Starting phenix.real_space_refine on Thu Feb 22 10:52:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hki_34852/02_2024/8hki_34852_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hki_34852/02_2024/8hki_34852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hki_34852/02_2024/8hki_34852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hki_34852/02_2024/8hki_34852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hki_34852/02_2024/8hki_34852_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hki_34852/02_2024/8hki_34852_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.124 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 189 5.16 5 C 21156 2.51 5 N 5930 2.21 5 O 6639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 15": "OE1" <-> "OE2" Residue "a GLU 68": "OE1" <-> "OE2" Residue "a PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 528": "OD1" <-> "OD2" Residue "a ASP 529": "OD1" <-> "OD2" Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 528": "OD1" <-> "OD2" Residue "b PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 18": "OE1" <-> "OE2" Residue "b GLU 19": "OE1" <-> "OE2" Residue "b PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 66": "OD1" <-> "OD2" Residue "b ASP 86": "OD1" <-> "OD2" Residue "b TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 460": "OD1" <-> "OD2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 49": "OD1" <-> "OD2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 26": "OD1" <-> "OD2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 46": "OD1" <-> "OD2" Residue "d ASP 63": "OD1" <-> "OD2" Residue "d ASP 73": "OD1" <-> "OD2" Residue "d TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 533": "OD1" <-> "OD2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 474": "OE1" <-> "OE2" Residue "E ASP 530": "OD1" <-> "OD2" Residue "e ASP 123": "OD1" <-> "OD2" Residue "e ASP 156": "OD1" <-> "OD2" Residue "e GLU 394": "OE1" <-> "OE2" Residue "e GLU 395": "OE1" <-> "OE2" Residue "e TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 506": "OE1" <-> "OE2" Residue "g GLU 473": "OE1" <-> "OE2" Residue "g GLU 476": "OE1" <-> "OE2" Residue "G TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 521": "OD1" <-> "OD2" Residue "h ASP 14": "OD1" <-> "OD2" Residue "h ASP 81": "OD1" <-> "OD2" Residue "h PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 147": "OD1" <-> "OD2" Residue "h PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H ASP 70": "OD1" <-> "OD2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 485": "OE1" <-> "OE2" Residue "q PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 26": "OE1" <-> "OE2" Residue "q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 158": "OD1" <-> "OD2" Residue "q PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 485": "OE1" <-> "OE2" Residue "Z ASP 32": "OD1" <-> "OD2" Residue "Z ASP 85": "OD1" <-> "OD2" Residue "Z ASP 107": "OD1" <-> "OD2" Residue "Z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 442": "OD1" <-> "OD2" Residue "Z PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 472": "OE1" <-> "OE2" Residue "z ASP 32": "OD1" <-> "OD2" Residue "z ASP 107": "OD1" <-> "OD2" Residue "z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 389": "OD1" <-> "OD2" Residue "z ASP 393": "OD1" <-> "OD2" Residue "z ASP 404": "OD1" <-> "OD2" Residue "z PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33926 Number of models: 1 Model: "" Number of chains: 22 Chain: "a" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2182 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 8, 'TRANS': 282} Chain breaks: 2 Chain: "A" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1918 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain breaks: 1 Chain: "b" Number of atoms: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2407 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 3 Chain: "B" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1842 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 6, 'TRANS': 243} Chain breaks: 1 Chain: "D" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1870 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 241} Chain breaks: 1 Chain: "d" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2086 Classifications: {'peptide': 278} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain breaks: 1 Chain: "E" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1916 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain breaks: 2 Chain: "e" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2433 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 8, 'TRANS': 312} Chain breaks: 2 Chain: "g" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1822 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 7, 'TRANS': 231} Chain breaks: 1 Chain: "G" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1946 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "h" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2585 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain breaks: 2 Chain: "H" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1929 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 9, 'TRANS': 245} Chain breaks: 2 Chain: "Q" Number of atoms: 1998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1998 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 252} Chain breaks: 1 Chain: "q" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2574 Classifications: {'peptide': 338} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 328} Chain breaks: 2 Chain: "Z" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1887 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain breaks: 1 Chain: "z" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2369 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "g" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.47, per 1000 atoms: 0.51 Number of scatterers: 33926 At special positions: 0 Unit cell: (187.156, 108.076, 181.884, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 189 16.00 P 12 15.00 O 6639 8.00 N 5930 7.00 C 21156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.86 Conformation dependent library (CDL) restraints added in 6.4 seconds 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8324 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 180 helices and 38 sheets defined 61.1% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.53 Creating SS restraints... Processing helix chain 'a' and resid 15 through 32 removed outlier: 3.757A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 64 Processing helix chain 'a' and resid 70 through 85 removed outlier: 3.506A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU a 81 " --> pdb=" O GLU a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 110 removed outlier: 3.561A pdb=" N GLU a 106 " --> pdb=" O LYS a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 135 Processing helix chain 'a' and resid 149 through 156 Processing helix chain 'a' and resid 160 through 163 removed outlier: 3.603A pdb=" N ILE a 163 " --> pdb=" O ILE a 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 160 through 163' Processing helix chain 'a' and resid 414 through 430 removed outlier: 3.811A pdb=" N ILE a 421 " --> pdb=" O ALA a 417 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET a 430 " --> pdb=" O TYR a 426 " (cutoff:3.500A) Processing helix chain 'a' and resid 435 through 455 removed outlier: 3.554A pdb=" N LEU a 445 " --> pdb=" O PHE a 441 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix Processing helix chain 'a' and resid 460 through 476 removed outlier: 3.517A pdb=" N GLN a 475 " --> pdb=" O HIS a 471 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 501 No H-bonds generated for 'chain 'a' and resid 498 through 501' Processing helix chain 'a' and resid 507 through 525 Processing helix chain 'A' and resid 15 through 32 removed outlier: 3.514A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.616A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 Processing helix chain 'A' and resid 114 through 132 Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.679A pdb=" N ILE A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 455 removed outlier: 3.564A pdb=" N LEU A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 507 through 525 removed outlier: 3.677A pdb=" N LEU A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 39 removed outlier: 3.755A pdb=" N LEU b 26 " --> pdb=" O GLU b 22 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE b 29 " --> pdb=" O ARG b 25 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE b 35 " --> pdb=" O GLY b 31 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL b 39 " --> pdb=" O ILE b 35 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 73 removed outlier: 3.572A pdb=" N ASN b 73 " --> pdb=" O THR b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 79 through 94 removed outlier: 3.766A pdb=" N GLN b 91 " --> pdb=" O MET b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 99 through 119 removed outlier: 3.504A pdb=" N THR b 103 " --> pdb=" O THR b 99 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER b 115 " --> pdb=" O ARG b 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 144 removed outlier: 3.580A pdb=" N GLY b 129 " --> pdb=" O THR b 125 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU b 141 " --> pdb=" O ALA b 137 " (cutoff:3.500A) Processing helix chain 'b' and resid 152 through 167 Processing helix chain 'b' and resid 171 through 173 No H-bonds generated for 'chain 'b' and resid 171 through 173' Processing helix chain 'b' and resid 209 through 211 No H-bonds generated for 'chain 'b' and resid 209 through 211' Processing helix chain 'b' and resid 380 through 402 Processing helix chain 'b' and resid 412 through 426 removed outlier: 3.753A pdb=" N ASN b 426 " --> pdb=" O THR b 422 " (cutoff:3.500A) Processing helix chain 'b' and resid 430 through 454 removed outlier: 3.858A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER b 438 " --> pdb=" O VAL b 434 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU b 446 " --> pdb=" O ALA b 442 " (cutoff:3.500A) Proline residue: b 447 - end of helix Processing helix chain 'b' and resid 458 through 470 Processing helix chain 'b' and resid 488 through 491 No H-bonds generated for 'chain 'b' and resid 488 through 491' Processing helix chain 'b' and resid 497 through 516 removed outlier: 3.511A pdb=" N ILE b 514 " --> pdb=" O ALA b 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.647A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 67 through 73 removed outlier: 3.790A pdb=" N ASN B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.711A pdb=" N SER B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 413 through 426 removed outlier: 3.730A pdb=" N ASN B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 3.960A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Proline residue: B 447 - end of helix Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'D' and resid 30 through 51 removed outlier: 4.089A pdb=" N PHE D 35 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 38 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER D 39 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 