Starting phenix.real_space_refine on Mon Sep 14 23:32:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nvo_12608/09_2026/7nvo_12608.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nvo_12608/09_2026/7nvo_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_12608/09_2026/7nvo_12608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nvo_12608/09_2026/7nvo_12608.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nvo_12608/09_2026/7nvo_12608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nvo_12608/09_2026/7nvo_12608.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7nvo_12608/09_2026/7nvo_12608.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nvo_12608/09_2026/7nvo_12608.cif" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.47, per 1000 atoms: 0.22 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: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 0.95 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: 6.80 Time building geometry restraints manager: 3.82 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: 0.07 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: 5.500 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: 0.050 Extract box with map and model: 0.610 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.100 Find NCS groups from input model: 0.320 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 are 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/Z covalent geometry : bond 0.00557 / 0.25 (34602) covalent geometry : angle 0.84829 / 0.43 (46880) hydrogen bonds : bond 0.18083 / 12.12 ( 1709) hydrogen bonds : angle 7.55635 / 5.33 ( 5004) Misc. bond : bond 0.60371 / 31.77 ( 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 : 1.148 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: 0.8017 (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: 0.9062 (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: 0.8783 (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: 0.8011 (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: 0.8724 (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: 0.8560 (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: 0.7962 (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: 0.2295 time to fit residues: 358.9768 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 : 1.449 ------------------------------------------------------------------------------- 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 ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.5122 > 50:) chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.9980 chunk 424 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 55 ASN E 129 HIS ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 GLN E 469 ASN E 522 GLN H 25 ASN ** H 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 ASN H 468 HIS H 480 ASN Q 58 ASN Q 67 ASN Q 80 HIS Q 140 HIS Q 461 ASN Z 31 GLN Z 68 GLN Z 71 HIS Z 105 GLN Z 386 GLN Z 434 GLN G 442 GLN G 454 ASN G 472 GLN G 481 ASN ** G 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN A 113 HIS A 455 ASN A 472 ASN D 125 GLN D 129 HIS D 482 ASN D 494 ASN B 399 GLN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN N 32 ASN N 100 ASN e 147 HIS e 469 ASN e 481 GLN e 522 GLN h 25 ASN ** h 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 468 HIS q 41 GLN q 58 ASN q 80 HIS q 140 HIS ** q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 185 GLN q 435 GLN z 31 GLN z 68 GLN z 71 HIS z 105 GLN z 132 GLN z 161 HIS z 382 HIS z 386 GLN z 434 GLN z 453 GLN z 470 HIS g 26 ASN g 111 HIS g 442 GLN g 454 ASN ** g 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 113 HIS a 435 GLN a 455 ASN a 472 ASN d 129 HIS d 482 ASN d 494 ASN d 502 ASN d 510 GLN b 391 HIS b 399 GLN ** b 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 464 GLN n 32 ASN n 100 ASN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.093527 restraints weight = 63427.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.096739 restraints weight = 32426.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.098889 restraints weight = 20802.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.100338 restraints weight = 15517.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.101254 restraints weight = 12714.981| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34603 Z= 0.162 Angle : 0.726 12.851 46880 Z= 0.354 Chirality : 0.043 0.206 5684 Planarity : 0.005 0.069 5936 Dihedral : 11.937 161.571 4918 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.38 % Favored : 93.57 % Rotamer: Outliers : 4.06 % Allowed : 20.13 % Favored : 75.81 % 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 are not related in a simple way. whole: -2.96 (0.12), residues: 4410 helix: -1.41 (0.09), residues: 2822 sheet: -2.47 (0.45), residues: 100 loop : -2.81 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 68 TYR 0.015 0.001 TYR Q 505 PHE 0.012 0.001 PHE h 455 TRP 0.008 0.001 TRP z 495 HIS 0.010 0.001 HIS g 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (34602) covalent geometry : angle 0.72597 / 0.35 (46880) hydrogen bonds : bond 0.04281 / 2.86 ( 1709) hydrogen bonds : angle 4.77916 / 3.39 ( 5004) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 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 798 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 650 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 29 MET cc_start: 0.6848 (ttm) cc_final: 0.6562 (ttm) REVERT: E 121 GLU cc_start: 0.8257 (tt0) cc_final: 0.7931 (tt0) REVERT: E 532 ASP cc_start: 0.7725 (t0) cc_final: 0.7420 (t0) REVERT: H 34 GLU cc_start: 0.8093 (tp30) cc_final: 0.7773 (tp30) REVERT: H 85 SER cc_start: 0.8935 (m) cc_final: 0.8597 (p) REVERT: H 86 GLN cc_start: 0.8775 (tp40) cc_final: 0.8557 (tp-100) REVERT: H 455 PHE cc_start: 0.8559 (m-10) cc_final: 0.8206 (m-10) REVERT: H 481 ASN cc_start: 0.8249 (p0) cc_final: 0.7979 (p0) REVERT: Q 113 GLU cc_start: 0.7727 (tt0) cc_final: 0.7435 (tt0) REVERT: Q 393 ASP cc_start: 0.7724 (t0) cc_final: 0.6903 (t0) REVERT: Q 397 ASN cc_start: 0.8795 (m-40) cc_final: 0.8194 (m-40) REVERT: Z 53 ASP cc_start: 0.7755 (m-30) cc_final: 0.7509 (m-30) REVERT: Z 170 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8143 (mm-30) REVERT: Z 502 LYS cc_start: 0.8472 (tttt) cc_final: 0.8203 (ttpp) REVERT: G 47 MET cc_start: 0.8656 (mmt) cc_final: 0.8207 (mmt) REVERT: G 110 GLU cc_start: 0.7493 (tm-30) cc_final: 0.6225 (tm-30) REVERT: G 114 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7014 (mt-10) REVERT: G 490 MET cc_start: 0.9162 (mmt) cc_final: 0.8543 (mmt) REVERT: A 446 LEU cc_start: 0.8757 (pp) cc_final: 0.8522 (pp) REVERT: D 39 SER cc_start: 0.9316 (OUTLIER) cc_final: 0.9059 (t) REVERT: D 483 ARG cc_start: 0.8807 (ttm-80) cc_final: 0.8353 (ttm-80) REVERT: B 70 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8826 (mt) REVERT: e 93 GLU cc_start: 0.7924 (tp30) cc_final: 0.7686 (mm-30) REVERT: e 138 GLU cc_start: 0.7942 (tp30) cc_final: 0.7691 (tp30) REVERT: e 149 ASP cc_start: 0.7689 (p0) cc_final: 0.7319 (t70) REVERT: e 522 GLN cc_start: 0.8243 (mt0) cc_final: 0.8015 (tt0) REVERT: q 52 MET cc_start: 0.8696 (mmm) cc_final: 0.8377 (mmm) REVERT: q 75 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7396 (mm-30) REVERT: q 79 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7594 (mt0) REVERT: q 111 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8586 (mp) REVERT: z 62 VAL cc_start: 0.9416 (t) cc_final: 0.9130 (t) REVERT: z 85 ASP cc_start: 0.7195 (p0) cc_final: 0.6737 (t0) REVERT: z 104 LYS cc_start: 0.8829 (tttt) cc_final: 0.8622 (tttp) REVERT: z 143 MET cc_start: 0.6654 (mmp) cc_final: 0.6287 (mmp) REVERT: g 57 ILE cc_start: 0.9242 (mm) cc_final: 0.8946 (mm) REVERT: g 73 GLN cc_start: 0.6975 (tp-100) cc_final: 0.6730 (tp-100) REVERT: g 110 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6705 (tm-30) REVERT: g 453 GLN cc_start: 0.8394 (tt0) cc_final: 0.8176 (tt0) REVERT: g 491 LYS cc_start: 0.8511 (mtmt) cc_final: 0.8215 (mttm) REVERT: a 17 ILE cc_start: 0.9079 (tt) cc_final: 0.8818 (mt) REVERT: a 82 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8390 (tm-30) REVERT: a 123 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8585 (mp) REVERT: a 440 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7876 (mm-30) REVERT: d 39 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8447 (t) REVERT: d 534 ASP cc_start: 0.6363 (OUTLIER) cc_final: 0.6059 (t70) REVERT: b 65 ASN cc_start: 0.8199 (t0) cc_final: 0.7950 (t0) REVERT: b 91 GLN cc_start: 0.9415 (mm-40) cc_final: 0.8175 (tm-30) REVERT: b 141 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8427 (pt) REVERT: b 399 GLN cc_start: 0.8377 (mm110) cc_final: 0.7632 (mm-40) REVERT: b 441 LYS cc_start: 0.8542 (mttt) cc_final: 0.8334 (mtpp) REVERT: b 488 MET cc_start: 0.9038 (mmp) cc_final: 0.8831 (mmt) REVERT: b 498 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7329 (mt0) outliers start: 148 outliers final: 85 residues processed: 763 average time/residue: 0.2089 time to fit residues: 264.4763 Evaluate side-chains 648 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 555 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 458 THR Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 65 HIS Chi-restraints excluded: chain Z residue 90 ASP Chi-restraints excluded: chain Z residue 149 ILE Chi-restraints excluded: chain Z residue 402 ILE Chi-restraints excluded: chain Z residue 406 CYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 450 CYS Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 442 THR Chi-restraints excluded: chain e residue 