190 removed outlier: 3.554A pdb=" N LEU q 179 " --> pdb=" O ASN q 175 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA q 186 " --> pdb=" O LEU q 182 " (cutoff:3.500A) Processing helix chain 'q' and resid 211 through 215 Processing helix chain 'q' and resid 385 through 405 Processing helix chain 'q' and resid 413 through 430 Processing helix chain 'q' and resid 433 through 446 removed outlier: 4.103A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 455 removed outlier: 3.514A pdb=" N ASN q 455 " --> pdb=" O ALA q 451 " (cutoff:3.500A) Processing helix chain 'q' and resid 459 through 474 removed outlier: 3.651A pdb=" N VAL q 470 " --> pdb=" O LYS q 466 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU q 473 " --> pdb=" O ALA q 469 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY q 474 " --> pdb=" O VAL q 470 " (cutoff:3.500A) Processing helix chain 'q' and resid 501 through 521 removed outlier: 3.669A pdb=" N ALA q 507 " --> pdb=" O GLY q 503 " (cutoff:3.500A) Processing helix chain 'z' and resid 17 through 35 removed outlier: 3.632A pdb=" N VAL z 22 " --> pdb=" O ALA z 18 " (cutoff:3.500A) Processing helix chain 'z' and resid 36 through 38 No H-bonds generated for 'chain 'z' and resid 36 through 38' Processing helix chain 'z' and resid 60 through 65 Processing helix chain 'z' and resid 71 through 83 removed outlier: 3.588A pdb=" N ALA z 83 " --> pdb=" O LYS z 79 " (cutoff:3.500A) Processing helix chain 'z' and resid 94 through 103 Processing helix chain 'z' and resid 104 through 112 removed outlier: 3.559A pdb=" N LEU z 108 " --> pdb=" O LYS z 104 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 136 removed outlier: 3.685A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU z 121 " --> pdb=" O ARG z 117 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 157 removed outlier: 3.897A pdb=" N SER z 155 " --> pdb=" O VAL z 151 " (cutoff:3.500A) Processing helix chain 'z' and resid 167 through 174 removed outlier: 4.139A pdb=" N ALA z 171 " --> pdb=" O VAL z 167 " (cutoff:3.500A) Processing helix chain 'z' and resid 383 through 405 removed outlier: 3.657A pdb=" N ASP z 404 " --> pdb=" O ASN z 400 " (cutoff:3.500A) Processing helix chain 'z' and resid 412 through 426 removed outlier: 3.535A pdb=" N LEU z 422 " --> pdb=" O MET z 418 " (cutoff:3.500A) Processing helix chain 'z' and resid 427 through 429 No H-bonds generated for 'chain 'z' and resid 427 through 429' Processing helix chain 'z' and resid 433 through 438 removed outlier: 3.634A pdb=" N VAL z 437 " --> pdb=" O ALA z 433 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 455 removed outlier: 3.615A pdb=" N SER z 455 " --> pdb=" O LEU z 451 " (cutoff:3.500A) Processing helix chain 'z' and resid 460 through 474 Processing helix chain 'z' and resid 488 through 493 Processing helix chain 'z' and resid 500 through 517 removed outlier: 3.759A pdb=" N LEU z 505 " --> pdb=" O LYS z 501 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS z 506 " --> pdb=" O LYS z 502 " (cutoff:3.500A) Processing helix chain 'g' and resid 26 through 38 removed outlier: 3.613A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 70 Processing helix chain 'g' and resid 74 through 89 Processing helix chain 'g' and resid 95 through 100 removed outlier: 4.199A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE g 100 " --> pdb=" O THR g 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 95 through 100' Processing helix chain 'g' and resid 103 through 108 Processing helix chain 'g' and resid 109 through 114 Processing helix chain 'g' and resid 118 through 137 removed outlier: 3.567A pdb=" N VAL g 122 " --> pdb=" O HIS g 118 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP g 131 " --> pdb=" O ARG g 127 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP g 132 " --> pdb=" O LYS g 128 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER g 135 " --> pdb=" O ASP g 131 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR g 136 " --> pdb=" O ASP g 132 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU g 137 " --> pdb=" O MET g 133 " (cutoff:3.500A) Processing helix chain 'g' and resid 412 through 426 Processing helix chain 'g' and resid 427 through 429 No H-bonds generated for 'chain 'g' and resid 427 through 429' Processing helix chain 'g' and resid 434 through 442 Processing helix chain 'g' and resid 445 through 454 Processing helix chain 'g' and resid 458 through 471 removed outlier: 3.909A pdb=" N SER g 465 " --> pdb=" O ARG g 461 " (cutoff:3.500A) Processing helix chain 'g' and resid 490 through 494 Processing helix chain 'g' and resid 502 through 516 removed outlier: 3.587A pdb=" N TYR g 506 " --> pdb=" O LYS g 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL g 514 " --> pdb=" O VAL g 510 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU g 516 " --> pdb=" O THR g 512 " (cutoff:3.500A) Processing helix chain 'a' and resid 18 through 33 Processing helix chain 'a' and resid 57 through 65 removed outlier: 3.820A pdb=" N ILE a 61 " --> pdb=" O ASP a 57 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS a 63 " --> pdb=" O ALA a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 69 through 86 Processing helix chain 'a' and resid 90 through 109 removed outlier: 3.938A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE a 95 " --> pdb=" O THR a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 129 removed outlier: 3.696A pdb=" N VAL a 129 " --> pdb=" O CYS a 125 " (cutoff:3.500A) Processing helix chain 'a' and resid 131 through 135 Processing helix chain 'a' and resid 413 through 429 removed outlier: 3.865A pdb=" N ILE a 421 " --> pdb=" O ALA a 417 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 438 through 443 removed outlier: 3.592A pdb=" N ARG a 443 " --> pdb=" O ALA a 439 " (cutoff:3.500A) Processing helix chain 'a' and resid 447 through 452 Processing helix chain 'a' and resid 460 through 471 removed outlier: 3.819A pdb=" N VAL a 464 " --> pdb=" O SER a 460 " (cutoff:3.500A) Processing helix chain 'a' and resid 472 through 475 Processing helix chain 'a' and resid 480 through 484 removed outlier: 3.783A pdb=" N LYS a 484 " --> pdb=" O LYS a 481 " (cutoff:3.500A) Processing helix chain 'a' and resid 506 through 526 removed outlier: 3.541A pdb=" N LYS a 510 " --> pdb=" O PRO a 506 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS a 512 " --> pdb=" O ILE a 508 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU a 519 " --> pdb=" O LYS a 515 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 34 Processing helix chain 'd' and resid 48 through 52 removed outlier: 3.562A pdb=" N SER d 51 " --> pdb=" O ILE d 48 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 80 removed outlier: 3.836A pdb=" N ILE d 77 " --> pdb=" O ASP d 73 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 102 removed outlier: 3.514A pdb=" N LEU d 94 " --> pdb=" O MET d 90 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER d 95 " --> pdb=" O LEU d 91 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS d 96 " --> pdb=" O VAL d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 107 through 126 removed outlier: 3.611A pdb=" N ILE d 111 " --> pdb=" O THR d 107 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU d 117 " --> pdb=" O ALA d 113 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 136 through 146 removed outlier: 3.995A pdb=" N LYS d 143 " --> pdb=" O LYS d 139 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU d 146 " --> pdb=" O GLU d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 426 through 