40 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS D 42 " --> pdb=" O SER D 39 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA D 43 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 47 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG D 49 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR D 50 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 106 through 125 removed outlier: 3.768A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 150 Processing helix chain 'D' and resid 427 through 442 removed outlier: 3.725A pdb=" N THR D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG D 441 " --> pdb=" O THR D 437 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 468 removed outlier: 3.882A pdb=" N SER D 448 " --> pdb=" O GLY D 445 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR D 449 " --> pdb=" O MET D 446 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 451 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG D 452 " --> pdb=" O TYR D 449 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA D 457 " --> pdb=" O PHE D 454 " (cutoff:3.500A) Proline residue: D 462 - end of helix removed outlier: 3.852A pdb=" N ALA D 466 " --> pdb=" O SER D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 486 Processing helix chain 'D' and resid 512 through 530 Processing helix chain 'd' and resid 30 through 49 removed outlier: 3.619A pdb=" N PHE d 35 " --> pdb=" O GLN d 32 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE d 38 " --> pdb=" O PHE d 35 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER d 39 " --> pdb=" O SER d 36 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA d 40 " --> pdb=" O ASN d 37 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA d 43 " --> pdb=" O ALA d 40 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA d 47 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG d 49 " --> pdb=" O ASP d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 81 Processing helix chain 'd' and resid 86 through 101 removed outlier: 3.691A pdb=" N LEU d 91 " --> pdb=" O ALA d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 125 removed outlier: 3.958A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN d 125 " --> pdb=" O THR d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 150 removed outlier: 3.605A pdb=" N GLU d 146 " --> pdb=" O GLU d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 173 removed outlier: 3.597A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 427 through 442 removed outlier: 3.564A pdb=" N ARG d 441 " --> pdb=" O THR d 437 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 468 removed outlier: 3.512A pdb=" N ARG d 452 " --> pdb=" O TYR d 449 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA d 453 " --> pdb=" O CYS d 450 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP d 456 " --> pdb=" O ALA d 453 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA d 457 " --> pdb=" O PHE d 454 " (cutoff:3.500A) Proline residue: d 462 - end of helix removed outlier: 3.605A pdb=" N ALA d 466 " --> pdb=" O SER d 463 " (cutoff:3.500A) Processing helix chain 'd' and resid 473 through 486 removed outlier: 3.739A pdb=" N VAL d 477 " --> pdb=" O PRO d 473 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN d 482 " --> pdb=" O THR d 478 " (cutoff:3.500A) Processing helix chain 'd' and resid 503 through 506 No H-bonds generated for 'chain 'd' and resid 503 through 506' Processing helix chain 'd' and resid 512 through 530 Processing helix chain 'E' and resid 29 through 47 removed outlier: 3.520A pdb=" N MET E 46 " --> pdb=" O VAL E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 78 Processing helix chain 'E' and resid 84 through 99 removed outlier: 3.524A pdb=" N MET E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 124 removed outlier: 3.635A pdb=" N VAL E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 147 removed outlier: 3.826A pdb=" N ASP E 147 " --> pdb=" O ILE E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 437 removed outlier: 3.938A pdb=" N ASP E 436 " --> pdb=" O SER E 432 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS E 437 " --> pdb=" O GLN E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 463 removed outlier: 3.565A pdb=" N TYR E 444 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG E 447 " --> pdb=" O TYR E 444 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 456 " --> pdb=" O LEU E 453 " (cutoff:3.500A) Proline residue: E 457 - end of helix removed outlier: 3.723A pdb=" N SER E 461 " --> pdb=" O MET E 458 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN E 463 " --> pdb=" O LEU E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 478 Processing helix chain 'E' and resid 499 through 502 No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 508 through 526 Processing helix chain 'e' and resid 29 through 49 removed outlier: 3.583A pdb=" N VAL e 42 " --> pdb=" O ALA e 38 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR e 48 " --> pdb=" O ASN e 44 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER e 49 " --> pdb=" O THR e 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 72 through 78 Processing helix chain 'e' and resid 84 through 96 removed outlier: 4.132A pdb=" N SER e 93 " --> pdb=" O MET e 89 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS e 94 " --> pdb=" O VAL e 90 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER e 95 " --> pdb=" O GLU e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 123 removed outlier: 3.861A pdb=" N GLN e 120 " --> pdb=" O GLU e 116 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU e 121 " --> pdb=" O GLU e 117 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP e 123 " --> pdb=" O GLU e 119 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 149 removed outlier: 3.568A pdb=" N ASP e 147 " --> pdb=" O ILE e 143 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS e 148 " --> pdb=" O GLU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 173 removed outlier: 3.824A pdb=" N GLN e 165 " --> pdb=" O GLU e 161 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA e 167 " --> pdb=" O LEU e 163 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR e 169 " --> pdb=" O GLN e 165 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY e 172 " --> pdb=" O LYS e 168 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER e 173 " --> pdb=" O THR e 169 " (cutoff:3.500A) Processing helix chain 'e' and resid 175 through 179 removed outlier: 4.371A pdb=" N SER e 178 " --> pdb=" O VAL e 175 " (cutoff:3.500A) Processing helix chain 'e' and resid 217 through 219 No H-bonds generated for 'chain 'e' and resid 217 through 219' Processing helix chain 'e' and resid 390 through 412 removed outlier: 3.547A pdb=" N LEU e 400 " --> pdb=" O ALA e 396 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA e 403 " --> pdb=" O SER e 399 " (cutoff:3.500A) Processing helix chain 'e' and resid 422 through 437 removed outlier: 3.559A pdb=" N LEU e 429 " --> pdb=" O ILE e 425 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP e 436 " --> pdb=" O SER e 432 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS e 437 " --> pdb=" O GLN e 433 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 464 removed outlier: 3.717A pdb=" N TYR e 444 " --> pdb=" O LEU e 441 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG e 447 " --> pdb=" O TYR e 444 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP e 451 " --> pdb=" O ALA e 448 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE e 456 " --> pdb=" O LEU e 453 " (cutoff:3.500A) Proline residue: e 457 - end of helix removed outlier: 4.026A pdb=" N SER e 461 " --> pdb=" O MET e 458 " (cutoff:3.500A) Processing helix chain 'e' and resid 468 through 480 Processing helix chain 'e' and resid 499 through 502 No H-bonds generated for 'chain 'e' and resid 499 through 502' Processing helix chain 'e' and resid 508 through 527 Processing helix chain 'g' and resid 19 through 36 removed outlier: 3.549A pdb=" N GLN g 23 " --> pdb=" O ARG g 20 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER g 24 " --> pdb=" O LYS g 21 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE g 27 " --> pdb=" O SER g 24 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS g 31 " --> pdb=" O ASN g 28 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE g 36 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 69 Processing helix chain 'g' and resid 75 through 90 Processing helix chain 'g' and resid 95 through 106 removed outlier: 3.659A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 138 removed outlier: 3.578A pdb=" N ASP g 131 " --> pdb=" O ARG g 127 " (cutoff:3.500A) Processing helix chain 'g' and resid 414 through 428 removed outlier: 3.546A pdb=" N ALA g 421 " --> pdb=" O ALA g 417 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 432 through 455 removed outlier: 3.508A pdb=" N TRP g 435 " --> pdb=" O VAL g 432 " (cutoff:3.500A) Proline residue: g 436 - end of helix removed outlier: 3.671A pdb=" N VAL g 440 " --> pdb=" O TYR g 437 " (cutoff:3.500A) Proline residue: g 448 - end of helix removed outlier: 3.808A pdb=" N ILE g 452 " --> pdb=" O ARG g 449 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN g 454 " --> pdb=" O LEU g 451 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS g 455 " --> pdb=" O ILE g 452 " (cutoff:3.500A) Processing helix chain 'g' and resid 459 through 472 Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'G' and resid 19 through 36 removed outlier: 3.513A pdb=" N GLN G 23 " --> pdb=" O ARG G 20 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER G 24 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN G 26 " --> pdb=" O GLN G 23 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE G 27 " --> pdb=" O SER G 24 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS G 31 " --> pdb=" O ASN G 28 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE G 33 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE G 36 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 69 Processing helix chain 'G' and resid 75 through 90 removed outlier: 3.638A pdb=" N SER G 84 " --> pdb=" O MET G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 106 removed outlier: 3.626A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 139 removed outlier: 3.760A pdb=" N LYS G 139 " --> pdb=" O SER G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 428 removed outlier: 3.858A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.558A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 3.609A pdb=" N VAL G 440 " --> pdb=" O TYR G 437 " (cutoff:3.500A) Proline residue: G 448 - end of helix removed outlier: 3.558A pdb=" N LEU G 451 " --> pdb=" O PRO G 448 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN G 454 " --> pdb=" O LEU G 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 472 Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'h' and resid 19 through 34 Processing helix chain 'h' and resid 62 through 69 Processing helix chain 'h' and resid 74 through 89 removed outlier: 3.573A pdb=" N LEU h 79 " --> pdb=" O ALA h 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 107 Processing helix chain 'h' and resid 109 through 113 Processing helix chain 'h' and resid 