476 GLU Chi-restraints excluded: chain e residue 503 GLN Chi-restraints excluded: chain e residue 509 THR Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 114 GLU Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain h residue 458 THR Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain h residue 515 SER Chi-restraints excluded: chain q residue 57 ILE Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 79 GLN Chi-restraints excluded: chain q residue 111 LEU Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 163 LEU Chi-restraints excluded: chain q residue 202 ILE Chi-restraints excluded: chain q residue 458 VAL Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 118 ILE Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 402 ILE Chi-restraints excluded: chain z residue 418 MET Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain a residue 435 GLN Chi-restraints excluded: chain a residue 464 VAL Chi-restraints excluded: chain a residue 513 SER 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 532 ILE Chi-restraints excluded: chain d residue 534 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 275 optimal weight: 0.6980 chunk 247 optimal weight: 10.0000 chunk 420 optimal weight: 8.9990 chunk 249 optimal weight: 0.6980 chunk 234 optimal weight: 6.9990 chunk 410 optimal weight: 0.3980 chunk 115 optimal weight: 0.9980 chunk 422 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 55 ASN E 147 HIS H 432 GLN H 459 ASN Q 50 ASN Z 470 HIS G 64 ASN ** G 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN B 453 ASN ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 86 GLN h 432 GLN z 61 ASN g 111 HIS ** g 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 125 GLN b 391 HIS b 453 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.095529 restraints weight = 62151.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.098890 restraints weight = 30902.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.101190 restraints weight = 19543.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102702 restraints weight = 14338.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.103700 restraints weight = 11664.016| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34603 Z= 0.131 Angle : 0.676 12.101 46880 Z= 0.325 Chirality : 0.041 0.194 5684 Planarity : 0.004 0.045 5936 Dihedral : 11.164 154.804 4896 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.34 % Favored : 93.62 % Rotamer: Outliers : 3.98 % Allowed : 21.22 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.12), residues: 4410 helix: -0.71 (0.10), residues: 2804 sheet: -1.26 (0.55), residues: 84 loop : -2.56 (0.14), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 483 TYR 0.020 0.001 TYR Q 505 PHE 0.011 0.001 PHE g 112 TRP 0.007 0.001 TRP z 495 HIS 0.010 0.001 HIS q 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (34602) covalent geometry : angle 0.67554 / 0.33 (46880) hydrogen bonds : bond 0.03698 / 2.47 ( 1709) hydrogen bonds : angle 4.37388 / 3.12 ( 5004) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 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 747 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 602 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 58 ASP cc_start: 0.7971 (m-30) cc_final: 0.7730 (m-30) REVERT: E 121 GLU cc_start: 0.8243 (tt0) cc_final: 0.7950 (tt0) REVERT: E 532 ASP cc_start: 0.7722 (t0) cc_final: 0.7250 (t0) REVERT: H 85 SER cc_start: 0.8848 (m) cc_final: 0.8589 (p) REVERT: H 455 PHE cc_start: 0.8480 (m-10) cc_final: 0.8137 (m-10) REVERT: H 481 ASN cc_start: 0.8275 (p0) cc_final: 0.7978 (p0) REVERT: Q 393 ASP cc_start: 0.7602 (t0) cc_final: 0.6598 (t0) REVERT: Q 397 ASN cc_start: 0.8726 (m-40) cc_final: 0.8269 (m110) REVERT: Z 502 LYS cc_start: 0.8573 (tttt) cc_final: 0.8318 (ttpp) REVERT: G 47 MET cc_start: 0.8622 (mmt) cc_final: 0.8137 (mmt) REVERT: G 110 GLU cc_start: 0.7554 (tm-30) cc_final: 0.6268 (tm-30) REVERT: G 114 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7025 (mt-10) REVERT: A 446 LEU cc_start: 0.8793 (pp) cc_final: 0.8444 (pp) REVERT: A 468 ARG cc_start: 0.8970 (ttp80) cc_final: 0.8691 (mtp-110) REVERT: B 70 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8792 (mt) REVERT: e 138 GLU cc_start: 0.8005 (tp30) cc_final: 0.7757 (tm-30) REVERT: e 149 ASP cc_start: 0.7679 (p0) cc_final: 0.7142 (t70) REVERT: e 522 GLN cc_start: 0.8255 (mt0) cc_final: 0.7959 (tt0) REVERT: q 52 MET cc_start: 0.8650 (mmm) cc_final: 0.8376 (mmm) REVERT: q 75 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7452 (mm-30) REVERT: q 85 MET cc_start: 0.8013 (mmm) cc_final: 0.7736 (mmp) REVERT: q 111 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8522 (mp) REVERT: z 54 ILE cc_start: 0.8715 (pt) cc_final: 0.8336 (pt) REVERT: z 65 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.7456 (t70) REVERT: z 143 MET cc_start: 0.6646 (mmp) cc_final: 0.6275 (mmt) REVERT: g 57 ILE cc_start: 0.8998 (mm) cc_final: 0.8739 (mm) REVERT: g 73 GLN cc_start: 0.6859 (tp-100) cc_final: 0.6584 (tp-100) REVERT: g 110 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6678 (tm-30) REVERT: g 115 GLN cc_start: 0.8673 (mt0) cc_final: 0.8457 (mt0) REVERT: g 491 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8223 (mttm) REVERT: a 17 ILE cc_start: 0.9030 (tt) cc_final: 0.8743 (mt) REVERT: a 82 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8367 (tm-30) REVERT: a 123 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8510 (mp) REVERT: a 450 ASN cc_start: 0.8671 (t0) cc_final: 0.8262 (t0) REVERT: d 39 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8601 (t) REVERT: d 446 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7896 (mmt) REVERT: b 65 ASN cc_start: 0.7938 (t0) cc_final: 0.7675 (t0) REVERT: b 91 GLN cc_start: 0.9420 (mm-40) cc_final: 0.8252 (tm-30) REVERT: b 141 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8460 (pt) REVERT: b 397 LEU cc_start: 0.9245 (mt) cc_final: 0.9041 (mt) REVERT: b 399 GLN cc_start: 0.8275 (mm110) cc_final: 0.7682 (mm-40) REVERT: b 441 LYS cc_start: 0.8536 (mttt) cc_final: 0.8318 (mtpp) REVERT: b 445 MET cc_start: 0.8512 (tpp) cc_final: 0.8216 (mmm) REVERT: b 498 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7372 (mt0) outliers start: 145 outliers final: 88 residues processed: 710 average time/residue: 0.2070 time to fit residues: 244.1834 Evaluate side-chains 628 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 533 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 141 GLU Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 65 HIS Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 402 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 450 CYS Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 436 GLU Chi-restraints excluded: chain e residue 442 THR Chi-restraints excluded: chain e residue 457 VAL Chi-restraints excluded: chain e residue 503 GLN Chi-restraints excluded: chain e residue 506 VAL Chi-restraints excluded: chain e residue 523 MET Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 492 VAL Chi-restraints excluded: chain h residue 515 SER Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 79 GLN Chi-restraints excluded: chain q residue 111 LEU Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 157 ILE Chi-restraints excluded: chain q residue 163 LEU Chi-restraints excluded: chain q residue 166 THR Chi-restraints excluded: chain z residue 15 ARG Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 56 LEU Chi-restraints excluded: chain z residue 65 HIS Chi-restraints excluded: chain z residue 67 MET Chi-restraints excluded: chain z residue 118 ILE Chi-restraints excluded: chain z residue 140 SER Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 402 ILE Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 476 LEU Chi-restraints excluded: chain z residue 522 MET Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 415 VAL Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain a residue 513 SER Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 450 CYS Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 141 LEU Chi-restraints excluded: chain b residue 436 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 378 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 382 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 83 optimal weight: 0.0030 chunk 281 optimal weight: 7.9990 chunk 363 optimal weight: 0.8980 chunk 226 optimal weight: 8.9990 chunk 164 optimal weight: 0.7980 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 459 ASN Q 67 ASN Q 185 GLN G 71 GLN ** G 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 129 HIS q 50 ASN z 454 ASN a 435 GLN b 391 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.094497 restraints weight = 69550.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.097901 restraints weight = 34530.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.100204 restraints weight = 21730.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.101741 restraints weight = 15924.