440 removed outlier: 3.973A pdb=" N LEU d 432 " --> pdb=" O PRO d 428 " (cutoff:3.500A) Processing helix chain 'd' and resid 446 through 459 removed outlier: 3.754A pdb=" N CYS d 450 " --> pdb=" O MET d 446 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ARG d 452 " --> pdb=" O SER d 448 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA d 453 " --> pdb=" O TYR d 449 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU d 459 " --> pdb=" O ALA d 455 " (cutoff:3.500A) Processing helix chain 'd' and resid 460 through 469 Processing helix chain 'd' and resid 472 through 486 removed outlier: 3.601A pdb=" N GLN d 486 " --> pdb=" O ASN d 482 " (cutoff:3.500A) Processing helix chain 'd' and resid 512 through 531 Processing helix chain 'b' and resid 29 through 39 removed outlier: 3.745A pdb=" N VAL b 39 " --> pdb=" O ILE b 35 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 94 removed outlier: 3.500A pdb=" N LYS b 82 " --> pdb=" O ASN b 78 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL b 83 " --> pdb=" O PRO b 79 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU b 84 " --> pdb=" O ALA b 80 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET b 87 " --> pdb=" O VAL b 83 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG b 89 " --> pdb=" O VAL b 85 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL b 90 " --> pdb=" O ASP b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 100 through 119 removed outlier: 3.621A pdb=" N ALA b 106 " --> pdb=" O VAL b 102 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU b 112 " --> pdb=" O GLU b 108 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU b 114 " --> pdb=" O LEU b 110 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER b 115 " --> pdb=" O ARG b 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 142 removed outlier: 3.619A pdb=" N ILE b 127 " --> pdb=" O PRO b 123 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA b 128 " --> pdb=" O GLN b 124 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU b 132 " --> pdb=" O ALA b 128 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 165 removed outlier: 3.600A pdb=" N ARG b 156 " --> pdb=" O GLU b 152 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN b 157 " --> pdb=" O VAL b 153 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET b 160 " --> pdb=" O ARG b 156 " (cutoff:3.500A) Processing helix chain 'b' and resid 386 through 403 Processing helix chain 'b' and resid 411 through 426 Processing helix chain 'b' and resid 432 through 444 removed outlier: 3.502A pdb=" N SER b 438 " --> pdb=" O VAL b 434 " (cutoff:3.500A) Processing helix chain 'b' and resid 444 through 453 removed outlier: 3.698A pdb=" N THR b 448 " --> pdb=" O ARG b 444 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 469 removed outlier: 4.154A pdb=" N ALA b 463 " --> pdb=" O ALA b 459 " (cutoff:3.500A) Processing helix chain 'b' and resid 497 through 516 Processing sheet with id=AA1, first strand: chain 'E' and resid 68 through 70 removed outlier: 6.611A pdb=" N ASP E 58 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN B 519 " --> pdb=" O ASP E 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 418 through 420 Processing sheet with id=AA3, first strand: chain 'E' and resid 530 through 534 removed outlier: 4.845A pdb=" N ILE E 530 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU H 48 " --> pdb=" O ILE E 530 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP E 532 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL H 50 " --> pdb=" O ASP E 532 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG E 534 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 405 through 407 Processing sheet with id=AA5, first strand: chain 'H' and resid 475 through 477 Processing