118 through 139 removed outlier: 3.598A pdb=" N ALA h 124 " --> pdb=" O ILE h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 146 through 148 No H-bonds generated for 'chain 'h' and resid 146 through 148' Processing helix chain 'h' and resid 151 through 163 Processing helix chain 'h' and resid 170 through 183 removed outlier: 4.569A pdb=" N ALA h 173 " --> pdb=" O GLN h 170 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET h 178 " --> pdb=" O PHE h 175 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL h 179 " --> pdb=" O ALA h 176 " (cutoff:3.500A) Processing helix chain 'h' and resid 379 through 401 removed outlier: 3.564A pdb=" N ARG h 387 " --> pdb=" O GLU h 383 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA h 392 " --> pdb=" O SER h 388 " (cutoff:3.500A) Processing helix chain 'h' and resid 411 through 426 removed outlier: 3.993A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 431 through 452 removed outlier: 3.548A pdb=" N LEU h 442 " --> pdb=" O TYR h 438 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE h 445 " --> pdb=" O ALA h 441 " (cutoff:3.500A) Proline residue: h 446 - end of helix Processing helix chain 'h' and resid 457 through 470 Processing helix chain 'h' and resid 496 through 514 Processing helix chain 'H' and resid 19 through 36 removed outlier: 3.794A pdb=" N ILE H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 69 removed outlier: 3.576A pdb=" N LEU H 68 " --> pdb=" O THR H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 89 removed outlier: 3.631A pdb=" N THR H 78 " --> pdb=" O PRO H 74 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU H 79 " --> pdb=" O ALA H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 107 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 118 through 138 removed outlier: 3.663A pdb=" N GLN H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 425 removed outlier: 3.550A pdb=" N ARG H 425 " --> pdb=" O ARG H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 452 removed outlier: 3.629A pdb=" N LEU H 442 " --> pdb=" O TYR H 438 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ILE H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix removed outlier: 3.538A pdb=" N LEU H 449 " --> pdb=" O ILE H 445 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS H 450 " --> pdb=" O PRO H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 470 removed outlier: 3.501A pdb=" N ALA H 469 " --> pdb=" O ARG H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 514 Processing helix chain 'Q' and resid 28 through 44 removed outlier: 3.517A pdb=" N ASN Q 32 " --> pdb=" O ALA Q 28 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS Q 36 " --> pdb=" O ASN Q 32 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU Q 39 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 Processing helix chain 'Q' and resid 81 through 94 removed outlier: 4.116A pdb=" N ILE Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 121 removed outlier: 4.038A pdb=" N GLU Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU Q 118 " --> pdb=" O LEU Q 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE Q 121 " --> pdb=" O GLU Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 143 removed outlier: 3.528A pdb=" N GLU Q 141 " --> pdb=" O ARG Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 414 through 429 Processing helix chain 'Q' and resid 434 through 455 removed outlier: 3.681A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU Q 446 " --> pdb=" O ALA Q 442 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA Q 447 " --> pdb=" O GLU Q 443 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE Q 448 " --> pdb=" O ALA Q 444 " (cutoff:3.500A) Proline residue: Q 449 - end of helix Processing helix chain 'Q' and resid 460 through 472 Processing helix chain 'Q' and resid 492 through 495 No H-bonds generated for 'chain 'Q' and resid 492 through 495' Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'q' and resid 28 through 44 removed outlier: 3.757A pdb=" N ASN q 32 " --> pdb=" O ALA q 28 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR q 42 " --> pdb=" O GLU q 38 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 75 Processing helix chain 'q' and resid 81 through 94 removed outlier: 4.128A pdb=" N ILE q 86 " --> pdb=" O ALA q 82 " (cutoff:3.500A) Processing helix chain 'q' and resid 101 through 121 removed outlier: 3.738A pdb=" N GLU q 117 " --> pdb=" O GLU q 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 125 through 146 Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 157 through 168 removed outlier: 3.554A pdb=" N ARG q 165 " --> pdb=" O SER q 161 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 186 removed outlier: 3.619A pdb=" N ALA q 186 " --> pdb=" O LEU q 182 " (cutoff:3.500A) Processing helix chain 'q' and resid 212 through 214 No H-bonds generated for 'chain 'q' and resid 212 through 214' Processing helix chain 'q' and resid 382 through 402 removed outlier: 3.579A pdb=" N ARG q 390 " --> pdb=" O ASP q 386 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE q 399 " --> pdb=" O GLY q 395 " (cutoff:3.500A) Processing helix chain 'q' and resid 414 through 429 Processing helix chain 'q' and resid 433 through 455 removed outlier: 3.520A pdb=" N TYR q 436 " --> pdb=" O LEU q 433 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS q 440 " --> pdb=" O ALA q 437 " (cutoff:3.500A) Proline residue: q 449 - end of helix removed outlier: 3.536A pdb=" N ALA q 453 " --> pdb=" O ARG q 450 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN q 455 " --> pdb=" O LEU q 452 " (cutoff:3.500A) Processing helix chain 'q' and resid 460 through 472 removed outlier: 3.632A pdb=" N LYS q 466 " --> pdb=" O GLU q 462 " (cutoff:3.500A) Processing helix chain 'q' and resid 492 through 495 No H-bonds generated for 'chain 'q' and resid 492 through 495' Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'Z' and resid 17 through 37 removed outlier: 3.520A pdb=" N VAL Z 22 " --> pdb=" O ALA Z 19 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE Z 24 " --> pdb=" O ALA Z 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU Z 34 " --> pdb=" O GLN Z 31 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG Z 35 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR Z 36 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 60 through 65 Processing helix chain 'Z' and resid 72 through 87 removed outlier: 3.713A pdb=" N LEU Z 76 " --> pdb=" O PRO Z 72 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE Z 77 " --> pdb=" O THR Z 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR Z 82 " --> pdb=" O ALA Z 78 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 110 Processing helix chain 'Z' and resid 116 through 136 removed outlier: 3.592A pdb=" N GLU Z 135 " --> pdb=" O LEU Z 131 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 423 Processing helix chain 'Z' and resid 432 through 454 removed outlier: 3.515A pdb=" N VAL Z 437 " --> pdb=" O GLN Z 434 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP Z 442 " --> pdb=" O ALA Z 439 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU Z 445 " --> pdb=" O ASP Z 442 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE Z 447 " --> pdb=" O LEU Z 444 " (cutoff:3.500A) Proline residue: Z 448 - end of helix removed outlier: 3.913A pdb=" N LEU Z 451 " --> pdb=" O PRO Z 448 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN Z 454 " --> pdb=" O LEU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 459 through 468 removed outlier: 3.565A pdb=" N LEU Z 463 " --> pdb=" O LEU Z 459 " (cutoff:3.500A) Processing helix chain 'Z' and resid 489 through 491 No H-bonds generated for 'chain 'Z' and resid 489 through 491' Processing helix chain 'Z' and resid 498 through 516 Processing helix chain 'z' and resid 17 through 37 removed outlier: 3.537A pdb=" N SER z 25 " --> pdb=" O VAL z 22 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG z 35 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR z 36 " --> pdb=" O VAL z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 62 through 65 No H-bonds generated for 'chain 'z' and resid 62 through 65' Processing helix chain 'z' and resid 72 through 87 removed outlier: 3.891A pdb=" N LEU z 76 " --> pdb=" O PRO z 72 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE z 77 " --> pdb=" O THR z 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE z 87 " --> pdb=" O ALA z 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 92 through 110 removed outlier: 3.589A pdb=" N LEU z 108 " --> pdb=" O LYS z 104 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 116 through 137 removed outlier: 3.599A pdb=" N GLU z 135 " --> pdb=" O LEU z 131 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU z 136 " --> pdb=" O GLN z 132 " (cutoff:3.500A) Processing helix chain 'z' and resid 145 through 159 removed outlier: 3.720A pdb=" N ASP z 150 " --> pdb=" O GLU z 146 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS z 159 " --> pdb=" O SER z 155 " (cutoff:3.500A) Processing helix chain 'z' and resid 201 through 203 No H-bonds generated for 'chain 'z' and resid 201 through 203' Processing helix chain 'z' and resid 381 through 403 Processing helix chain 'z' and resid 413 through 423 Processing helix chain 'z' and resid 432 through 454 removed outlier: 3.552A pdb=" N GLN z 438 " --> pdb=" O LEU z 435 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP z 442 " --> pdb=" O ALA z 439 " (cutoff:3.500A) Proline residue: z 448 - end of helix removed outlier: 3.859A pdb=" N ASN z 454 " --> pdb=" O LEU z 451 " (cutoff:3.500A) Processing helix chain 'z' and resid 459 through 468 removed outlier: 3.717A pdb=" N LEU z 463 " --> pdb=" O LEU z 459 " (cutoff:3.500A) Processing helix chain 'z' and resid 489 through 492 No H-bonds generated for 'chain 'z' and resid 489 through 492' Processing helix chain 'z' and resid 498 through 516 removed outlier: 3.590A pdb=" N VAL z 510 " --> pdb=" O HIS z 506 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'a' and resid 10 through 13 Processing sheet with id= B, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= C, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.575A pdb=" N LYS a 494 " --> pdb=" O ASP a 489 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 11 through 13 Processing sheet with id= E, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= F, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= G, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= H, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= I, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.023A pdb=" N ILE B 520 " --> pdb=" O GLU B 19 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 50 through 52 Processing sheet with id= K, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= L, first strand: chain 'D' and resid 59 through 62 removed outlier: 3.696A pdb=" N THR D 71 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 61 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= N, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.819A pdb=" N GLY D 492 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= P, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= Q, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= R, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= S, first