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.102719 restraints weight = 12920.749| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34603 Z= 0.146 Angle : 0.665 11.600 46880 Z= 0.319 Chirality : 0.042 0.289 5684 Planarity : 0.004 0.042 5936 Dihedral : 10.795 153.009 4892 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.18 % Favored : 93.78 % Rotamer: Outliers : 5.02 % Allowed : 20.68 % Favored : 74.30 % 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 are not related in a simple way. whole: -1.70 (0.12), residues: 4410 helix: -0.40 (0.10), residues: 2822 sheet: -1.09 (0.57), residues: 88 loop : -2.45 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 483 TYR 0.016 0.001 TYR Q 505 PHE 0.011 0.001 PHE q 64 TRP 0.007 0.001 TRP N 105 HIS 0.008 0.001 HIS q 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (34602) covalent geometry : angle 0.66456 / 0.32 (46880) hydrogen bonds : bond 0.03551 / 2.36 ( 1709) hydrogen bonds : angle 4.19186 / 2.99 ( 5004) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 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 744 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 561 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 58 ASP cc_start: 0.7998 (m-30) cc_final: 0.7752 (m-30) REVERT: E 121 GLU cc_start: 0.8262 (tt0) cc_final: 0.7920 (tt0) REVERT: E 532 ASP cc_start: 0.7737 (t0) cc_final: 0.7306 (t0) REVERT: H 85 SER cc_start: 0.8975 (m) cc_final: 0.8715 (p) REVERT: H 92 ASP cc_start: 0.7399 (t0) cc_final: 0.7178 (t0) REVERT: H 455 PHE cc_start: 0.8508 (m-10) cc_final: 0.8164 (m-10) REVERT: H 481 ASN cc_start: 0.8300 (p0) cc_final: 0.7993 (p0) REVERT: Q 393 ASP cc_start: 0.7626 (t0) cc_final: 0.6607 (t0) REVERT: Q 397 ASN cc_start: 0.8633 (m-40) cc_final: 0.8221 (m110) REVERT: Z 393 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7397 (t70) REVERT: Z 459 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8579 (pp) REVERT: Z 502 LYS cc_start: 0.8627 (tttt) cc_final: 0.8355 (ttpp) REVERT: G 110 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7133 (tm-30) REVERT: G 490 MET cc_start: 0.9088 (mmt) cc_final: 0.8768 (mmt) REVERT: A 430 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7445 (ttp) REVERT: A 446 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8469 (pp) REVERT: A 468 ARG cc_start: 0.8912 (ttp80) cc_final: 0.8594 (mtp-110) REVERT: D 73 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8497 (p0) REVERT: D 446 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7626 (mmt) REVERT: D 479 GLU cc_start: 0.7924 (tp30) cc_final: 0.7558 (tp30) REVERT: B 70 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8765 (mt) REVERT: e 149 ASP cc_start: 0.7736 (p0) cc_final: 0.7110 (t70) REVERT: e 485 MET cc_start: 0.8185 (mmm) cc_final: 0.7976 (mpp) REVERT: e 522 GLN cc_start: 0.8337 (mt0) cc_final: 0.7959 (tt0) REVERT: h 448 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7209 (tp40) REVERT: q 52 MET cc_start: 0.8648 (mmm) cc_final: 0.8381 (mmm) REVERT: q 85 MET cc_start: 0.8058 (mmm) cc_final: 0.7830 (mmp) REVERT: q 111 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8561 (mp) REVERT: z 44 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8312 (mtt) REVERT: z 54 ILE cc_start: 0.8715 (pt) cc_final: 0.8329 (pt) REVERT: z 65 HIS cc_start: 0.7741 (OUTLIER) cc_final: 0.7391 (t-170) REVERT: z 118 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8605 (pt) REVERT: z 143 MET cc_start: 0.6635 (mmp) cc_final: 0.6281 (mmt) REVERT: g 57 ILE cc_start: 0.9020 (mm) cc_final: 0.8820 (mm) REVERT: g 110 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6670 (tm-30) REVERT: g 491 LYS cc_start: 0.8464 (mtmt) cc_final: 0.8226 (mttm) REVERT: g 504 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: a 17 ILE cc_start: 0.9029 (tt) cc_final: 0.8733 (mt) REVERT: a 82 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8380 (tm-30) REVERT: a 123 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8574 (mp) REVERT: a 446 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8432 (pp) REVERT: a 450 ASN cc_start: 0.8694 (t0) cc_final: 0.8307 (t0) REVERT: d 446 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7863 (mmt) REVERT: d 494 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7660 (p0) REVERT: b 65 ASN cc_start: 0.8037 (t0) cc_final: 0.7694 (t0) REVERT: b 91 GLN cc_start: 0.9407 (mm-40) cc_final: 0.8289 (tm-30) REVERT: b 141 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8409 (pt) REVERT: b 399 GLN cc_start: 0.8332 (mm110) cc_final: 0.7822 (mm-40) REVERT: b 441 LYS cc_start: 0.8551 (mttt) cc_final: 0.8327 (mtpp) REVERT: b 445 MET cc_start: 0.8521 (tpp) cc_final: 0.8193 (mmm) REVERT: b 498 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7539 (mt0) outliers start: 183 outliers final: 119 residues processed: 698 average time/residue: 0.2041 time to fit residues: 240.4274 Evaluate side-chains 659 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 522 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 458 THR Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 141 GLU Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 65 HIS Chi-restraints excluded: chain Z residue 90 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 393 ASP Chi-restraints excluded: chain Z residue 402 ILE Chi-restraints excluded: chain Z residue 406 CYS Chi-restraints excluded: chain Z residue 459 LEU Chi-restraints excluded: chain Z residue 476 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 450 CYS Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 102 ILE Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 436 GLU Chi-restraints excluded: chain e residue 442 THR Chi-restraints excluded: chain e residue 457 VAL Chi-restraints excluded: chain e residue 476 GLU Chi-restraints excluded: chain e residue 503 GLN Chi-restraints excluded: chain e residue 506 VAL Chi-restraints excluded: chain e residue 523 MET Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 114 GLU Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain h residue 448 GLN Chi-restraints excluded: chain h residue 458 THR Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain h residue 492 VAL Chi-restraints excluded: chain h residue 515 SER Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 79 GLN Chi-restraints excluded: chain q residue 111 LEU Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 157 ILE Chi-restraints excluded: chain q residue 163 LEU Chi-restraints excluded: chain q residue 166 THR Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 56 LEU Chi-restraints excluded: chain z residue 65 HIS Chi-restraints excluded: chain z residue 67 MET Chi-restraints excluded: chain z residue 118 ILE Chi-restraints excluded: chain z residue 140 SER Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 402 ILE Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain z residue 459 LEU Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 476 LEU Chi-restraints excluded: chain z residue 499 CYS Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 95 THR Chi-restraints excluded: chain g residue 504 GLN Chi-restraints excluded: chain g residue 505 THR Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 415 VAL Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain a residue 435 GLN Chi-restraints excluded: chain a residue 446 LEU Chi-restraints excluded: chain a residue 464 VAL Chi-restraints excluded: chain a residue 473 GLU Chi-restraints excluded: chain a residue 513 SER Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 450 CYS Chi-restraints excluded: chain d residue 494 ASN Chi-restraints excluded: chain d residue 532 ILE Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 141 LEU Chi-restraints excluded: chain b residue 144 SER Chi-restraints excluded: chain b residue 153 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 91 optimal weight: 0.0020 chunk 245 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 286 optimal weight: 9.9990 chunk 401 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 434 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 405 optimal weight: 0.8980 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 459 ASN Q 185 GLN Q 461 ASN G 434 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 499 ASN g 115 GLN g 453 GLN ** g 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 435 GLN ** d 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.096814 restraints weight = 58281.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.100010 restraints weight = 30282.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.102143 restraints weight = 19607.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.103602 restraints weight = 14654.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.104551 restraints weight = 12015.773| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 34603 Z= 0.124 Angle : 0.646 11.366 46880 Z= 0.309 Chirality : 0.041 0.203 5684 Planarity : 0.004 0.041 5936 Dihedral : 10.517 158.059 4891 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.86 % Favored : 94.10 % Rotamer: Outliers : 4.83 % Allowed : 21.11 % Favored : 74.05 % 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 are not related in a simple way. whole: -1.37 (0.13), residues: 4410 helix: -0.13 (0.10), residues: 2822 sheet: -0.97 (0.57), residues: 88 loop : -2.35 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG e 142 TYR 0.025 0.001 TYR z 498 PHE 0.011 0.001 PHE q 64 TRP 0.006 0.001 TRP z 495 HIS 0.007 0.001 HIS q 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (34602) covalent geometry : angle 0.64623 / 0.31 (46880) hydrogen bonds : bond 0.03369 / 2.25 ( 1709) hydrogen bonds : angle 4.06737 / 2.90 ( 5004) Misc. bond : bond 0.00052 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 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 741 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 565 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 58 ASP cc_start: 0.7960 (m-30) cc_final: 0.7727 (m-30) REVERT: E 91 MET cc_start: 0.8491 (mtp) cc_final: 0.8239 (mtp) REVERT: E 448 MET cc_start: 0.8523 (mtp) cc_final: 0.8125 (mtt) REVERT: E 501 MET cc_start: 0.8885 (mmt) cc_final: 0.8656 (mmt) REVERT: E 532 ASP cc_start: 0.7568 (t0) cc_final: 0.7182 (t0) REVERT: H 34 GLU cc_start: 0.8030 (tp30) cc_final: 0.7646 (tp30) REVERT: H 85 SER cc_start: 0.8978 (m) cc_final: 0.8733 (p) REVERT: H 455 PHE cc_start: 0.8422 (m-10) cc_final: 0.8088 (m-10) REVERT: H 481 ASN cc_start: 0.8294 (p0) cc_final: 0.7972 (p0) REVERT: Q 393 ASP cc_start: 0.7624 (t0) cc_final: 0.6641 (t0) REVERT: Q 397 ASN cc_start: 0.8528 (m-40) cc_final: 0.8174 (m110) REVERT: Z 46 MET cc_start: 0.8126 (tpt) cc_final: 0.7913 (tpt) REVERT: Z 459 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8581 (pp) REVERT: Z 502 LYS cc_start: 0.8608 (tttt) cc_final: 0.8386 (ttpp) REVERT: G 64 ASN cc_start: 0.8411 (m110) cc_final: 0.8189 (m-40) REVERT: G 68 ARG cc_start: 0.7786 (mtm110) cc_final: 0.7321 (mtm180) REVERT: G 110 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7239 (tm-30) REVERT: A 430 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7293 (ttp) REVERT: A 446 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8486 (pp) REVERT: D 80 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7463 (pp30) REVERT: D 483 ARG cc_start: 0.8641 (ttm-80) cc_final: 0.8389 (ptm160) REVERT: B 91 GLN cc_start: 0.9426 (mm-40) cc_final: 0.8270 (tm-30) REVERT: e 135 ASP cc_start: 0.8059 (m-30) cc_final: 0.7515 (m-30) REVERT: e 149 ASP cc_start: 0.7587 (p0) cc_final: 0.6968 (t70) REVERT: e 522 GLN cc_start: 0.8317 (mt0) cc_final: 0.7972 (tt0) REVERT: h 448 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.7173 (tp40) REVERT: h 451 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7684 (m-30) REVERT: q 52 MET cc_start: 0.8575 (mmm) cc_final: 0.8350 (mmm) REVERT: q 111 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8493 (mp) REVERT: z 44 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8271 (mtt) REVERT: z 65 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.7294 (t70) REVERT: z 143 MET cc_start: 0.6573 (mmp) cc_final: 0.6187 (mmt) REVERT: g 57 ILE cc_start: 0.8975 (mm) cc_final: 0.8772 (mm) REVERT: g 110 GLU cc_start: 0.7482 (tm-30) cc_final: 0.6738 (tm-30) REVERT: g 491 LYS cc_start: 0.8407 (mtmt) cc_final: 0.8176 (mttm) REVERT: g 504 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: a 17 ILE cc_start: 0.8939 (tt) cc_final: 0.8658 (mt) REVERT: a 82 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8346 (tm-30) REVERT: a 123 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8605 (mp) REVERT: a 446 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8404 (pp) REVERT: a 450 ASN cc_start: 0.8635 (t0) cc_final: 0.8254 (t0) REVERT: d 36 SER cc_start: 0.9078 (m) cc_final: 0.8840 (m) REVERT: d 446 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7881 (mmt) REVERT: b 91 GLN cc_start: 0.9362 (mm-40) cc_final: 0.9039 (tp-100) REVERT: b 141 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8444 (pt) REVERT: b 397 LEU cc_start: 0.9253 (mt) cc_final: 0.8997 (mt) REVERT: b 399 GLN cc_start: 0.8263 (mm110) cc_final: 0.7698 (mm-40) REVERT: b 441 LYS cc_start: 0.8527 (mttt) cc_final: 0.8308 (mtpp) REVERT: b 445 MET cc_start: 0.8572 (tpp) cc_final: 0.8238 (mmm) REVERT: b 498 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7351 (mt0) outliers start: 176 outliers final: 115 residues processed: 695 average time/residue: 0.2023 time to fit residues: 235.2837 Evaluate side-chains 662 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 533 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 458 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 141 GLU Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 65 HIS Chi-restraints excluded: chain Z residue 90 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 402 ILE Chi-restraints excluded: chain Z residue 406 CYS Chi-restraints excluded: chain Z residue 459 LEU Chi-restraints excluded: chain Z residue 476 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 505 THR Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain D residue 80 GLN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 450 CYS Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 436 GLU Chi-restraints excluded: chain e residue 442 THR Chi-restraints excluded: chain e residue 457 VAL Chi-restraints excluded: chain e residue 476 GLU Chi-restraints excluded: chain e residue 499 ASN Chi-restraints excluded: chain e residue 523 MET Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 448 GLN Chi-restraints excluded: chain h residue 451 ASP Chi-restraints excluded: chain h residue 458 THR Chi-restraints excluded: chain h residue 492 VAL Chi-restraints excluded: chain h residue 515 SER Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 79 GLN Chi-restraints excluded: chain q residue 111 LEU Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 157 ILE Chi-restraints excluded: chain q residue 163 LEU Chi-restraints excluded: chain q residue 166 THR Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 13 VAL Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 56 LEU Chi-restraints excluded: chain z residue 65 HIS Chi-restraints excluded: chain z residue 67 MET Chi-restraints excluded: chain z residue 90 ASP Chi-restraints excluded: chain z residue 140 SER Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 393 ASP Chi-restraints excluded: chain z residue 402 ILE Chi-restraints excluded: chain z residue 429 VAL Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain z residue 459 LEU Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 476 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 504 GLN Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 415 VAL Chi-restraints excluded: chain a residue 446 LEU Chi-restraints excluded: chain a residue 464 VAL Chi-restraints excluded: chain a residue 513 SER Chi-restraints excluded: chain a residue 529 ASP Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 450 CYS Chi-restraints excluded: chain d residue 532 ILE Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 141 LEU Chi-restraints excluded: chain b residue 144 SER Chi-restraints excluded: chain b residue 496 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 335 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 206 optimal weight: 0.5980 chunk 380 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 263 optimal weight: 5.9990 chunk 260 optimal weight: 0.0870 chunk 132 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 333 optimal weight: 0.9980 overall best weight: 1.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 445 GLN ** H 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 ASN Q 185 GLN Q 461 ASN G 71 GLN G 434 GLN D 494 ASN B 423 GLN B 469 HIS ** h 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 61 ASN ** z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 434 GLN ** g 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS b 469 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.091898 restraints weight = 64078.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.095066 restraints weight = 32830.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.097219 restraints weight = 21204.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.098664 restraints weight = 15884.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.099634 restraints weight = 13055.222| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 34603 Z= 0.200 Angle : 0.703 11.630 46880 Z= 0.336 Chirality : 0.043 0.237 5684 Planarity : 0.004 0.048 5936 Dihedral : 10.459 160.999 4888 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.49 % Favored : 93.46 % Rotamer: Outliers : 5.08 % Allowed : 21.44 % Favored : 73.48 % 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 are not related in a simple way. whole: -1.35 (0.13), residues: 4410 helix: -0.13 (0.10), residues: 2846 sheet: -0.93 (0.58), residues: 88 loop : -2.32 (0.14), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG g 38 TYR 0.020 0.002 TYR z 498 PHE 0.012 0.001 PHE q 64 TRP 0.006 0.001 TRP g 478 HIS 0.006 0.001 HIS q 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (34602) covalent geometry : angle 0.70284 / 0.34 (46880) hydrogen bonds : bond 0.03675 / 2.45 ( 1709) hydrogen bonds : angle 4.10488 / 2.92 ( 5004) Misc. bond : bond 0.00078 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 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 733 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 548 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: E 58 ASP cc_start: 0.8052 (m-30) cc_final: 0.7786 (m-30) REVERT: H 34 GLU cc_start: 0.8069 (tp30) cc_final: 0.7678 (tp30) REVERT: H 85 SER cc_start: 0.8993 (m) cc_final: 0.8784 (p) REVERT: H 455 PHE cc_start: 0.8476 (m-10) cc_final: 0.8095 (m-10) REVERT: H 481 ASN cc_start: 0.8331 (p0) cc_final: 0.7978 (p0) REVERT: Q 59 HIS cc_start: 0.7712 (p90) cc_final: 0.7468 (p90) REVERT: Q 393 ASP cc_start: 0.7653 (t0) cc_final: 0.6606 (t0) REVERT: Q 397 ASN cc_start: 0.8613 (m-40) cc_final: 0.8197 (m110) REVERT: Z 438 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8665 (tp40) REVERT: Z 442 ASP cc_start: 0.7654 (m-30) cc_final: 0.7430 (m-30) REVERT: Z 459 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8572 (pp) REVERT: Z 502 LYS cc_start: 0.8673 (tttt) cc_final: 0.8376 (ttpp) REVERT: G 71 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.7151 (mp-120) REVERT: G 110 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 430 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7329 (ttp) REVERT: A 446 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8550 (pp) REVERT: D 80 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7501 (pp30) REVERT: D 138 GLN cc_start: 0.8413 (tp40) cc_final: 0.8092 (tp40) REVERT: D 446 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7692 (mmt) REVERT: B 82 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8361 (mmtm) REVERT: e 149 ASP cc_start: 0.7746 (p0) cc_final: 0.7044 (t70) REVERT: e 522 GLN cc_start: 0.8402 (mt0) cc_final: 0.7863 (tt0) REVERT: q 111 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8583 (mp) REVERT: q 462 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: z 44 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8305 (mtt) REVERT: z 65 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7431 (t-170) REVERT: g 73 GLN cc_start: 0.6751 (tp-100) cc_final: 0.6469 (tp-100) REVERT: g 110 GLU cc_start: 0.7443 (tm-30) cc_final: 0.6665 (tm-30) REVERT: g 491 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8267 (mttm) REVERT: g 504 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: a 17 ILE cc_start: 0.8969 (tt) cc_final: 0.8697 (mt) REVERT: a 51 ASP cc_start: 0.7948 (t0) cc_final: 0.7746 (t0) REVERT: a 82 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8389 (tm-30) REVERT: a 123 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8611 (mp) REVERT: a 443 ARG cc_start: 0.8588 (ttp80) cc_final: 0.8186 (ttp80) REVERT: a 446 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8531 (pp) REVERT: a 450 ASN cc_start: 0.8701 (t0) cc_final: 0.8459 (t0) REVERT: d 36 SER cc_start: 0.9107 (m) cc_final: 0.8850 (m) REVERT: d 446 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7721 (mmt) REVERT: d 497 LYS cc_start: 0.7446 (pttm) cc_final: 0.6560 (ttmt) REVERT: b 91 GLN cc_start: 0.9429 (mm-40) cc_final: 0.9059 (tp-100) REVERT: b 141 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8474 (pt) REVERT: b 399 GLN cc_start: 0.8389 (mm110) cc_final: 0.7701 (mm-40) REVERT: b 498 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7400 (mt0) outliers start: 185 outliers final: 130 residues processed: 685 average time/residue: 0.2092 time to fit residues: 240.0094 Evaluate side-chains 662 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 515 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 458 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 141 GLU Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Q residue 461 ASN Chi-restraints excluded: chain Q residue 500 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 65 HIS Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 402 ILE Chi-restraints excluded: chain Z residue 406 CYS Chi-restraints excluded: chain Z residue 437 VAL Chi-restraints excluded: chain Z residue 438 GLN Chi-restraints excluded: chain Z residue 459 LEU Chi-restraints excluded: chain Z residue 476 LEU Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 505 THR Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 80 GLN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 450 CYS Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 436 GLU Chi-restraints excluded: chain e residue 442 THR Chi-restraints excluded: chain e residue 457 VAL Chi-restraints excluded: chain e residue 503 GLN Chi-restraints excluded: chain e residue 523 MET Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 114 GLU Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain h residue 458 THR Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain h residue 492 VAL Chi-restraints excluded: chain h residue 512 LEU Chi-restraints excluded: chain h residue 515 SER Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 79 GLN Chi-restraints excluded: chain q residue 111 LEU Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 157 ILE Chi-restraints excluded: chain q residue 163 LEU Chi-restraints excluded: chain q residue 166 THR Chi-restraints excluded: chain q residue 462 GLU Chi-restraints excluded: chain z residue 13 VAL Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 56 LEU Chi-restraints excluded: chain z residue 65 HIS Chi-restraints excluded: chain z residue 67 MET Chi-restraints excluded: chain z residue 90 ASP Chi-restraints excluded: chain z residue 140 SER Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 393 ASP Chi-restraints excluded: chain z residue 402 ILE Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain z residue 437 VAL Chi-restraints excluded: chain z residue 459 LEU Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 476 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 504 GLN Chi-restraints excluded: chain g residue 505 THR Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 415 VAL Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain a residue 446 LEU Chi-restraints excluded: chain a residue 464 VAL Chi-restraints excluded: chain a residue 513 SER Chi-restraints excluded: chain a residue 529 ASP Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 450 CYS Chi-restraints excluded: chain d residue 532 ILE Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 141 LEU Chi-restraints excluded: chain b residue 144 SER Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 496 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 53 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 429 optimal weight: 0.9980 chunk 400 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 423 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 384 optimal weight: 0.0670 chunk 418 optimal weight: 0.9980 chunk 343 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 459 ASN Q 185 GLN Q 219 HIS Q 461 ASN G 71 GLN e 499 ASN ** h 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 434 GLN ** g 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.094356 restraints weight = 61212.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.097690 restraints weight = 30698.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.099952 restraints weight = 19606.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.101435 restraints weight = 14513.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.102435 restraints weight = 11866.496| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34603 Z= 0.123 Angle : 0.660 10.853 46880 Z= 0.313 Chirality : 0.041 0.212 5684 Planarity : 0.003 0.042 5936 Dihedral : 10.217 157.783 4887 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.44 % Rotamer: Outliers : 4.31 % Allowed : 22.71 % Favored : 72.98 % 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 are not related in a simple way. whole: -1.02 (0.13), residues: 4410 helix: 0.13 (0.10), residues: 2820 sheet: -0.83 (0.57), residues: 88 loop : -2.16 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 117 TYR 0.019 0.001 TYR z 498 PHE 0.012 0.001 PHE q 64 TRP 0.005 0.001 TRP Z 495 HIS 0.007 0.001 HIS q 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (34602) covalent geometry : angle 0.65977 / 0.31 (46880) hydrogen bonds : bond 0.03361 / 2.24 ( 1709) hydrogen bonds : angle 3.99477 / 2.85 ( 5004) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 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 712 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 555 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 58 ASP cc_start: 0.8005 (m-30) cc_final: 0.7742 (m-30) REVERT: E 448 MET cc_start: 0.8497 (mtp) cc_final: 0.7995 (mtt) REVERT: E 532 ASP cc_start: 0.7524 (t0) cc_final: 0.7238 (t0) REVERT: H 34 GLU cc_start: 0.8079 (tp30) cc_final: 0.7646 (tp30) REVERT: H 85 SER cc_start: 0.8998 (m) cc_final: 0.8733 (p) REVERT: H 481 ASN cc_start: 0.8300 (p0) cc_final: 0.7909 (p0) REVERT: Q 393 ASP cc_start: 0.7666 (t0) cc_final: 0.6663 (t0) REVERT: Q 397 ASN cc_start: 0.8526 (m-40) cc_final: 0.8136 (m110) REVERT: Z 46 MET cc_start: 0.8265 (tpt) cc_final: 0.8065 (mmm) REVERT: Z 438 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8674 (tp40) REVERT: Z 459 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8521 (pp) REVERT: Z 502 LYS cc_start: 0.8630 (tttt) cc_final: 0.8319 (ttpp) REVERT: G 68 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7356 (mtm180) REVERT: G 69 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6900 (tt0) REVERT: G 110 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7248 (tm-30) REVERT: A 430 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7233 (ttp) REVERT: A 446 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8453 (pp) REVERT: D 73 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8515 (p0) REVERT: D 80 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.7512 (pp30) REVERT: D 101 GLU cc_start: 0.8036 (tp30) cc_final: 0.7792 (mm-30) REVERT: D 446 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7765 (mmt) REVERT: D 483 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8377 (ptm160) REVERT: B 82 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8331 (mmtm) REVERT: e 39 MET cc_start: 0.8391 (mmp) cc_final: 0.8128 (mmp) REVERT: e 135 ASP cc_start: 0.8093 (m-30) cc_final: 0.7379 (m-30) REVERT: e 149 ASP cc_start: 0.7775 (p0) cc_final: 0.7012 (t70) REVERT: e 522 GLN cc_start: 0.8384 (mt0) cc_final: 0.7821 (tt0) REVERT: h 451 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7705 (m-30) REVERT: q 111 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8467 (mp) REVERT: q 462 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: z 44 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8158 (mtt) REVERT: z 65 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.7431 (t-170) REVERT: z 67 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8455 (ptm) REVERT: g 68 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.7636 (mtm180) REVERT: g 73 GLN cc_start: 0.6715 (tp-100) cc_final: 0.6416 (tp-100) REVERT: g 110 GLU cc_start: 0.7405 (tm-30) cc_final: 0.6636 (tm-30) REVERT: g 491 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8280 (mttm) REVERT: g 504 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: a 17 ILE cc_start: 0.8925 (tt) cc_final: 0.8628 (mt) REVERT: a 51 ASP cc_start: 0.7972 (t0) cc_final: 0.7750 (t0) REVERT: a 446 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8428 (pp) REVERT: d 32 GLN cc_start: 0.7935 (mt0) cc_final: 0.7408 (mt0) REVERT: d 36 SER cc_start: 0.9040 (m) cc_final: 0.8684 (m) REVERT: d 446 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7795 (mmt) REVERT: d 497 LYS cc_start: 0.7461 (pttm) cc_final: 0.6614 (ttmt) REVERT: b 91 GLN cc_start: 0.9389 (mm-40) cc_final: 0.9032 (tp-100) REVERT: b 399 GLN cc_start: 0.8389 (mm110) cc_final: 0.7722 (mm-40) REVERT: b 498 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7427 (mt0) outliers start: 157 outliers final: 106 residues processed: 671 average time/residue: 0.2044 time to fit residues: 229.2682 Evaluate side-chains 646 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 522 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 458 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 141 GLU Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 445 PHE Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Q residue 461 ASN Chi-restraints excluded: chain Q residue 500 THR Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 65 HIS Chi-restraints excluded: chain Z residue 90 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 402 ILE Chi-restraints excluded: chain Z residue 406 CYS Chi-restraints excluded: chain Z residue 438 GLN Chi-restraints excluded: chain Z residue 459 LEU Chi-restraints excluded: chain Z residue 476 LEU Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 505 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 80 GLN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain e residue 436 GLU Chi-restraints excluded: chain e residue 442 THR Chi-restraints excluded: chain e residue 457 VAL Chi-restraints excluded: chain e residue 499 ASN Chi-restraints excluded: chain e residue 523 MET Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain h residue 451 ASP Chi-restraints excluded: chain h residue 458 THR Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain h residue 492 VAL Chi-restraints excluded: chain h residue 515 SER Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 79 GLN Chi-restraints excluded: chain q residue 111 LEU Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 157 ILE Chi-restraints excluded: chain q residue 163 LEU Chi-restraints excluded: chain q residue 166 THR Chi-restraints excluded: chain q residue 462 GLU Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 56 LEU Chi-restraints excluded: chain z residue 65 HIS Chi-restraints excluded: chain z residue 67 MET Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 393 ASP Chi-restraints excluded: chain z residue 402 ILE Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 429 VAL Chi-restraints excluded: chain z residue 437 VAL Chi-restraints excluded: chain z residue 459 LEU Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 476 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 133 MET Chi-restraints excluded: chain g residue 504 GLN Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 42 ASP Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 415 VAL Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain a residue 446 LEU Chi-restraints excluded: chain a residue 464 VAL Chi-restraints excluded: chain a residue 513 SER Chi-restraints excluded: chain a residue 529 ASP Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 450 CYS Chi-restraints excluded: chain d residue 532 ILE Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 496 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 327 optimal weight: 0.6980 chunk 338 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 191 optimal weight: 10.0000 chunk 297 optimal weight: 0.8980 chunk 409 optimal weight: 0.9990 chunk 224 optimal weight: 0.0470 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 459 ASN Q 185 GLN Q 461 ASN Q 523 GLN ** G 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 499 ASN ** h 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 438 GLN g 64 ASN g 434 GLN ** g 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 125 GLN ** d 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 537 ASN b 391 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.115945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.094926 restraints weight = 78839.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.098546 restraints weight = 37199.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.101019 restraints weight = 22686.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.102661 restraints weight = 16336.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.103775 restraints weight = 13094.310| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34603 Z= 0.121 Angle : 0.658 10.521 46880 Z= 0.311 Chirality : 0.041 0.243 5684 Planarity : 0.003 0.043 5936 Dihedral : 10.011 155.504 4886 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 4.04 % Allowed : 23.26 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.13), residues: 4410 helix: 0.27 (0.10), residues: 2822 sheet: -0.77 (0.57), residues: 88 loop : -2.10 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG e 142 TYR 0.017 0.001 TYR z 498 PHE 0.011 0.001 PHE q 64 TRP 0.006 0.001 TRP Z 495 HIS 0.007 0.001 HIS q 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (34602) covalent geometry : angle 0.65797 / 0.31 (46880) hydrogen bonds : bond 0.03278 / 2.19 ( 1709) hydrogen bonds : angle 3.93630 / 2.81 ( 5004) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 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 691 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 544 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 58 ASP cc_start: 0.7975 (m-30) cc_final: 0.7725 (m-30) REVERT: E 448 MET cc_start: 0.8529 (mtp) cc_final: 0.8072 (mtt) REVERT: E 532 ASP cc_start: 0.7554 (t0) cc_final: 0.7190 (t0) REVERT: H 34 GLU cc_start: 0.8032 (tp30) cc_final: 0.7598 (tp30) REVERT: H 85 SER cc_start: 0.8981 (m) cc_final: 0.8775 (p) REVERT: H 481 ASN cc_start: 0.8306 (p0) cc_final: 0.8062 (p0) REVERT: Q 393 ASP cc_start: 0.7629 (t0) cc_final: 0.6749 (t0) REVERT: Q 397 ASN cc_start: 0.8435 (m-40) cc_final: 0.8051 (m110) REVERT: Z 459 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8499 (pp) REVERT: Z 502 LYS cc_start: 0.8607 (tttt) cc_final: 0.8308 (ttpp) REVERT: G 68 ARG cc_start: 0.7704 (mtm110) cc_final: 0.7374 (mtm180) REVERT: G 110 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7054 (tm-30) REVERT: A 430 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7235 (ttp) REVERT: A 446 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8507 (pp) REVERT: D 73 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8494 (p0) REVERT: D 80 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7514 (pp30) REVERT: D 446 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7678 (mmt) REVERT: e 39 MET cc_start: 0.8389 (mmp) cc_final: 0.8133 (mmp) REVERT: e 135 ASP cc_start: 0.8101 (m-30) cc_final: 0.7401 (m-30) REVERT: e 149 ASP cc_start: 0.7709 (p0) cc_final: 0.6994 (t70) REVERT: e 522 GLN cc_start: 0.8341 (mt0) cc_final: 0.7767 (tt0) REVERT: h 451 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7691 (m-30) REVERT: q 111 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8465 (mp) REVERT: q 462 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: z 67 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8421 (ptm) REVERT: g 68 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7620 (mtm180) REVERT: g 73 GLN cc_start: 0.6623 (tp-100) cc_final: 0.6325 (tp-100) REVERT: g 110 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6536 (tm-30) REVERT: g 491 LYS cc_start: 0.8486 (mtmt) cc_final: 0.8253 (mttm) REVERT: g 504 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7152 (tm-30) REVERT: a 17 ILE cc_start: 0.8903 (tt) cc_final: 0.8632 (mt) REVERT: a 51 ASP cc_start: 0.7981 (t0) cc_final: 0.7767 (t0) REVERT: a 446 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8427 (pp) REVERT: d 32 GLN cc_start: 0.7906 (mt0) cc_final: 0.7360 (mt0) REVERT: d 36 SER cc_start: 0.9026 (m) cc_final: 0.8682 (m) REVERT: d 446 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7796 (mmt) REVERT: d 497 LYS cc_start: 0.7348 (pttm) cc_final: 0.6498 (ttmt) REVERT: b 91 GLN cc_start: 0.9365 (mm-40) cc_final: 0.9013 (tp-100) REVERT: b 397 LEU cc_start: 0.9302 (mt) cc_final: 0.9026 (mt) REVERT: b 399 GLN cc_start: 0.8403 (mm110) cc_final: 0.7826 (mm-40) REVERT: b 498 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7425 (mt0) outliers start: 147 outliers final: 107 residues processed: 654 average time/residue: 0.2007 time to fit residues: 219.5514 Evaluate side-chains 627 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 507 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 458 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 141 GLU Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 445 PHE Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Q residue 461 ASN Chi-restraints excluded: chain Q residue 500 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 65 HIS Chi-restraints excluded: chain Z residue 90 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 402 ILE Chi-restraints excluded: chain Z residue 406 CYS Chi-restraints excluded: chain