sheet with id=AA6, first strand: chain 'H' and resid 519 through 521 removed outlier: 6.340A pdb=" N ILE H 520 " --> pdb=" O ILE Q 57 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL Q 56 " --> pdb=" O PHE Q 64 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE Q 64 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 203 through 204 removed outlier: 6.912A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 408 through 410 Processing sheet with id=AA9, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AB1, first strand: chain 'Z' and resid 478 through 479 Processing sheet with id=AB2, first strand: chain 'Z' and resid 518 through 523 removed outlier: 4.048A pdb=" N VAL Z 518 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N MET G 49 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU Z 520 " --> pdb=" O MET G 49 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU G 51 " --> pdb=" O GLU Z 520 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N MET Z 522 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 407 through 409 Processing sheet with id=AB4, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AB5, first strand: chain 'G' and resid 519 through 524 removed outlier: 7.413A pdb=" N MET A 44 " --> pdb=" O ASP G 520 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE G 522 " --> pdb=" O MET A 44 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 46 " --> pdb=" O ILE G 522 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N SER G 524 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 486 through 487 Processing sheet with id=AB7, first strand: chain 'A' and resid 527 through 532 removed outlier: 4.333A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR D 71 " --> pdb=" O LYS D 59 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 421 through 423 Processing sheet with id=AB9, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AC1, first strand: chain 'D' and resid 536 through 537 Processing sheet with id=AC2, first strand: chain 'B' and resid 406 through 408 Processing sheet with id=AC3, first strand: chain 'N' and resid 2 through 3 Processing sheet with id=AC4, first strand: chain 'N' and resid 33 through 35 removed outlier: 3.832A pdb=" N ASP N 33 " --> pdb=" O ASN N 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'e' and resid 68 through 70 removed outlier: 6.504A pdb=" N ASP e 58 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN b 519 " --> pdb=" O ASP e 58 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 418 through 420 Processing sheet with id=AC7, first strand: chain 'e' and resid 530 through 534 removed outlier: 4.871A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG e 534 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'h' and resid 405 through 407 Processing sheet with id=AC9, first strand: chain 'h' and resid 475 through 477 Processing sheet with id=AD1, first strand: chain 'h' and resid 519 through 521 removed outlier: 6.322A pdb=" N ILE h 520 " --> pdb=" O ILE q 57 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL q 56 " --> pdb=" O PHE q 64 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE q 64 " --> pdb=" O VAL q 56 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'q' and resid 203 through 204 removed outlier: 6.911A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'q' and resid 408 through 410 Processing sheet with id=AD4, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AD5, first strand: chain 'z' and resid 478 through 479 Processing sheet with id=AD6, first strand: chain 'z' and resid 518 through 523 removed outlier: 3.947A pdb=" N VAL z 518 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N MET g 49 " --> pdb=" O VAL z 518 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU z 520 " --> pdb=" O MET g 49 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU g 51 " --> pdb=" O GLU z 520 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET z 522 " --> pdb=" O LEU g 51 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'g' and resid 407 through 409 Processing sheet with id=AD8, first strand: chain 'g' and resid 478 through 480 Processing sheet with id=AD9, first strand: chain 'g' and resid 519 through 524 removed outlier: 4.353A pdb=" N ILE g 519 " --> pdb=" O ASP a 42 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N MET a 44 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP g 521 " --> pdb=" O MET a 44 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL a 46 " --> pdb=" O ASP g 521 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL g 523 " --> pdb=" O VAL a 46 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'a' and resid 486 through 487 Processing sheet with id=AE2, first strand: chain 'a' and resid 527 through 532 removed outlier: 4.364A pdb=" N ILE a 527 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE a 531 " --> pdb=" O GLN d 62 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR d 71 " --> pdb=" O LYS d 59 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 421 through 423 Processing sheet with id=AE4, first strand: chain 'd' and resid 493 through 494 Processing sheet with id=AE5, first strand: chain 'd' and resid 536 through 537 Processing sheet with id=AE6, first strand: chain 'b' and resid 406 through 408 Processing sheet with id=AE7, first strand: chain 'n' and resid 2 through 3 Processing sheet with id=AE8, first strand: chain 'n' and resid 33 through 35 removed outlier: 3.832A pdb=" N ASP n 33 " --> pdb=" O ASN n 98 " (cutoff:3.500A) 1709 hydrogen bonds defined for protein. 5004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.77 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11486 1.34 - 1.46: 4778 1.46 - 1.58: 17926 1.58 - 1.69: 88 1.69 - 1.81: 324 Bond restraints: 34602 Sorted by residual: bond pdb=" C4 ADP G 601 " pdb=" C5 ADP G 601 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP q 601 " pdb=" C5 ADP q 601 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C4 ADP g 601 " pdb=" C5 ADP g 601 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C4 ADP Q 601 " pdb=" C5 ADP Q 601 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C5 ADP Q 601 " pdb=" C6 ADP Q 601 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 34597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 46122 2.83 - 5.66: 647 5.66 - 8.49: 74 8.49 - 11.32: 34 11.32 - 14.15: 3 Bond angle restraints: 46880 Sorted by residual: angle pdb=" C GLY q 122 " pdb=" N LEU q 123 " pdb=" CA LEU q 123 " ideal model delta sigma weight residual 121.64 107.49 14.15 2.13e+00 2.20e-01 4.42e+01 angle pdb=" C GLY Q 122 " pdb=" N LEU Q 123 " pdb=" CA LEU Q 123 " ideal model delta sigma weight residual 121.64 107.55 14.09 2.13e+00 2.20e-01 4.38e+01 angle pdb=" CA LYS D 497 " pdb=" CB LYS D 497 " pdb=" CG LYS D 497 " ideal model delta sigma weight residual 114.10 124.59 -10.49 2.00e+00 2.50e-01 2.75e+01 angle pdb=" CA LYS d 497 " pdb=" CB LYS d 497 " pdb=" CG LYS d 497 " ideal model delta sigma weight residual 114.10 124.55 -10.45 2.00e+00 2.50e-01 2.73e+01 angle pdb=" N GLN z 17 " pdb=" CA GLN z 17 " pdb=" C GLN z 17 " ideal model delta sigma weight residual 113.55 107.63 5.92 1.26e+00 6.30e-01 2.21e+01 ... (remaining 46875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 20480 35.79 - 71.57: 648 71.57 - 107.36: 50 107.36 - 143.14: 9 143.14 - 178.93: 13 Dihedral angle restraints: 21200 sinusoidal: 8362 harmonic: 12838 Sorted by residual: dihedral pdb=" O1B ADP G 601 " pdb=" O3A ADP G 601 " pdb=" PB ADP G 601 " pdb=" PA ADP G 601 " ideal model delta sinusoidal sigma