strand: chain 'e' and resid 24 through 27 removed outlier: 3.529A pdb=" N LYS e 533 " --> pdb=" O SER e 24 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU e 26 " --> pdb=" O ILE e 531 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE e 531 " --> pdb=" O LEU e 26 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'e' and resid 57 through 60 Processing sheet with id= U, first strand: chain 'e' and resid 416 through 418 Processing sheet with id= V, first strand: chain 'G' and resid 16 through 18 Processing sheet with id= W, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= X, first strand: chain 'h' and resid 15 through 17 removed outlier: 4.101A pdb=" N SER h 16 " --> pdb=" O THR h 519 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR h 519 " --> pdb=" O SER h 16 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= Z, first strand: chain 'h' and resid 197 through 200 removed outlier: 5.748A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= AB, first strand: chain 'h' and resid 475 through 477 Processing sheet with id= AC, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AD, first strand: chain 'H' and resid 475 through 477 Processing sheet with id= AE, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AF, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AG, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= AH, first strand: chain 'q' and resid 408 through 410 Processing sheet with id= AI, first strand: chain 'q' and resid 478 through 480 removed outlier: 3.530A pdb=" N LYS q 490 " --> pdb=" O GLY q 479 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Z' and resid 407 through 409 Processing sheet with id= AK, first strand: chain 'z' and resid 407 through 409 Processing sheet with id= AL, first strand: chain 'z' and resid 477 through 479 1835 hydrogen bonds defined for protein. 4890 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: 11.40 Time building geometry restraints manager: 15.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 11527 1.35 - 1.47: 6451 1.47 - 1.59: 15947 1.59 - 1.71: 18 1.71 - 1.83: 330 Bond restraints: 34273 Sorted by residual: bond pdb=" C ASN A 477 " pdb=" N PRO A 478 " ideal model delta sigma weight residual 1.331 1.346 -0.015 7.90e-03 1.60e+04 3.49e+00 bond pdb=" CA PHE b 12 " pdb=" CB PHE b 12 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.35e-02 5.49e+03 1.49e+00 bond pdb=" N GLY A 9 " pdb=" CA GLY A 9 " ideal model delta sigma weight residual 1.453 1.443 0.010 8.60e-03 1.35e+04 1.36e+00 bond pdb=" C LEU Z 7 " pdb=" N ASN Z 8 " ideal model delta sigma weight residual 1.327 1.358 -0.031 2.86e-02 1.22e+03 1.21e+00 bond pdb=" C VAL G 408 " pdb=" N PRO G 409 " ideal model delta sigma weight residual 1.335 1.344 -0.009 8.70e-03 1.32e+04 1.17e+00 ... (remaining 34268 not shown) Histogram of bond angle deviations from ideal: 100.07 - 107.30: 956 107.30 - 114.53: 21267 114.53 - 121.76: 16914 121.76 - 128.99: 6959 128.99 - 136.22: 225 Bond angle restraints: 46321 Sorted by residual: angle pdb=" N ILE G 495 " pdb=" CA ILE G 495 " pdb=" C ILE G 495 " ideal model delta sigma weight residual 111.91 108.69 3.22 8.90e-01 1.26e+00 1.31e+01 angle pdb=" N ILE g 495 " pdb=" CA ILE g 495 " pdb=" C ILE g 495 " ideal model delta sigma weight residual 111.91 108.69 3.22 8.90e-01 1.26e+00 1.31e+01 angle pdb=" N VAL Z 429 " pdb=" CA VAL Z 429 " pdb=" C VAL Z 429 " ideal model delta sigma weight residual 112.12 109.33 2.79 8.40e-01 1.42e+00 1.10e+01 angle pdb=" N VAL e 153 " pdb=" CA VAL e 153 " pdb=" C VAL e 153 " ideal model delta sigma weight residual 111.62 109.25 2.37 7.90e-01 1.60e+00 9.00e+00 angle pdb=" C VAL e 155 " pdb=" N ASP e 156 " pdb=" CA ASP e 156 " ideal model delta sigma weight residual 121.54 126.75 -5.21 1.91e+00 2.74e-01 7.45e+00 ... (remaining 46316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.20: 20408 22.20 - 44.40: 693 44.40 - 66.60: 65 66.60 - 88.80: 13 88.80 - 111.01: 7 Dihedral angle restraints: 21186 sinusoidal: 8353 harmonic: 12833 Sorted by residual: dihedral pdb=" O1B ADP Q 601 " pdb=" O3A ADP Q 601 " pdb=" PB ADP Q 601 " pdb=" PA ADP Q 601 " ideal model delta sinusoidal sigma weight residual -60.00 -171.01 111.01 1 2.00e+01 2.50e-03 3.26e+01 dihedral pdb=" O1B ADP Z 601 " pdb=" O3A ADP Z 601 " pdb=" PB ADP Z 601 " pdb=" PA ADP Z 601 " ideal model delta sinusoidal sigma weight residual -60.00 -171.01 111.00 1 2.00e+01 2.50e-03 3.26e+01 dihedral pdb=" O1B ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PB ADP z 601 " pdb=" PA ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 -171.00 110.99 1 2.00e+01 2.50e-03 3.26e+01 ... (remaining 21183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3869 0.030 - 0.059: 1083 0.059 - 0.089: 397 0.089 - 0.118: 211 0.118 - 0.148: 57 Chirality restraints: 5617 Sorted by residual: chirality pdb=" CA ILE A 112 " pdb=" N ILE A 112 " pdb=" C ILE A 112 " pdb=" CB ILE A 112 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA VAL a 409 " pdb=" N VAL a 409 " pdb=" C VAL a 409 " pdb=" CB VAL a 409 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE a 112 " pdb=" N ILE a 112 " pdb=" C ILE a 112 " pdb=" CB ILE a 112 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 5614 not shown) Planarity restraints: 5931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 428 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO B 429 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 429 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 429 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN e 484 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO e 485 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO e 485 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO e 485 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR b 428 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO b 429 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO b 429 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO b 429 " 0.024 5.00e-02 4.00e+02 ... (remaining 5928 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 41 2.32 - 2.96: 14393 2.96 - 3.61: 51069 3.61 - 4.25: 78670 4.25 - 4.90: 129159 Nonbonded interactions: 273332 Sorted by model distance: nonbonded pdb=" OD1 ASP G 93 " pdb=" O3A ADP G 601 " model vdw 1.675 3.040 nonbonded pdb=" NZ LYS e 527 " pdb=" OE2 GLU h 384 " model vdw 1.679 2.520 nonbonded pdb=" OD2 ASP G 93 " pdb=" O1A ADP G 601 " model vdw 1.682 3.040 nonbonded pdb=" OD1 ASP g 93 " pdb=" O3A ADP g 601 " model vdw 1.689 3.040 nonbonded pdb=" OD1 ASP g 93 " pdb=" O1A ADP g 601 " model vdw 1.863 3.040 ... (remaining 273327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'a' and (resid 5 through 133 or resid 408 through 533)) } ncs_group { reference = chain 'D' selection = (chain 'd' and (resid 24 through 151 or resid 418 through 539)) } ncs_group { reference = (chain 'G' and (resid 15 through 139 or resid 413 through 526 or resid 601)) selection = chain 'g' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.550 Check model and map are aligned: 0.510 Set scattering table: 0.330 Process input model: 90.050 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.160 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 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 : 0.003 0.032 34273 Z= 0.183 Angle : 0.531 6.171 46321 Z= 0.269 Chirality : 0.038 0.148 5617 Planarity : 0.003 0.046 5931 Dihedral : 11.382 111.005 12862 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.05 % Allowed : 0.69 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.10), residues: 4407 helix: -2.43 (0.07), residues: 2835 sheet: -1.66 (0.36), residues: 172 loop : -1.90 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP g 478 HIS 0.002 0.000 HIS q 59 PHE 0.014 0.001 PHE G 112 TYR 0.006 0.001 TYR g 437 ARG 0.004 0.000 ARG e 398 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1669 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1667 time to evaluate : 3.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 146 ASP cc_start: 0.4141 (t0) cc_final: 0.3928 (t0) REVERT: a 460 SER cc_start: 0.8396 (p) cc_final: 0.8001 (t) REVERT: A 20 GLN cc_start: 0.8650 (mt0) cc_final: 0.8313 (mt0) REVERT: A 52 VAL cc_start: 0.7776 (p) cc_final: 0.7561 (t) REVERT: A 489 ASP cc_start: 0.1888 (t0) cc_final: 0.1252 (t70) REVERT: b 97 ASP cc_start: 0.5663 (t0) cc_final: 0.5054 (m-30) REVERT: b 120 LYS cc_start: 0.8433 (mtmt) cc_final: 0.7735 (mmtm) REVERT: b 485 ILE cc_start: 0.5865 (mt) cc_final: 0.5306 (mt) REVERT: B 52 LEU cc_start: 0.8154 (mt) cc_final: 0.7687 (mt) REVERT: B 448 THR cc_start: 0.7941 (m) cc_final: 0.7297 (p) REVERT: B 452 ASP cc_start: 0.6536 (m-30) cc_final: 0.6158 (m-30) REVERT: B 522 LYS cc_start: 0.8397 (mttt) cc_final: 0.8007 (ptpt) REVERT: D 57 MET cc_start: 0.8455 (mmm) cc_final: 0.7673 (mmm) REVERT: D 460 VAL cc_start: 0.7996 (p) cc_final: 0.7664 (t) REVERT: E 58 MET cc_start: 0.8563 (ttm) cc_final: 0.8235 (ttm) REVERT: E 71 ASP cc_start: 0.7607 (t70) cc_final: 0.7385 (t0) REVERT: E 82 ASP cc_start: 0.7062 (m-30) cc_final: 0.6841 (m-30) REVERT: E 98 ASP cc_start: 0.7333 (m-30) cc_final: 0.6907 (m-30) REVERT: E 474 GLU cc_start: 0.5689 (mt-10) cc_final: 0.5199 (mt-10) REVERT: e 32 LEU cc_start: 0.8322 (mt) cc_final: 0.7897 (tp) REVERT: e 87 LYS cc_start: 0.8549 (mttt) cc_final: 0.7563 (mttp) REVERT: g 48 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7210 (mmtm) REVERT: G 145 ASP cc_start: 0.7023 (t0) cc_final: 0.6603 (m-30) REVERT: G 449 ARG cc_start: 0.6845 (ttm170) cc_final: 0.6551 (ttm110) REVERT: G 495 ILE cc_start: 0.7471 (mm) cc_final: 0.6869 (mm) REVERT: h 46 ASP cc_start: 0.7525 (m-30) cc_final: 0.7298 (m-30) REVERT: h 49 ILE cc_start: 0.8973 (mt) cc_final: 0.8671 (mm) REVERT: h 57 THR cc_start: 0.8748 (m) cc_final: 0.8501 (p) REVERT: h 77 LYS cc_start: 0.8245 (mttt) cc_final: 0.8010 (mttm) REVERT: h 197 ILE cc_start: 0.6173 (mt) cc_final: 0.5970 (mm) REVERT: H 51 ASP cc_start: 0.5728 (p0) cc_final: 0.5182 (p0) REVERT: H 95 THR cc_start: 0.7969 (m) cc_final: 0.7707 (p) REVERT: H 135 LYS cc_start: 0.8459 (tptt) cc_final: 0.8190 (tptm) REVERT: H 452 ASN cc_start: 0.7630 (m-40) cc_final: 0.7150 (m-40) REVERT: H 481 ASN cc_start: 0.6902 (t0) cc_final: 0.6639 (t0) REVERT: H 484 ILE cc_start: 0.8132 (pt) cc_final: 0.7804 (pt) REVERT: H 521 LYS cc_start: 0.8116 (tttt) cc_final: 0.7674 (ttpp) REVERT: Q 446 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6866 (mt-10) REVERT: Q 505 TYR cc_start: 0.7401 (t80) cc_final: 0.6899 (t80) REVERT: q 30 TYR cc_start: 0.7532 (m-10) cc_final: 0.7310 (m-10) REVERT: q 31 ARG cc_start: 0.8095 (mmt180) cc_final: 0.7755 (mmt-90) REVERT: q 34 GLN cc_start: 0.8259 (tp40) cc_final: 0.8037 (mm110) REVERT: Z 432 ARG cc_start: 0.7854 (mtm180) cc_final: 0.7492 (mtm180) REVERT: Z 460 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7353 (mm-40) REVERT: Z 507 SER cc_start: 0.8452 (t) cc_final: 0.8178 (t) REVERT: z 23 ASN cc_start: 0.8165 (m-40) cc_final: 0.7589 (m110) REVERT: z 37 ASN cc_start: 0.8115 (p0) cc_final: 0.7849 (p0) REVERT: z 66 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7688 (mt-10) REVERT: z 414 VAL cc_start: 0.8602 (t) cc_final: 0.8352 (m) REVERT: z 453 GLN cc_start: 0.7904 (mt0) cc_final: 0.7222 (mt0) REVERT: z 518 VAL cc_start: 0.8797 (t) cc_final: 0.8556 (m) outliers start: 2 outliers final: 0 residues processed: 1667 average time/residue: 0.5261 time to fit residues: 1325.5709 Evaluate side-chains 874 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 874 time to evaluate : 3.