Z residue 437 VAL Chi-restraints excluded: chain Z residue 459 LEU Chi-restraints excluded: chain Z residue 476 LEU Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 505 THR Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 80 GLN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 450 CYS Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain e residue 442 THR Chi-restraints excluded: chain e residue 523 MET Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain h residue 451 ASP Chi-restraints excluded: chain h residue 458 THR Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain h residue 492 VAL Chi-restraints excluded: chain h residue 515 SER Chi-restraints excluded: chain q residue 79 GLN Chi-restraints excluded: chain q residue 111 LEU Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 163 LEU Chi-restraints excluded: chain q residue 166 THR Chi-restraints excluded: chain q residue 462 GLU Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 56 LEU Chi-restraints excluded: chain z residue 65 HIS Chi-restraints excluded: chain z residue 67 MET Chi-restraints excluded: chain z residue 118 ILE Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 393 ASP Chi-restraints excluded: chain z residue 402 ILE Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 429 VAL Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain z residue 437 VAL Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 476 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 504 GLN Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 42 ASP Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 415 VAL Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain a residue 446 LEU Chi-restraints excluded: chain a residue 464 VAL Chi-restraints excluded: chain a residue 513 SER Chi-restraints excluded: chain a residue 529 ASP Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 450 CYS Chi-restraints excluded: chain d residue 532 ILE Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 496 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 8 optimal weight: 0.8980 chunk 392 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 395 optimal weight: 3.9990 chunk 320 optimal weight: 0.9980 chunk 235 optimal weight: 0.7980 chunk 354 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 459 ASN Q 185 GLN Q 461 ASN Q 523 GLN G 71 GLN e 499 ASN h 60 ASN ** h 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 219 HIS g 111 HIS g 434 GLN ** g 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 492 ASN ** d 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 125 GLN ** d 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.094743 restraints weight = 76104.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.098296 restraints weight = 36589.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.100718 restraints weight = 22576.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.102325 restraints weight = 16431.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.103409 restraints weight = 13233.279| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34603 Z= 0.132 Angle : 0.671 11.776 46880 Z= 0.317 Chirality : 0.041 0.250 5684 Planarity : 0.003 0.043 5936 Dihedral : 9.944 155.843 4886 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.44 % Rotamer: Outliers : 4.06 % Allowed : 23.31 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 4410 helix: 0.36 (0.10), residues: 2816 sheet: -0.56 (0.58), residues: 84 loop : -2.06 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG g 38 TYR 0.021 0.001 TYR Q 505 PHE 0.011 0.001 PHE q 64 TRP 0.005 0.001 TRP N 105 HIS 0.009 0.001 HIS q 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (34602) covalent geometry : angle 0.67084 / 0.32 (46880) hydrogen bonds : bond 0.03278 / 2.19 ( 1709) hydrogen bonds : angle 3.91795 / 2.79 ( 5004) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 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 669 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 521 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 58 ASP cc_start: 0.7989 (m-30) cc_final: 0.7730 (m-30) REVERT: E 448 MET cc_start: 0.8527 (mtp) cc_final: 0.8100 (mtt) REVERT: H 34 GLU cc_start: 0.8027 (tp30) cc_final: 0.7716 (tp30) REVERT: H 481 ASN cc_start: 0.8320 (p0) cc_final: 0.8065 (p0) REVERT: Q 393 ASP cc_start: 0.7624 (t0) cc_final: 0.6731 (t0) REVERT: Q 397 ASN cc_start: 0.8424 (m-40) cc_final: 0.8039 (m110) REVERT: Z 87 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7457 (tp) REVERT: Z 459 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8508 (pp) REVERT: Z 502 LYS cc_start: 0.8583 (tttt) cc_final: 0.8315 (ttpp) REVERT: G 68 ARG cc_start: 0.7680 (mtm110) cc_final: 0.7340 (mtm180) REVERT: G 71 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6978 (mp-120) REVERT: G 110 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7056 (tm-30) REVERT: A 430 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7253 (ttp) REVERT: A 446 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8538 (pp) REVERT: D 73 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8453 (p0) REVERT: D 446 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7669 (mmt) REVERT: e 39 MET cc_start: 0.8442 (mmp) cc_final: 0.8193 (mmp) REVERT: e 149 ASP cc_start: 0.7706 (p0) cc_final: 0.6985 (t70) REVERT: e 522 GLN cc_start: 0.8330 (mt0) cc_final: 0.7762 (tt0) REVERT: h 451 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7714 (m-30) REVERT: q 111 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8492 (mp) REVERT: q 462 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: z 44 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8157 (mtt) REVERT: g 68 ARG cc_start: 0.7874 (mtm-85) cc_final: 0.7670 (mtm180) REVERT: g 73 GLN cc_start: 0.6598 (tp-100) cc_final: 0.6292 (tp-100) REVERT: g 110 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6548 (tm-30) REVERT: g 491 LYS cc_start: 0.8479 (mtmt) cc_final: 0.8250 (mttm) REVERT: g 504 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: a 17 ILE cc_start: 0.8847 (tt) cc_final: 0.8558 (mt) REVERT: a 51 ASP cc_start: 0.8006 (t0) cc_final: 0.7790 (t0) REVERT: a 446 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8454 (pp) REVERT: d 32 GLN cc_start: 0.7941 (mt0) cc_final: 0.7353 (mt0) REVERT: d 36 SER cc_start: 0.9022 (m) cc_final: 0.8684 (m) REVERT: d 446 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7798 (mmt) REVERT: d 497 LYS cc_start: 0.7321 (pttm) cc_final: 0.6529 (ttmt) REVERT: b 39 VAL cc_start: 0.9501 (p) cc_final: 0.9293 (p) REVERT: b 91 GLN cc_start: 0.9366 (mm-40) cc_final: 0.9006 (tp-100) REVERT: b 397 LEU cc_start: 0.9267 (mt) cc_final: 0.9011 (mt) REVERT: b 399 GLN cc_start: 0.8402 (mm110) cc_final: 0.7944 (mm-40) REVERT: b 498 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7484 (mt0) outliers start: 148 outliers final: 114 residues processed: 632 average time/residue: 0.1996 time to fit residues: 211.5874 Evaluate side-chains 633 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 505 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 458 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 141 GLU Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 445 PHE Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Q residue 461 ASN Chi-restraints excluded: chain Q residue 500 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 65 HIS Chi-restraints excluded: chain Z residue 87 ILE Chi-restraints excluded: chain Z residue 90 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 402 ILE Chi-restraints excluded: chain Z residue 406 CYS Chi-restraints excluded: chain Z residue 437 VAL Chi-restraints excluded: chain Z residue 459 LEU Chi-restraints excluded: chain Z residue 476 LEU Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 505 THR Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 450 CYS Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain e residue 436 GLU Chi-restraints excluded: chain e residue 442 THR Chi-restraints excluded: chain e residue 457 VAL Chi-restraints excluded: chain e residue 499 ASN Chi-restraints excluded: chain e residue 523 MET Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain h residue 451 ASP Chi-restraints excluded: chain h residue 458 THR Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain h residue 492 VAL Chi-restraints excluded: chain h residue 515 SER Chi-restraints excluded: chain q residue 79 GLN Chi-restraints excluded: chain q residue 111 LEU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 163 LEU Chi-restraints excluded: chain q residue 166 THR Chi-restraints excluded: chain q residue 462 GLU Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 56 LEU Chi-restraints excluded: chain z residue 65 HIS Chi-restraints excluded: chain z residue 67 MET Chi-restraints excluded: chain z residue 118 ILE Chi-restraints excluded: chain z residue 140 SER Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 393 ASP Chi-restraints excluded: chain z residue 402 ILE Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 429 VAL Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain z residue 437 VAL Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 476 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 504 GLN Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 42 ASP Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 415 VAL Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain a residue 446 LEU Chi-restraints excluded: chain a residue 464 VAL Chi-restraints excluded: chain a residue 513 SER Chi-restraints excluded: chain a residue 529 ASP Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 450 CYS Chi-restraints excluded: chain d residue 532 ILE Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 144 SER Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 496 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 0.9980 chunk 157 optimal weight: 0.0770 chunk 100 optimal weight: 0.0170 chunk 81 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 403 optimal weight: 0.0970 chunk 395 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 chunk 359 optimal weight: 0.1980 chunk 148 optimal weight: 0.8980 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 459 ASN Q 185 GLN Q 461 ASN Q 523 GLN G 71 GLN e 499 ASN ** h 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 472 GLN ** g 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 125 GLN ** d 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.097913 restraints weight = 65954.