weight residual -60.00 118.92 -178.93 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP d 602 " pdb=" O5' ADP d 602 " pdb=" PA ADP d 602 " pdb=" O2A ADP d 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.28 177.73 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP D 602 " pdb=" O5' ADP D 602 " pdb=" PA ADP D 602 " pdb=" O2A ADP D 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.32 177.68 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 21197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4526 0.054 - 0.109: 992 0.109 - 0.163: 134 0.163 - 0.217: 30 0.217 - 0.272: 2 Chirality restraints: 5684 Sorted by residual: chirality pdb=" CB ILE e 507 " pdb=" CA ILE e 507 " pdb=" CG1 ILE e 507 " pdb=" CG2 ILE e 507 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE E 507 " pdb=" CA ILE E 507 " pdb=" CG1 ILE E 507 " pdb=" CG2 ILE E 507 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE b 51 " pdb=" CA ILE b 51 " pdb=" CG1 ILE b 51 " pdb=" CG2 ILE b 51 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 5681 not shown) Planarity restraints: 5936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 101 " 0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C SER B 101 " -0.068 2.00e-02 2.50e+03 pdb=" O SER B 101 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL B 102 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS e 89 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C LYS e 89 " 0.068 2.00e-02 2.50e+03 pdb=" O LYS e 89 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU e 90 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER b 101 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER b 101 " -0.068 2.00e-02 2.50e+03 pdb=" O SER b 101 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL b 102 " 0.023 2.00e-02 2.50e+03 ... (remaining 5933 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 171 2.40 - 3.03: 21175 3.03 - 3.65: 51377 3.65 - 4.28: 79436 4.28 - 4.90: 133726 Nonbonded interactions: 285885 Sorted by model distance: nonbonded pdb=" O3A ADP Q 601 " pdb="MG MG Q 602 " model vdw 1.778 2.170 nonbonded pdb=" O3A ADP q 601 " pdb="MG MG q 602 " model vdw 1.804 2.170 nonbonded pdb="MG MG d 601 " pdb=" O1A ADP d 602 " model vdw 1.949 2.170 nonbonded pdb="MG MG D 601 " pdb=" O1A ADP D 602 " model vdw 1.950 2.170 nonbonded pdb=" O3A ADP h 601 " pdb="MG MG h 602 " model vdw 1.979 2.170 ... (remaining 285880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'z' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'N' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 4.870 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: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 34.010 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.006 0.604 34603 Z= 0.407 Angle : 0.848 14.153 46880 Z= 0.435 Chirality : 0.046 0.272 5684 Planarity : 0.005 0.044 5936 Dihedral : 17.645 178.925 12876 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.81 % Favored : 92.01 % Rotamer: Outliers : 1.87 % Allowed : 18.12 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.70 (0.10), residues: 4410 helix: -2.79 (0.08), residues: 2784 sheet: -2.71 (0.38), residues: 124 loop : -3.49 (0.12), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG a 526 TYR 0.014 0.001 TYR E 420 PHE 0.020 0.002 PHE q 445 TRP 0.014 0.001 TRP N 109 HIS 0.010 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00557 (34602) covalent geometry : angle 0.84829 (46880) hydrogen bonds : bond 0.18083 ( 1709) hydrogen bonds : angle 7.55635 ( 5004) Misc. bond : bond 0.60371 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 942 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 138 GLU cc_start: 0.8147 (tp30) cc_final: 0.7869 (tp30) REVERT: E 426 GLU cc_start: 0.8488 (mp0) cc_final: 0.8260 (mp0) REVERT: E 501 MET cc_start: 0.8986 (mmp) cc_final: 0.8093 (mmt) REVERT: E 532 ASP cc_start: 0.7973 (t0) cc_final: 0.7650 (t0) REVERT: H 455 PHE cc_start: 0.8559 (m-10) cc_final: 0.8224 (m-10) REVERT: Q 52 MET cc_start: 0.8945 (mmm) cc_final: 0.8659 (mmm) REVERT: Q 85 MET cc_start: 0.8370 (mtm) cc_final: 0.7574 (mtt) REVERT: Q 113 GLU cc_start: 0.8018 (tt0) cc_final: 0.7729 (tt0) REVERT: Q 393 ASP cc_start: 0.7731 (t0) cc_final: 0.7496 (t0) REVERT: Z 79 LYS cc_start: 0.9061 (tmtt) cc_final: 0.8833 (tttp) REVERT: Z 101 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7936 (mm-30) REVERT: Z 104 LYS cc_start: 0.9035 (tttt) cc_final: 0.8784 (tttm) REVERT: Z 170 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7923 (mm-30) REVERT: Z 498 TYR cc_start: 0.7824 (t80) cc_final: 0.7589 (t80) REVERT: Z 502 LYS cc_start: 0.8482 (tttt) cc_final: 0.8107 (ttpp) REVERT: G 21 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8119 (mmtt) REVERT: G 47 MET cc_start: 0.8686 (mmt) cc_final: 0.8103 (mmt) REVERT: G 90 GLU cc_start: 0.7659 (tp30) cc_final: 0.7446 (tp30) REVERT: G 104 GLU cc_start: 0.8178 (tp30) cc_final: 0.7945 (tp30) REVERT: G 110 GLU cc_start: 0.7655 (tm-30) cc_final: 0.6241 (tm-30) REVERT: G 114 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7224 (mt-10) REVERT: A 430 MET cc_start: 0.8252 (ttm) cc_final: 0.7782 (ttm) REVERT: D 39 SER cc_start: 0.9380 (OUTLIER) cc_final: 0.9148 (m) REVERT: D 57 MET cc_start: 0.8866 (mmm) cc_final: 0.8649 (mmp) REVERT: D 60 MET cc_start: 0.7851 (mtm) cc_final: 0.7538 (mtm) REVERT: D 479 GLU cc_start: 0.8111 (tp30) cc_final: 0.7897 (tp30) REVERT: D 483 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8022 (ttm-80) REVERT: B 94 GLU cc_start: 0.7899 (tt0) cc_final: 0.7092 (tm-30) REVERT: B 108 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7465 (mm-30) REVERT: B 112 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7404 (mp0) REVERT: B 120 LYS cc_start: 0.8738 (mtmm) cc_final: 0.8524 (ttmm) REVERT: B 160 MET cc_start: 0.8869 (mmm) cc_final: 0.8669 (mmm) REVERT: B 414 GLU cc_start: 0.7894 (mp0) cc_final: 0.7553 (mp0) REVERT: e 39 MET cc_start: 0.8266 (tpp) cc_final: 0.8010 (mmm) REVERT: e 149 ASP cc_start: 0.7950 (p0) cc_final: 0.7727 (t70) REVERT: e 485 MET cc_start: 0.8173 (mmm) cc_final: 0.7959 (mpp) REVERT: e 486 ASN cc_start: 0.8548 (t0) cc_final: 0.8235 (t0) REVERT: e 489 LEU cc_start: 0.8651 (mp) cc_final: 0.8123 (mt) REVERT: e 522 GLN cc_start: 0.8242 (mt0) cc_final: 0.7911 (tt0) REVERT: q 52 MET cc_start: 0.8723 (mmm) cc_final: 0.8317 (mmm) REVERT: q 165 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7955 (mtp-110) REVERT: q 462 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7683 (mp0) REVERT: z 46 MET cc_start: 0.8379 (tpt) cc_final: 0.8015 (tpp) REVERT: z 62 VAL cc_start: 0.9358 (t) cc_final: 0.9092 (t) REVERT: z 79 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8792 (ttpp) REVERT: z 85 ASP cc_start: 0.7561 (p0) cc_final: 0.7163 (t0) REVERT: z 104 LYS cc_start: 0.8811 (tttt) cc_final: 0.8469 (tttp) REVERT: z 519 ASP cc_start: 0.8244 (m-30) cc_final: 0.7931 (m-30) REVERT: g 59 MET cc_start: 0.8235 (mtm) cc_final: 0.8031 (mtm) REVERT: g 83 ILE cc_start: 0.8829 (mm) cc_final: 0.8614 (mt) REVERT: g 110 GLU cc_start: 0.7453 (tm-30) cc_final: 0.6304 (tm-30) REVERT: g 114 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7098 (mt-10) REVERT: g 115 GLN cc_start: 0.8777 (mt0) cc_final: 0.8516 (mt0) REVERT: g 489 ASP cc_start: 0.8546 (t0) cc_final: 0.8238 (t0) REVERT: g 491 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8203 (mttm) REVERT: a 17 ILE cc_start: 0.9096 (tt) cc_final: 0.8848 (mt) REVERT: a 42 ASP cc_start: 0.7873 (m-30) cc_final: 0.7655 (m-30) REVERT: a 82 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8409 (tm-30) REVERT: a 440 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8238 (mm-30) REVERT: a 450 ASN cc_start: 0.8792 (t0) cc_final: 0.8448 (t0) REVERT: d 39 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8546 (t) REVERT: d 118 ASP cc_start: 0.7846 (t0) cc_final: 0.7294 (t0) REVERT: d 479 GLU cc_start: 0.8143 (tp30) cc_final: 0.7584 (tp30) REVERT: d 483 ARG cc_start: 0.8561 (ttm-80) cc_final: 0.8229 (mmm-85) REVERT: d 534 ASP cc_start: 0.6238 (OUTLIER) cc_final: 0.5892 (t70) REVERT: b 76 VAL cc_start: 0.8559 (t) cc_final: 0.8338 (m) REVERT: b 135 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8320 (ttmm) REVERT: b 390 LEU cc_start: 0.9014 (tp) cc_final: 0.8647 (tp) REVERT: b 441 LYS cc_start: 0.8556 (mttt) cc_final: 0.8291 (mtpp) REVERT: b 498 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7597 (mt0) REVERT: n 98 ASN cc_start: 0.6763 (t0) cc_final: 0.6370 (t0) outliers start: 68 outliers final: 17 residues processed: 989 average time/residue: 0.2482 time to fit residues: 384.3225 Evaluate side-chains 621 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 600 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 127 GLU Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 450 CYS Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain q residue 127 GLU Chi-restraints excluded: chain z residue 15 ARG Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 450 CYS Chi-restraints excluded: chain d residue 534 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.5122 > 50: distance: 92 - 115: 31.463 distance: 101 - 126: 25.770 distance: 107 - 131: 32.350 distance: 110 - 115: 29.276 distance: 111 - 138: 27.195 distance: 116 - 117: 19.822 distance: 116 - 119: 34.969 distance: 117 - 118: 50.149 distance: 117 - 126: 33.652 distance: 118 - 143: 59.731 distance: 119 - 120: 38.314 distance: 120 - 121: 34.606 distance: 121 - 122: 21.460 distance: 122 - 123: 34.718 distance: 123 - 124: 20.608 distance: 123 - 125: 27.786 distance: 126 - 127: 40.487 distance: 127 - 128: 57.476 distance: 127 - 130: 30.622 distance: 128 - 129: 46.626 distance: 128 - 131: 56.416 distance: 131 - 132: 39.808 distance: 132 - 133: 60.986 distance: 132 - 135: 39.394 distance: 133 - 134: 59.428 distance: 133 - 138: 13.140 distance: 135 - 136: 42.339 distance: 135 - 137: 42.606 distance: 138 - 139: 42.067 distance: 139 - 140: 51.387 distance: 139 - 142: 36.536 distance: 140 - 141: 41.126 distance: 140 - 143: 62.800 distance: 143 - 144: 56.647 distance: 144 - 145: 34.043 distance: 144 - 147: 31.902 distance: 145 - 146: 51.544 distance: 145 - 152: 49.612 distance: 147 - 148: 43.175 distance: 148 - 149: 27.870 distance: 149 - 150: 7.909 distance: 149 - 151: 9.503 distance: 153 - 154: 57.598 distance: 153 - 156: 54.777 distance: 154 - 155: 33.685 distance: 154 - 157: 28.827 distance: 157 - 158: 10.213 distance: 158 - 159: 18.219 distance: 158 - 161: 3.895 distance: 159 - 160: 28.712 distance: 159 - 165: 28.581 distance: 161 - 162: 18.494 distance: 162 - 163: 37.455 distance: 162 - 164: 22.542 distance: 165 - 166: 35.813 distance: 166 - 167: 26.558 distance: 166 - 169: 8.419 distance: 167 - 168: 26.492 distance: 167 - 174: 43.783 distance: 168 - 196: 28.044 distance: 169 - 170: 17.718 distance: 170 - 171: 7.994 distance: 171 - 172: 16.661 distance: 171 - 173: 24.957 distance: 174 - 175: 17.118 distance: 175 - 176: 19.823 distance: 175 - 178: 14.243 distance: 176 - 177: 7.941 distance: 176 - 181: 9.438 distance: 177 - 203: 10.365 distance: 178 - 179: 47.064 distance: 178 - 180: 40.793 distance: 181 - 182: 15.613 distance: 182 - 183: 40.936 distance: 182 - 185: 16.934 distance: 183 - 184: 40.638 distance: 183 - 189: 20.451 distance: 184 - 209: 28.693 distance: 185 - 186: 26.354 distance: 185 - 187: 23.240 distance: 186 - 188: 5.752