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 372 optimal weight: 0.9980 chunk 334 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 345 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 400 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 135 ASN a 150 ASN a 450 ASN A 475 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 148 HIS b 174 HIS b 175 HIS b 195 ASN b 464 GLN B 464 GLN D 98 GLN ** d 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 98 GLN d 165 ASN E 120 GLN E 443 GLN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 ASN ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 HIS g 472 GLN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 175 ASN q 477 ASN Z 61 ASN Z 132 GLN Z 434 GLN z 382 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34273 Z= 0.248 Angle : 0.627 9.184 46321 Z= 0.317 Chirality : 0.042 0.219 5617 Planarity : 0.004 0.058 5931 Dihedral : 5.000 102.496 4773 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.63 % Allowed : 15.27 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.12), residues: 4407 helix: 0.07 (0.09), residues: 2838 sheet: -1.15 (0.35), residues: 200 loop : -1.31 (0.16), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP z 495 HIS 0.007 0.001 HIS H 468 PHE 0.023 0.002 PHE a 516 TYR 0.019 0.002 TYR h 419 ARG 0.014 0.001 ARG h 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 965 time to evaluate : 4.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 150 ASN cc_start: 0.6327 (OUTLIER) cc_final: 0.6125 (m110) REVERT: a 426 TYR cc_start: 0.7587 (t80) cc_final: 0.7027 (t80) REVERT: a 527 ILE cc_start: 0.8658 (mm) cc_final: 0.8288 (mt) REVERT: A 528 ASP cc_start: 0.8406 (p0) cc_final: 0.8099 (p0) REVERT: b 78 ASN cc_start: 0.7825 (t0) cc_final: 0.7538 (t0) REVERT: b 82 LYS cc_start: 0.9115 (ttmm) cc_final: 0.8763 (mtmm) REVERT: b 97 ASP cc_start: 0.6417 (t0) cc_final: 0.5149 (m-30) REVERT: b 120 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8570 (mmtm) REVERT: b 452 ASP cc_start: 0.7601 (m-30) cc_final: 0.7189 (m-30) REVERT: b 458 SER cc_start: 0.7940 (p) cc_final: 0.7580 (t) REVERT: B 77 ASP cc_start: 0.7314 (p0) cc_final: 0.6118 (m-30) REVERT: B 91 GLN cc_start: 0.7297 (tp40) cc_final: 0.6942 (tp40) REVERT: B 448 THR cc_start: 0.8438 (m) cc_final: 0.7739 (p) REVERT: B 452 ASP cc_start: 0.7129 (m-30) cc_final: 0.6425 (m-30) REVERT: D 57 MET cc_start: 0.8546 (mmm) cc_final: 0.7847 (mmm) REVERT: D 80 GLN cc_start: 0.8646 (mp10) cc_final: 0.8131 (mp10) REVERT: D 454 PHE cc_start: 0.8791 (t80) cc_final: 0.8551 (t80) REVERT: E 36 ILE cc_start: 0.8999 (mt) cc_final: 0.8764 (mm) REVERT: E 58 MET cc_start: 0.8489 (ttm) cc_final: 0.7943 (ttp) REVERT: E 59 MET cc_start: 0.8157 (mtm) cc_final: 0.7742 (mmm) REVERT: E 79 MET cc_start: 0.8160 (tpp) cc_final: 0.7680 (tpt) REVERT: E 472 MET cc_start: 0.6622 (mmm) cc_final: 0.6147 (mmm) REVERT: e 521 MET cc_start: 0.7709 (ttm) cc_final: 0.7388 (ttm) REVERT: g 132 ASP cc_start: 0.6750 (m-30) cc_final: 0.6351 (m-30) REVERT: g 503 LEU cc_start: 0.8277 (mt) cc_final: 0.8037 (mt) REVERT: G 49 MET cc_start: 0.7656 (tpp) cc_final: 0.7333 (mtp) REVERT: G 87 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7791 (tm-30) REVERT: G 145 ASP cc_start: 0.7678 (t0) cc_final: 0.7141 (m-30) REVERT: h 46 ASP cc_start: 0.7776 (m-30) cc_final: 0.7545 (m-30) REVERT: h 49 ILE cc_start: 0.9056 (mt) cc_final: 0.8621 (tt) REVERT: h 51 ASP cc_start: 0.7224 (p0) cc_final: 0.6952 (p0) REVERT: h 57 THR cc_start: 0.9139 (m) cc_final: 0.8842 (p) REVERT: H 87 ASP cc_start: 0.5735 (t0) cc_final: 0.5470 (t0) REVERT: H 521 LYS cc_start: 0.8298 (tttt) cc_final: 0.7866 (ttpp) REVERT: Q 14 MET cc_start: 0.4588 (ppp) cc_final: 0.3364 (ptt) REVERT: Q 68 ASP cc_start: 0.7671 (t70) cc_final: 0.7464 (t70) REVERT: Q 505 TYR cc_start: 0.7867 (t80) cc_final: 0.7412 (t80) REVERT: q 75 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6466 (mm-30) REVERT: q 114 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8741 (mm) REVERT: q 523 GLN cc_start: 0.7849 (tt0) cc_final: 0.7552 (tp40) REVERT: q 526 MET cc_start: 0.6040 (mtm) cc_final: 0.5788 (mpp) REVERT: Z 128 GLU cc_start: 0.6461 (tp30) cc_final: 0.6211 (tp30) REVERT: Z 135 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6785 (mm-30) REVERT: z 23 ASN cc_start: 0.8554 (m-40) cc_final: 0.7981 (m-40) REVERT: z 453 GLN cc_start: 0.7974 (mt0) cc_final: 0.7718 (mt0) outliers start: 132 outliers final: 66 residues processed: 1045 average time/residue: 0.4675 time to fit residues: 777.6179 Evaluate side-chains 850 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 782 time to evaluate : 3.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 150 ASN Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 450 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 529 ILE Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain e residue 531 ILE Chi-restraints excluded: chain g residue 33 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 488 VAL Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 442 GLN Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain h residue 17 GLN Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 388 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 513 ASN Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 166 THR Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 517 THR Chi-restraints excluded: chain q residue 524 ILE Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain z residue 36 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 408 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 222 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 333 optimal weight: 6.9990 chunk 272 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 401 optimal weight: 2.9990 chunk 433 optimal weight: 0.8980 chunk 357 optimal weight: 0.9980 chunk 397 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 321 optimal weight: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN b 157 GLN b 161 ASN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 98 GLN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 44 ASN g 111 HIS g 453 GLN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN H 462 ASN H 487 ASN ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 13 GLN q 140 HIS Z 61 ASN Z 132 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34273 Z= 0.190 Angle : 0.578 7.844 46321 Z= 0.285 Chirality : 0.040 0.197 5617 Planarity : 0.004 0.052 5931 Dihedral : 4.834 101.204 4773 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.32 % Allowed : 17.69 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.12), residues: 4407 helix: 0.91 (0.09), residues: 2828 sheet: -0.65 (0.34), residues: 208 loop : -1.08 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 435 HIS 0.017 0.001 HIS z 161 PHE 0.013 0.001 PHE a 516 TYR 0.011 0.001 TYR h 419 ARG 0.008 0.001 ARG g 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 877 time to evaluate : 4.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 443 ARG cc_start: 0.7892 (mtm110) cc_final: 0.7461 (ttp-110) REVERT: a 527 ILE cc_start: 0.8703 (mm) cc_final: 0.8379 (mt) REVERT: A 81 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6024 (mm) REVERT: A 458 GLN cc_start: 0.7295 (mm-40) cc_final: 0.7030 (mm110) REVERT: b 78 ASN cc_start: 0.7980 (t0) cc_final: 0.7663 (t0) REVERT: b 97 ASP cc_start: 0.6438 (t0) cc_final: 0.5399 (m-30) REVERT: b 142 LEU cc_start: 0.8445 (tp) cc_final: 0.8150 (tp) REVERT: b 162 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7723 (tt) REVERT: b 452 ASP cc_start: 0.7643 (m-30) cc_final: 0.7295 (m-30) REVERT: b 458 SER cc_start: 0.7869 (p) cc_final: 0.7472 (t) REVERT: b 480 MET cc_start: 0.6351 (pmm) cc_final: 0.5957 (mpp) REVERT: b 502 GLN cc_start: 0.7948 (mt0) cc_final: 0.7747 (mt0) REVERT: B 91 GLN cc_start: 0.7563 (tp-100) cc_final: 0.7222 (tp40) REVERT: D 42 LYS cc_start: 0.8362 (ttpp) cc_final: 0.8149 (ptmm) REVERT: D 57 MET cc_start: 0.8574 (mmm) cc_final: 0.7942 (mmm) REVERT: D 80 GLN cc_start: 0.8442 (mp10) cc_final: 0.7771 (mp10) REVERT: D 82 GLN cc_start: 0.7663 (mm110) cc_final: 0.6552 (tm-30) REVERT: D 454 PHE cc_start: 0.8812 (t80) cc_final: 0.8595 (t80) REVERT: D 460 VAL cc_start: 0.8643 (p) cc_final: 0.8330 (t) REVERT: E 58 MET cc_start: 0.8231 (ttm) cc_final: 0.7725 (ttm) REVERT: E 79 MET cc_start: 0.8008 (tpp) cc_final: 0.7341 (tpt) REVERT: E 137 GLN cc_start: 0.7007 (mt0) cc_final: 0.6682 (mt0) REVERT: E 512 LYS cc_start: 0.7934 (mttt) cc_final: 0.7717 (mtpp) REVERT: e 80 ASP cc_start: 0.7500 (p0) cc_final: 0.7149 (t0) REVERT: e 458 MET cc_start: 0.8166 (ttm) cc_final: 0.7526 (ttm) REVERT: e 521 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7497 (ttm) REVERT: g 503 LEU cc_start: 0.8274 (mt) cc_final: 0.8056 (mt) REVERT: G 145 ASP cc_start: 0.7932 (t0) cc_final: 0.7342 (m-30) REVERT: h 49 ILE cc_start: 0.9004 (mt) cc_final: 0.8792 (mm) REVERT: h 374 LEU cc_start: 0.7135 (mt) cc_final: 0.6321 (mt) REVERT: h 382 MET cc_start: 0.4887 (mmp) cc_final: 0.4043 (mmp) REVERT: h 394 MET cc_start: 0.7816 (mmp) cc_final: 0.7506 (mmp) REVERT: H 25 ASN cc_start: 0.8978 (m-40) cc_final: 0.8612 (m110) REVERT: H 483 ASP cc_start: 0.6586 (p0) cc_final: 0.6368 (p0) REVERT: H 519 THR cc_start: 0.8325 (t) cc_final: 0.8047 (t) REVERT: H 521 LYS cc_start: 0.8225 (tttt) cc_final: 0.7792 (ttpp) REVERT: Q 14 MET cc_start: 0.4450 (ppp) cc_final: 0.3396 (ptt) REVERT: Q 31 ARG cc_start: 0.7281 (mmt180) cc_final: 0.6999 (mmt90) REVERT: Q 68 ASP cc_start: 0.7628 (t70) cc_final: 0.7394 (t70) REVERT: Q 116 GLU cc_start: 0.6822 (tp30) cc_final: 0.6551 (tp30) REVERT: q 34 GLN cc_start: 0.8217 (tp40) cc_final: 0.7936 (mm110) REVERT: q 41 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7934 (mm-40) REVERT: q 52 MET cc_start: 0.8004 (mmm) cc_final: 0.7734 (mmm) REVERT: q 114 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8705 (mm) REVERT: q 385 MET cc_start: 0.3799 (mtt) cc_final: 0.3181 (ttt) REVERT: q 526 MET cc_start: 0.6425 (mtm) cc_final: 0.6171 (mpp) REVERT: z 23 ASN cc_start: 0.8391 (m-40) cc_final: 0.7985 (m-40) outliers start: 121 outliers final: 74 residues processed: 954 average time/residue: 0.4712 time to fit residues: 710.9409 Evaluate side-chains 839 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 761 time to evaluate : 4.