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.101336 restraints weight = 32970.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.103658 restraints weight = 20861.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.105203 restraints weight = 15341.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106228 restraints weight = 12468.975| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34603 Z= 0.111 Angle : 0.664 11.941 46880 Z= 0.312 Chirality : 0.041 0.255 5684 Planarity : 0.003 0.043 5936 Dihedral : 9.752 154.074 4885 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.22 % Favored : 94.73 % Rotamer: Outliers : 3.54 % Allowed : 23.89 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.13), residues: 4410 helix: 0.54 (0.10), residues: 2798 sheet: -0.56 (0.58), residues: 84 loop : -1.98 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG g 38 TYR 0.022 0.001 TYR Q 505 PHE 0.010 0.001 PHE q 64 TRP 0.006 0.001 TRP Z 495 HIS 0.010 0.001 HIS q 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (34602) covalent geometry : angle 0.66356 / 0.31 (46880) hydrogen bonds : bond 0.03147 / 2.10 ( 1709) hydrogen bonds : angle 3.87132 / 2.76 ( 5004) Misc. bond : bond 0.00020 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 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 681 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 552 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 58 ASP cc_start: 0.7915 (m-30) cc_final: 0.7601 (m-30) REVERT: E 448 MET cc_start: 0.8495 (mtp) cc_final: 0.8084 (mtt) REVERT: H 34 GLU cc_start: 0.8038 (tp30) cc_final: 0.7667 (tp30) REVERT: H 481 ASN cc_start: 0.8304 (p0) cc_final: 0.8048 (p0) REVERT: Q 393 ASP cc_start: 0.7620 (t0) cc_final: 0.6745 (t0) REVERT: Q 397 ASN cc_start: 0.8342 (m-40) cc_final: 0.7996 (m110) REVERT: Z 459 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8459 (pp) REVERT: Z 502 LYS cc_start: 0.8572 (tttt) cc_final: 0.8308 (ttpp) REVERT: G 57 ILE cc_start: 0.8488 (mm) cc_final: 0.8277 (mm) REVERT: G 68 ARG cc_start: 0.7677 (mtm110) cc_final: 0.7385 (mtm180) REVERT: G 96 THR cc_start: 0.9306 (t) cc_final: 0.9014 (m) REVERT: G 110 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7032 (tm-30) REVERT: A 430 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.6978 (ttp) REVERT: A 446 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8480 (pp) REVERT: D 60 MET cc_start: 0.7707 (mtm) cc_final: 0.7449 (mtp) REVERT: D 446 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7599 (mmt) REVERT: e 39 MET cc_start: 0.8406 (mmp) cc_final: 0.8187 (mmp) REVERT: e 76 THR cc_start: 0.6756 (p) cc_final: 0.6535 (p) REVERT: e 81 MET cc_start: 0.4931 (OUTLIER) cc_final: 0.4153 (ppp) REVERT: h 451 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7676 (m-30) REVERT: q 462 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: z 44 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8108 (mtt) REVERT: z 430 LYS cc_start: 0.6332 (mmmt) cc_final: 0.5781 (mmtm) REVERT: g 73 GLN cc_start: 0.6553 (tp-100) cc_final: 0.6269 (tp-100) REVERT: g 110 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6540 (tm-30) REVERT: g 504 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: a 17 ILE cc_start: 0.8739 (tt) cc_final: 0.8458 (mt) REVERT: a 51 ASP cc_start: 0.8023 (t0) cc_final: 0.7811 (t0) REVERT: a 446 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8385 (pp) REVERT: d 32 GLN cc_start: 0.7884 (mt0) cc_final: 0.7303 (mt0) REVERT: d 36 SER cc_start: 0.8958 (m) cc_final: 0.8624 (m) REVERT: d 132 ILE cc_start: 0.9231 (mt) cc_final: 0.9006 (mt) REVERT: d 446 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7765 (mmt) REVERT: d 497 LYS cc_start: 0.7223 (pttm) cc_final: 0.6366 (ttmm) REVERT: b 91 GLN cc_start: 0.9309 (mm-40) cc_final: 0.8936 (tp-100) REVERT: b 397 LEU cc_start: 0.9240 (mt) cc_final: 0.9036 (mt) REVERT: b 399 GLN cc_start: 0.8396 (mm110) cc_final: 0.7964 (mm-40) REVERT: b 498 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7476 (mt0) outliers start: 129 outliers final: 103 residues processed: 645 average time/residue: 0.2037 time to fit residues: 220.4472 Evaluate side-chains 638 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 524 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 458 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 141 GLU Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 445 PHE Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Q residue 461 ASN Chi-restraints excluded: chain Q residue 500 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 65 HIS Chi-restraints excluded: chain Z residue 87 ILE Chi-restraints excluded: chain Z residue 90 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 402 ILE Chi-restraints excluded: chain Z residue 406 CYS Chi-restraints excluded: chain Z residue 437 VAL Chi-restraints excluded: chain Z residue 459 LEU Chi-restraints excluded: chain Z residue 476 LEU Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 505 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 450 CYS Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain e residue 436 GLU Chi-restraints excluded: chain e residue 457 VAL Chi-restraints excluded: chain e residue 476 GLU Chi-restraints excluded: chain e residue 523 MET Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 451 ASP Chi-restraints excluded: chain h residue 458 THR Chi-restraints excluded: chain h residue 492 VAL Chi-restraints excluded: chain h residue 515 SER Chi-restraints excluded: chain q residue 79 GLN Chi-restraints excluded: chain q residue 163 LEU Chi-restraints excluded: chain q residue 166 THR Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain q residue 462 GLU Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 13 VAL Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 56 LEU Chi-restraints excluded: chain z residue 65 HIS Chi-restraints excluded: chain z residue 67 MET Chi-restraints excluded: chain z residue 140 SER Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 393 ASP Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 429 VAL Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain z residue 459 LEU Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain g residue 504 GLN Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 42 ASP Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 415 VAL Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain a residue 446 LEU Chi-restraints excluded: chain a residue 464 VAL Chi-restraints excluded: chain a residue 529 ASP Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 450 CYS Chi-restraints excluded: chain d residue 532 ILE Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 496 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 290 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 268 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 276 optimal weight: 0.8980 chunk 364 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 293 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 459 ASN Q 185 GLN Q 461 ASN Q 523 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN e 499 ASN ** h 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN ** d 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 125 GLN ** d 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.097196 restraints weight = 63925.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.100543 restraints weight = 32528.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.102814 restraints weight = 20805.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.104323 restraints weight = 15395.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.105330 restraints weight = 12584.674| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 34603 Z= 0.127 Angle : 0.666 11.775 46880 Z= 0.314 Chirality : 0.041 0.251 5684 Planarity : 0.003 0.043 5936 Dihedral : 9.679 152.380 4885 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.40 % Favored : 94.55 % Rotamer: Outliers : 3.54 % Allowed : 24.00 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.13), residues: 4410 helix: 0.60 (0.10), residues: 2804 sheet: -0.60 (0.57), residues: 84 loop : -1.96 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG a 443 TYR 0.021 0.001 TYR Q 505 PHE 0.010 0.001 PHE q 64 TRP 0.007 0.001 TRP N 101 HIS 0.010 0.001 HIS q 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (34602) covalent geometry : angle 0.66644 / 0.31 (46880) hydrogen bonds : bond 0.03191 / 2.14 ( 1709) hydrogen bonds : angle 3.86134 / 2.74 ( 5004) Misc. bond : bond 0.00041 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7147.77 seconds wall clock time: 123 minutes 59.01 seconds (7439.01 seconds total)