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 150 ASN Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain a residue 499 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 493 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 484 ASN Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 466 MET Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain e residue 521 MET Chi-restraints excluded: chain e residue 531 ILE Chi-restraints excluded: chain g residue 33 ILE Chi-restraints excluded: chain g residue 64 ASN Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 523 VAL Chi-restraints excluded: chain h residue 17 GLN Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 518 GLU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 513 ASN Chi-restraints excluded: chain Q residue 518 VAL Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 166 THR Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 517 THR Chi-restraints excluded: chain q residue 524 ILE Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 483 THR Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 22 VAL Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 499 CYS Chi-restraints excluded: chain z residue 518 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 396 optimal weight: 0.8980 chunk 301 optimal weight: 0.0570 chunk 208 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 402 optimal weight: 2.9990 chunk 426 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 chunk 381 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 110 GLN a 150 ASN a 435 GLN ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN A 103 ASN b 161 ASN b 195 ASN b 453 ASN D 25 GLN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** d 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 GLN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN H 487 ASN ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 GLN Q 435 GLN q 50 ASN Z 68 GLN z 453 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34273 Z= 0.199 Angle : 0.579 8.351 46321 Z= 0.286 Chirality : 0.040 0.166 5617 Planarity : 0.004 0.047 5931 Dihedral : 4.706 98.585 4773 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.76 % Allowed : 18.05 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.12), residues: 4407 helix: 1.30 (0.10), residues: 2812 sheet: -0.36 (0.35), residues: 198 loop : -0.97 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 435 HIS 0.009 0.001 HIS z 161 PHE 0.023 0.001 PHE H 455 TYR 0.018 0.001 TYR q 30 ARG 0.007 0.001 ARG g 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 821 time to evaluate : 4.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 GLN cc_start: 0.8388 (mt0) cc_final: 0.8157 (mm-40) REVERT: a 65 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7658 (tt) REVERT: b 78 ASN cc_start: 0.7959 (t0) cc_final: 0.7638 (t0) REVERT: b 97 ASP cc_start: 0.6512 (t0) cc_final: 0.5153 (m-30) REVERT: b 142 LEU cc_start: 0.8581 (tp) cc_final: 0.8260 (tp) REVERT: b 441 LYS cc_start: 0.8785 (mptt) cc_final: 0.8464 (mptt) REVERT: b 502 GLN cc_start: 0.7990 (mt0) cc_final: 0.7613 (tt0) REVERT: B 91 GLN cc_start: 0.7915 (tp-100) cc_final: 0.7550 (tp40) REVERT: B 522 LYS cc_start: 0.8184 (mttt) cc_final: 0.7907 (ptpp) REVERT: D 57 MET cc_start: 0.8659 (mmm) cc_final: 0.8058 (mmm) REVERT: D 80 GLN cc_start: 0.8467 (mp10) cc_final: 0.7810 (mp10) REVERT: D 82 GLN cc_start: 0.7477 (mm110) cc_final: 0.6472 (tm-30) REVERT: D 460 VAL cc_start: 0.8661 (p) cc_final: 0.8277 (t) REVERT: E 46 MET cc_start: 0.7628 (mtp) cc_final: 0.7396 (ttt) REVERT: E 58 MET cc_start: 0.7974 (ttm) cc_final: 0.7588 (ttt) REVERT: E 78 MET cc_start: 0.8463 (mtm) cc_final: 0.8172 (ptm) REVERT: E 79 MET cc_start: 0.7876 (tpp) cc_final: 0.7389 (tpt) REVERT: E 512 LYS cc_start: 0.8114 (mttt) cc_final: 0.7818 (mtpp) REVERT: e 442 GLU cc_start: 0.6805 (tt0) cc_final: 0.6481 (tt0) REVERT: e 521 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7558 (ttm) REVERT: e 533 LYS cc_start: 0.7568 (tptm) cc_final: 0.7336 (tptm) REVERT: g 132 ASP cc_start: 0.6652 (m-30) cc_final: 0.6417 (m-30) REVERT: G 62 ASP cc_start: 0.6715 (OUTLIER) cc_final: 0.5879 (t70) REVERT: G 145 ASP cc_start: 0.8090 (t0) cc_final: 0.7590 (m-30) REVERT: h 45 MET cc_start: 0.7887 (mmm) cc_final: 0.7446 (mmm) REVERT: h 374 LEU cc_start: 0.7388 (mt) cc_final: 0.6828 (mt) REVERT: h 382 MET cc_start: 0.4755 (mmp) cc_final: 0.4151 (mmp) REVERT: h 394 MET cc_start: 0.8035 (mmp) cc_final: 0.7767 (mmp) REVERT: h 451 ASP cc_start: 0.7639 (m-30) cc_final: 0.7233 (m-30) REVERT: H 25 ASN cc_start: 0.9006 (m-40) cc_final: 0.8610 (m110) REVERT: H 519 THR cc_start: 0.8719 (t) cc_final: 0.8489 (t) REVERT: H 521 LYS cc_start: 0.8397 (tttt) cc_final: 0.7863 (ttpp) REVERT: Q 14 MET cc_start: 0.4052 (ppp) cc_final: 0.3090 (ptt) REVERT: Q 31 ARG cc_start: 0.7319 (mmt180) cc_final: 0.7036 (mmt90) REVERT: Q 41 GLN cc_start: 0.8494 (tp40) cc_final: 0.8164 (tp40) REVERT: Q 68 ASP cc_start: 0.7662 (t70) cc_final: 0.7429 (t70) REVERT: Q 116 GLU cc_start: 0.6847 (tp30) cc_final: 0.6414 (tp30) REVERT: q 34 GLN cc_start: 0.8218 (tp40) cc_final: 0.7887 (mm110) REVERT: q 385 MET cc_start: 0.4311 (mtt) cc_final: 0.3479 (ttt) REVERT: q 524 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9044 (mp) REVERT: q 526 MET cc_start: 0.6581 (mtm) cc_final: 0.6267 (mpp) REVERT: z 23 ASN cc_start: 0.8292 (m-40) cc_final: 0.7962 (m-40) REVERT: z 35 ARG cc_start: 0.8727 (ptm160) cc_final: 0.8389 (ptm160) REVERT: z 453 GLN cc_start: 0.8364 (mt0) cc_final: 0.8105 (mt0) outliers start: 137 outliers final: 86 residues processed: 904 average time/residue: 0.4683 time to fit residues: 670.8892 Evaluate side-chains 821 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 731 time to evaluate : 3.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain a residue 499 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 493 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 460 VAL Chi-restraints excluded: chain d residue 461 ILE Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 484 ASN Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 466 MET Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain e residue 521 MET Chi-restraints excluded: chain e residue 531 ILE Chi-restraints excluded: chain g residue 64 ASN Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 501 VAL Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 523 VAL Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain Q residue 513 ASN Chi-restraints excluded: chain Q residue 518 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 383 ASN Chi-restraints excluded: chain q residue 517 THR Chi-restraints excluded: chain q residue 524 ILE Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 22 VAL Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 61 ASN Chi-restraints excluded: chain z residue 69 ILE Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 88 THR Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 499 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 355 optimal weight: 8.9990 chunk 241 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 317 optimal weight: 0.6980 chunk 175 optimal weight: 7.9990 chunk 363 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 217 optimal weight: 0.6980 chunk 382 optimal weight: 2.9990 chunk 107 optimal weight: 0.0970 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 110 GLN a 482 ASN A 21 ASN b 391 HIS b 453 ASN D 37 ASN D 468 ASN ** d 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 443 GLN h 21 GLN H 487 ASN ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 23 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34273 Z= 0.171 Angle : 0.564 9.631 46321 Z= 0.275 Chirality : 0.040 0.195 5617 Planarity : 0.003 0.046 5931 Dihedral : 4.642 98.660 4773 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.99 % Allowed : 20.00 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.13), residues: 4407 helix: 1.51 (0.10), residues: 2807 sheet: -0.09 (0.37), residues: 198 loop : -0.88 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP h 493 HIS 0.009 0.001 HIS b 391 PHE 0.016 0.001 PHE h 381 TYR 0.021 0.001 TYR q 505 ARG 0.006 0.001 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 796 time to evaluate : 3.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8621 (mmtp) cc_final: 0.8277 (mmtp) REVERT: b 78 ASN cc_start: 0.7919 (t0) cc_final: 0.7590 (t0) REVERT: b 97 ASP cc_start: 0.6547 (t0) cc_final: 0.5113 (m-30) REVERT: b 142 LEU cc_start: 0.8397 (tp) cc_final: 0.8090 (tp) REVERT: B 452 ASP cc_start: 0.7340 (m-30) cc_final: 0.6694 (m-30) REVERT: B 522 LYS cc_start: 0.8087 (mttt) cc_final: 0.7749 (ptpp) REVERT: D 57 MET cc_start: 0.8665 (mmm) cc_final: 0.8070 (mmm) REVERT: D 80 GLN cc_start: 0.8491 (mp10) cc_final: 0.7870 (mp10) REVERT: D 82 GLN cc_start: 0.7523 (mm110) cc_final: 0.6606 (tm-30) REVERT: D 460 VAL cc_start: 0.8715 (p) cc_final: 0.8331 (t) REVERT: d 81 MET cc_start: 0.6788 (mmm) cc_final: 0.6542 (mmm) REVERT: d 90 MET cc_start: 0.6516 (mtm) cc_final: 0.5698 (mtm) REVERT: E 46 MET cc_start: 0.7740 (mtp) cc_final: 0.7433 (ttt) REVERT: E 58 MET cc_start: 0.8206 (ttm) cc_final: 0.7841 (ttp) REVERT: E 79 MET cc_start: 0.8003 (tpp) cc_final: 0.7293 (tpt) REVERT: E 512 LYS cc_start: 0.8164 (mttt) cc_final: 0.7850 (mtpp) REVERT: e 87 LYS cc_start: 0.8669 (mmtt) cc_final: 0.8453 (mmtp) REVERT: e 442 GLU cc_start: 0.6935 (tt0) cc_final: 0.6609 (tt0) REVERT: e 521 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7579 (ttm) REVERT: e 531 ILE cc_start: 0.9032 (pt) cc_final: 0.8785 (mm) REVERT: g 435 TRP cc_start: 0.7753 (m100) cc_final: 0.7469 (m100) REVERT: G 62 ASP cc_start: 0.6586 (OUTLIER) cc_final: 0.5475 (t70) REVERT: h 373 ILE cc_start: 0.6094 (OUTLIER) cc_final: 0.5647 (mp) REVERT: h 382 MET cc_start: 0.5156 (mmp) cc_final: 0.4264 (mmp) REVERT: h 394 MET cc_start: 0.8023 (mmp) cc_final: 0.7717 (mmp) REVERT: H 519 THR cc_start: 0.8657 (t) cc_final: 0.8440 (t) REVERT: H 521 LYS cc_start: 0.8425 (tttt) cc_final: 0.7907 (ttpp) REVERT: Q 14 MET cc_start: 0.3975 (ppp) cc_final: 0.3118 (ptt) REVERT: Q 41 GLN cc_start: 0.8456 (tp40) cc_final: 0.8055 (tp40) REVERT: Q 68 ASP cc_start: 0.7697 (t70) cc_final: 0.7466 (t70) REVERT: Q 78 VAL cc_start: 0.8529 (t) cc_final: 0.8218 (m) REVERT: Q 79 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8484 (mp10) REVERT: Q 90 SER cc_start: 0.9410 (OUTLIER) cc_final: 0.9063 (p) REVERT: Q 116 GLU cc_start: 0.6904 (tp30) cc_final: 0.6263 (tp30) REVERT: Q 120 ARG cc_start: 0.8150 (mmt90) cc_final: 0.7508 (mmt180) REVERT: q 34 GLN cc_start: 0.8069 (tp40) cc_final: 0.7794 (mm110) REVERT: q 385 MET cc_start: 0.4442 (mtt) cc_final: 0.3632 (ttt) REVERT: q 526 MET cc_start: 0.6313 (mtm) cc_final: 0.5940 (mpp) REVERT: z 23 ASN cc_start: 0.8248 (m-40) cc_final: 0.7963 (m-40) REVERT: z 35 ARG cc_start: 0.8685 (ptm160) cc_final: 0.8335 (ptm160) REVERT: z 88 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8202 (t) REVERT: z 453 GLN cc_start: 0.8265 (mt0) cc_final: 0.7991 (mt0) outliers start: 109 outliers final: 67 residues processed: 866 average time/residue: 0.4970 time to fit residues: 681.8223 Evaluate side-chains 778 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 706 time to evaluate : 4.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain a residue 499 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 493 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 460 VAL Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 466 MET Chi-restraints excluded: chain e residue 521 MET Chi-restraints excluded: chain g residue 33 ILE Chi-restraints excluded: chain g residue 64 ASN Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 383 ASN Chi-restraints excluded: chain q residue 497 ILE Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 22 VAL Chi-restraints excluded: chain z residue 61 ASN Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 88 THR Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 500 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 143 optimal weight: 2.9990 chunk 383 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 250 optimal weight: 10.0000 chunk 105 optimal weight: 0.3980 chunk 426 optimal weight: 5.9990 chunk 354 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 141 optimal weight: 0.0000 chunk 224 optimal weight: 5.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 110 GLN b 391 HIS D 468 ASN D 502 ASN ** d 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS Z 23 ASN Z 65 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.6589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34273 Z= 0.183 Angle : 0.582 11.063 46321 Z= 0.282 Chirality : 0.040 0.266 5617 Planarity : 0.004 0.058 5931 Dihedral : 4.676 98.201 4773 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.43 % Allowed : 20.66 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.13), residues: 4407 helix: 1.62 (0.10), residues: 2808 sheet: -0.05 (0.36), residues: 209 loop : -0.79 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 496 HIS 0.009 0.001 HIS b 391 PHE 0.022 0.001 PHE q 103 TYR 0.021 0.001 TYR a 426 ARG 0.010 0.001 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 747 time to evaluate : 4.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 GLN cc_start: 0.8425 (mt0) cc_final: 0.8097 (mp10) REVERT: A 20 GLN cc_start: 0.8739 (mt0) cc_final: 0.8391 (mt0) REVERT: A 109 LYS cc_start: 0.8773 (mmtp) cc_final: 0.8488 (mmtp) REVERT: b 78 ASN cc_start: 0.7853 (t0) cc_final: 0.7490 (t0) REVERT: b 97 ASP cc_start: 0.5856 (t0) cc_final: 0.4723 (m-30) REVERT: b 162 ILE cc_start: 0.8641 (mt) cc_final: 0.8371 (tt) REVERT: b 441 LYS cc_start: 0.8935 (mptt) cc_final: 0.8479 (mptt) REVERT: B 89 ARG cc_start: 0.8024 (tpp80) cc_final: 0.7714 (tpp80) REVERT: B 91 GLN cc_start: 0.7994 (tp-100) cc_final: 0.7457 (tp40) REVERT: B 417 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7826 (mtp) REVERT: B 452 ASP cc_start: 0.7350 (m-30) cc_final: 0.6709 (m-30) REVERT: B 522 LYS cc_start: 0.8145 (mttt) cc_final: 0.7783 (ptpp) REVERT: D 57 MET cc_start: 0.8591 (mmm) cc_final: 0.8088 (mmm) REVERT: D 82 GLN cc_start: 0.7343 (mm110) cc_final: 0.7091 (pt0) REVERT: D 460 VAL cc_start: 0.8871 (p) cc_final: 0.8387 (t) REVERT: E 58 MET cc_start: 0.8157 (ttm) cc_final: 0.7858 (ttp) REVERT: E 79 MET cc_start: 0.8106 (tpp) cc_final: 0.7473 (tpt) REVERT: E 472 MET cc_start: 0.6612 (mmm) cc_final: 0.6282 (mmm) REVERT: E 512 LYS cc_start: 0.8213 (mttt) cc_final: 0.7883 (mtpp) REVERT: e 87 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8477 (mmtp) REVERT: e 442 GLU cc_start: 0.6909 (tt0) cc_final: 0.6563 (tt0) REVERT: e 521 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7544 (ttm) REVERT: g 435 TRP cc_start: 0.7735 (m100) cc_final: 0.7437 (m100) REVERT: G 38 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.6996 (tmm-80) REVERT: G 62 ASP cc_start: 0.6438 (OUTLIER) cc_final: 0.5531 (t70) REVERT: h 382 MET cc_start: 0.5207 (mmp) cc_final: 0.4407 (mmp) REVERT: h 394 MET cc_start: 0.7998 (mmp) cc_final: 0.7712 (mmp) REVERT: H 521 LYS cc_start: 0.8432 (tttt) cc_final: 0.7929 (ttpp) REVERT: Q 14 MET cc_start: 0.3816 (ppp) cc_final: 0.2980 (ptt) REVERT: Q 41 GLN cc_start: 0.8356 (tp40) cc_final: 0.7915 (tp40) REVERT: Q 78 VAL cc_start: 0.8543 (t) cc_final: 0.8192 (m) REVERT: Q 79 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8470 (mp10) REVERT: Q 90 SER cc_start: 0.9444 (OUTLIER) cc_final: 0.9111 (p) REVERT: Q 116 GLU cc_start: 0.6911 (tp30) cc_final: 0.6243 (tp30) REVERT: Q 120 ARG cc_start: 0.8090 (mmt90) cc_final: 0.7413 (mmt180) REVERT: q 385 MET cc_start: 0.4581 (mtt) cc_final: 0.3864 (ttt) REVERT: q 524 ILE cc_start: 0.9171 (mp) cc_final: 0.8949 (mm) REVERT: q 526 MET cc_start: 0.6528 (mtm) cc_final: 0.6156 (mpp) REVERT: z 23 ASN cc_start: 0.8198 (m-40) cc_final: 0.7934 (m110) REVERT: z 35 ARG cc_start: 0.8619 (ptm160) cc_final: 0.8266 (ptm160) REVERT: z 46 MET cc_start: 0.8541 (tpp) cc_final: 0.8141 (tpp) REVERT: z 453 GLN cc_start: 0.8263 (mt0) cc_final: 0.7944 (mt0) outliers start: 125 outliers final: 76 residues processed: 821 average time/residue: 0.4703 time to fit residues: 612.5806 Evaluate side-chains 775 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 694 time to evaluate : 4.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain a residue 499 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 460 VAL Chi-restraints excluded: chain d residue 461 ILE Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 466 MET Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain e residue 521 MET Chi-restraints excluded: chain g residue 33 ILE Chi-restraints excluded: chain g residue 64 ASN Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 97 SER Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain G residue 523 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 383 ASN Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 65 HIS Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 22 VAL Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 497 ASN Chi-restraints excluded: chain z residue 500 VAL Chi-restraints excluded: chain z residue 522 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 411 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 311 optimal weight: 4.9990 chunk 241 optimal weight: 1.9990 chunk 359 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 chunk 425 optimal weight: 3.9990 chunk 266 optimal weight: 0.8980 chunk 259 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS D 37 ASN D 468 ASN ** d 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 484 ASN h 21 GLN q 13 GLN q 34 GLN Z 65 HIS ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.6923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34273 Z= 0.210 Angle : 0.604 10.984 46321 Z= 0.296 Chirality : 0.041 0.190 5617 Planarity : 0.004 0.044 5931 Dihedral : 4.744 97.486 4773 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.19 % Allowed : 20.77 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.13), residues: 4407 helix: 1.61 (0.10), residues: 2815 sheet: -0.08 (0.34), residues: 223 loop : -0.77 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 496 HIS 0.010 0.001 HIS b 391 PHE 0.020 0.001 PHE q 399 TYR 0.022 0.002 TYR q 505 ARG 0.007 0.000 ARG Q 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 742 time to evaluate : 4.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 GLN cc_start: 0.8490 (mt0) cc_final: 0.8076 (mp10) REVERT: A 20 GLN cc_start: 0.8658 (mt0) cc_final: 0.8270 (mt0) REVERT: A 109 LYS cc_start: 0.8787 (mmtp) cc_final: 0.8545 (mmtp) REVERT: b 48 MET cc_start: 0.8224 (mmm) cc_final: 0.7855 (mmp) REVERT: b 78 ASN cc_start: 0.7905 (t0) cc_final: 0.7546 (t0) REVERT: b 97 ASP cc_start: 0.5611 (t0) cc_final: 0.4680 (m-30) REVERT: b 111 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8398 (ptp-110) REVERT: b 162 ILE cc_start: 0.8746 (mt) cc_final: 0.8486 (tt) REVERT: b 441 LYS cc_start: 0.8899 (mptt) cc_final: 0.8489 (mptt) REVERT: B 452 ASP cc_start: 0.7388 (m-30) cc_final: 0.6793 (m-30) REVERT: D 57 MET cc_start: 0.8709 (mmm) cc_final: 0.8067 (mmm) REVERT: D 460 VAL cc_start: 0.8880 (p) cc_final: 0.8370 (t) REVERT: E 58 MET cc_start: 0.8148 (ttm) cc_final: 0.7819 (ttp) REVERT: E 79 MET cc_start: 0.8051 (tpp) cc_final: 0.7453 (tpt) REVERT: E 133 ASP cc_start: 0.7614 (t0) cc_final: 0.7163 (t0) REVERT: E 472 MET cc_start: 0.6719 (mmm) cc_final: 0.6443 (mmm) REVERT: E 524 MET cc_start: 0.8289 (tpp) cc_final: 0.7908 (tpp) REVERT: e 87 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8511 (mmtp) REVERT: e 89 MET cc_start: 0.8868 (mtm) cc_final: 0.8507 (mtp) REVERT: e 442 GLU cc_start: 0.6898 (tt0) cc_final: 0.6649 (tt0) REVERT: g 435 TRP cc_start: 0.7715 (m100) cc_final: 0.7376 (m100) REVERT: G 38 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7379 (tmm-80) REVERT: G 59 MET cc_start: 0.8052 (tpp) cc_final: 0.7642 (tpp) REVERT: h 382 MET cc_start: 0.4826 (mmp) cc_final: 0.4485 (mmp) REVERT: h 387 ARG cc_start: 0.6921 (ptm-80) cc_final: 0.6527 (ptm160) REVERT: h 394 MET cc_start: 0.8007 (mmp) cc_final: 0.7736 (mmp) REVERT: H 45 MET cc_start: 0.6725 (ttm) cc_final: 0.6492 (ttt) REVERT: H 521 LYS cc_start: 0.8532 (tttt) cc_final: 0.7589 (tmtt) REVERT: Q 14 MET cc_start: 0.3924 (ppp) cc_final: 0.3130 (ptt) REVERT: Q 41 GLN cc_start: 0.8379 (tp40) cc_final: 0.7945 (tp40) REVERT: Q 78 VAL cc_start: 0.8577 (t) cc_final: 0.8227 (m) REVERT: Q 79 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8435 (mp10) REVERT: Q 90 SER cc_start: 0.9424 (OUTLIER) cc_final: 0.9071 (p) REVERT: Q 116 GLU cc_start: 0.6974 (tp30) cc_final: 0.6329 (tp30) REVERT: Q 120 ARG cc_start: 0.7951 (mmt90) cc_final: 0.7474 (mmt-90) REVERT: q 385 MET cc_start: 0.4752 (mtt) cc_final: 0.3975 (ttt) REVERT: q 524 ILE cc_start: 0.9149 (mp) cc_final: 0.8945 (mm) REVERT: q 526 MET cc_start: 0.6436 (mtm) cc_final: 0.6085 (mpp) REVERT: Z 35 ARG cc_start: 0.7678 (ptm160) cc_final: 0.7457 (ptp-170) REVERT: z 23 ASN cc_start: 0.8304 (m-40) cc_final: 0.8030 (m-40) REVERT: z 46 MET cc_start: 0.8655 (tpp) cc_final: 0.8143 (tpp) outliers start: 116 outliers final: 78 residues processed: 813 average time/residue: 0.4720 time to fit residues: 602.7317 Evaluate side-chains 777 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 696 time to evaluate : 3.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain a residue 499 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 111 ARG Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 478 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 460 VAL Chi-restraints excluded: chain d residue 461 ILE Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 456 ILE Chi-restraints excluded: chain e residue 466 MET Chi-restraints excluded: chain g residue 64 ASN Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain h residue 518 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 517 THR Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 85 ASP Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 22 VAL Chi-restraints excluded: chain z residue 36 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 497 ASN Chi-restraints excluded: chain z residue 522 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 262 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 253 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 270 optimal weight: 7.9990 chunk 289 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 334 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS B 453 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** d 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 ASN h 21 GLN Z 31 GLN ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS z 386 GLN ** z 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.7187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34273 Z= 0.213 Angle : 0.622 11.925 46321 Z= 0.302 Chirality : 0.041 0.292 5617 Planarity : 0.004 0.051 5931 Dihedral : 4.802 97.533 4773 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.10 % Allowed : 21.65 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.13), residues: 4407 helix: 1.60 (0.10), residues: 2818 sheet: -0.01 (0.34), residues: 223 loop : -0.75 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 496 HIS 0.010 0.001 HIS b 391 PHE 0.018 0.001 PHE q 399 TYR 0.023 0.001 TYR q 426 ARG 0.012 0.001 ARG a 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 745 time to evaluate : 4.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 GLN cc_start: 0.8428 (mt0) cc_final: 0.8151 (mm-40) REVERT: a 105 ASP cc_start: 0.7641 (m-30) cc_final: 0.7359 (m-30) REVERT: A 105 ASP cc_start: 0.8068 (t0) cc_final: 0.7855 (t0) REVERT: b 53 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6647 (pp) REVERT: b 78 ASN cc_start: 0.8011 (t0) cc_final: 0.7658 (t0) REVERT: b 97 ASP cc_start: 0.5287 (t0) cc_final: 0.4573 (m-30) REVERT: b 111 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8516 (ptp-110) REVERT: b 441 LYS cc_start: 0.8873 (mptt) cc_final: 0.8435 (mptt) REVERT: B 89 ARG cc_start: 0.7844 (tpp80) cc_final: 0.7641 (tpp80) REVERT: B 91 GLN cc_start: 0.8002 (tp-100) cc_final: 0.7411 (tp40) REVERT: B 438 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8666 (p) REVERT: B 522 LYS cc_start: 0.8219 (mttt) cc_final: 0.7860 (ptpp) REVERT: D 57 MET cc_start: 0.8732 (mmm) cc_final: 0.8090 (mmm) REVERT: D 80 GLN cc_start: 0.8654 (mp10) cc_final: 0.7993 (mp10) REVERT: D 460 VAL cc_start: 0.8927 (p) cc_final: 0.8458 (t) REVERT: d 527 ARG cc_start: 0.7868 (mtp180) cc_final: 0.7656 (mtm180) REVERT: E 58 MET cc_start: 0.8192 (ttm) cc_final: 0.7945 (ttp) REVERT: E 79 MET cc_start: 0.8132 (tpp) cc_final: 0.7508 (tpt) REVERT: E 133 ASP cc_start: 0.7669 (t0) cc_final: 0.7390 (t0) REVERT: E 524 MET cc_start: 0.8361 (tpp) cc_final: 0.7957 (tpp) REVERT: e 442 GLU cc_start: 0.7037 (tt0) cc_final: 0.6813 (tt0) REVERT: e 458 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7680 (tpp) REVERT: G 38 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7455 (tmm-80) REVERT: G 59 MET cc_start: 0.8023 (tpp) cc_final: 0.7339 (tpp) REVERT: h 387 ARG cc_start: 0.6892 (ptm-80) cc_final: 0.6585 (ptm160) REVERT: h 394 MET cc_start: 0.8016 (mmp) cc_final: 0.7728 (mmp) REVERT: H 45 MET cc_start: 0.7085 (ttm) cc_final: 0.6727 (ttt) REVERT: H 106 LYS cc_start: 0.8269 (ttpt) cc_final: 0.8046 (ttpt) REVERT: H 521 LYS cc_start: 0.8496 (tttt) cc_final: 0.7712 (tmtt) REVERT: Q 14 MET cc_start: 0.4002 (ppp) cc_final: 0.2970 (ptp) REVERT: Q 41 GLN cc_start: 0.8385 (tp40) cc_final: 0.7925 (tp40) REVERT: Q 78 VAL cc_start: 0.8658 (t) cc_final: 0.8320 (m) REVERT: Q 79 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8435 (mp10) REVERT: Q 90 SER cc_start: 0.9423 (OUTLIER) cc_final: 0.9095 (p) REVERT: Q 116 GLU cc_start: 0.7061 (tp30) cc_final: 0.6375 (tp30) REVERT: Q 120 ARG cc_start: 0.8029 (mmt90) cc_final: 0.7657 (mmt-90) REVERT: q 385 MET cc_start: 0.4456 (mtt) cc_final: 0.3739 (ttt) REVERT: q 524 ILE cc_start: 0.9048 (mp) cc_final: 0.8843 (mm) REVERT: q 526 MET cc_start: 0.6432 (mtm) cc_final: 0.6077 (mpp) REVERT: Z 35 ARG cc_start: 0.7826 (ptm160) cc_final: 0.7499 (ptp-170) REVERT: z 46 MET cc_start: 0.8789 (tpp) cc_final: 0.8425 (tpp) REVERT: z 388 LYS cc_start: 0.6949 (tptt) cc_final: 0.6725 (tppt) REVERT: z 526 MET cc_start: 0.2385 (mmm) cc_final: 0.1677 (mmm) outliers start: 113 outliers final: 78 residues processed: 817 average time/residue: 0.4784 time to fit residues: 616.1087 Evaluate side-chains 768 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 684 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain a residue 499 LYS Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 111 ARG Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 478 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 460 VAL Chi-restraints excluded: chain d residue 461 ILE Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 456 ILE Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain e residue 466 MET Chi-restraints excluded: chain g residue 64 ASN Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 501 VAL Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain h residue 518 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 517 THR Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 85 ASP Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 22 VAL Chi-restraints excluded: chain z residue 36 THR Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 386 GLN Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 497 ASN Chi-restraints excluded: chain z residue 522 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 386 optimal weight: 5.9990 chunk 407 optimal weight: 0.7980 chunk 371 optimal weight: 0.8980 chunk 396 optimal weight: 0.9990 chunk 238 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 chunk 311 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 357 optimal weight: 5.9990 chunk 374 optimal weight: 5.9990 chunk 394 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 110 GLN A 110 GLN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS b 426 ASN D 37 ASN D 468 ASN D 494 ASN ** d 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS h 21 GLN h 448 GLN H 30 GLN H 462 ASN Z 37 ASN Z 453 GLN z 386 GLN z 434 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.7327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34273 Z= 0.170 Angle : 0.621 12.538 46321 Z= 0.302 Chirality : 0.041 0.321 5617 Planarity : 0.004 0.041 5931 Dihedral : 4.692 99.841 4773 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.39 % Allowed : 22.72 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.13), residues: 4407 helix: 1.68 (0.10), residues: 2813 sheet: 0.21 (0.34), residues: 223 loop : -0.64 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 496 HIS 0.011 0.001 HIS b 391 PHE 0.020 0.001 PHE Z 457 TYR 0.024 0.001 TYR H 423 ARG 0.011 0.000 ARG a 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 754 time to evaluate : 4.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 105 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: A 105 ASP cc_start: 0.8108 (t0) cc_final: 0.7815 (t0) REVERT: b 53 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6707 (pp) REVERT: b 78 ASN cc_start: 0.7925 (t0) cc_final: 0.7577 (t0) REVERT: b 441 LYS cc_start: 0.8827 (mptt) cc_final: 0.8414 (mptt) REVERT: B 89 ARG cc_start: 0.7832 (tpp80) cc_final: 0.7601 (tpp80) REVERT: B 91 GLN cc_start: 0.7987 (tp-100) cc_final: 0.7467 (tp40) REVERT: B 93 ASP cc_start: 0.7250 (m-30) cc_final: 0.7043 (m-30) REVERT: B 438 SER cc_start: 0.8990 (m) cc_final: 0.8662 (p) REVERT: D 57 MET cc_start: 0.8831 (mmm) cc_final: 0.8235 (mmm) REVERT: D 80 GLN cc_start: 0.8622 (mp10) cc_final: 0.7934 (mp10) REVERT: D 460 VAL cc_start: 0.8873 (p) cc_final: 0.8400 (t) REVERT: d 65 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7882 (mmtt) REVERT: E 79 MET cc_start: 0.8148 (tpp) cc_final: 0.7414 (tpt) REVERT: E 100 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7290 (mm) REVERT: E 133 ASP cc_start: 0.7642 (t0) cc_final: 0.7315 (t0) REVERT: E 472 MET cc_start: 0.6733 (mmm) cc_final: 0.6333 (mmm) REVERT: E 524 MET cc_start: 0.8345 (tpp) cc_final: 0.7962 (tpp) REVERT: e 442 GLU cc_start: 0.6973 (tt0) cc_final: 0.6731 (tt0) REVERT: e 458 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7727 (tpp) REVERT: e 533 LYS cc_start: 0.6910 (tptt) cc_final: 0.6421 (tptm) REVERT: G 38 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7403 (tmm-80) REVERT: h 387 ARG cc_start: 0.6888 (ptm-80) cc_final: 0.6613 (ptm160) REVERT: h 394 MET cc_start: 0.7984 (mmp) cc_final: 0.7709 (mmp) REVERT: H 45 MET cc_start: 0.7144 (ttm) cc_final: 0.6834 (ttt) REVERT: H 521 LYS cc_start: 0.8446 (tttt) cc_final: 0.7685 (tmtt) REVERT: Q 14 MET cc_start: 0.3682 (ppp) cc_final: 0.2780 (ptp) REVERT: Q 41 GLN cc_start: 0.8342 (tp40) cc_final: 0.7895 (tp40) REVERT: Q 78 VAL cc_start: 0.8568 (t) cc_final: 0.8235 (m) REVERT: Q 79 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8337 (mp10) REVERT: Q 90 SER cc_start: 0.9431 (OUTLIER) cc_final: 0.9119 (p) REVERT: Q 116 GLU cc_start: 0.7011 (tp30) cc_final: 0.6366 (tp30) REVERT: Q 120 ARG cc_start: 0.8015 (mmt90) cc_final: 0.7660 (mpt-90) REVERT: q 385 MET cc_start: 0.4191 (mtt) cc_final: 0.3569 (ttt) REVERT: q 523 GLN cc_start: 0.8409 (tp40) cc_final: 0.7695 (tp40) REVERT: q 524 ILE cc_start: 0.9047 (mp) cc_final: 0.8807 (mm) REVERT: q 526 MET cc_start: 0.6461 (mtm) cc_final: 0.6135 (mpp) REVERT: Z 483 THR cc_start: 0.7592 (p) cc_final: 0.7294 (p) outliers start: 87 outliers final: 63 residues processed: 807 average time/residue: 0.4710 time to fit residues: 604.7595 Evaluate side-chains 765 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 696 time to evaluate : 4.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 105 ASP Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain a residue 499 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 391 HIS Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 478 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 460 VAL Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain g residue 64 ASN Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain h residue 508 GLU Chi-restraints excluded: chain h residue 518 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 133 GLU Chi-restraints excluded: chain q residue 383 ASN Chi-restraints excluded: chain q residue 517 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain Z residue 511 ILE Chi-restraints excluded: chain z residue 36 THR Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 434 GLN Chi-restraints excluded: chain z residue 497 ASN Chi-restraints excluded: chain z residue 522 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 260 optimal weight: 0.0570 chunk 418 optimal weight: 0.8980 chunk 255 optimal weight: 0.0670 chunk 198 optimal weight: 7.9990 chunk 291 optimal weight: 2.9990 chunk 439 optimal weight: 0.9980 chunk 404 optimal weight: 0.8980 chunk 349 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 270 optimal weight: 4.9990 chunk 214 optimal weight: 0.0870 overall best weight: 0.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS D 37 ASN D 468 ASN D 494 ASN ** d 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 468 ASN E 493 HIS h 21 GLN q 34 GLN ** Z 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 453 GLN z 23 ASN z 514 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.7423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34273 Z= 0.169 Angle : 0.642 11.925 46321 Z= 0.312 Chirality : 0.040 0.258 5617 Planarity : 0.004 0.041 5931 Dihedral : 4.627 100.253 4773 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.12 % Allowed : 23.32 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.13), residues: 4407 helix: 1.75 (0.10), residues: 2799 sheet: 0.32 (0.34), residues: 223 loop : -0.56 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP g 435 HIS 0.013 0.001 HIS b 391 PHE 0.016 0.001 PHE Z 457 TYR 0.029 0.001 TYR a 426 ARG 0.010 0.000 ARG a 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 744 time to evaluate : 4.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 105 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: A 105 ASP cc_start: 0.8225 (t0) cc_final: 0.7900 (t0) REVERT: b 78 ASN cc_start: 0.7884 (t0) cc_final: 0.7509 (t0) REVERT: b 441 LYS cc_start: 0.8814 (mptt) cc_final: 0.8413 (mptt) REVERT: B 89 ARG cc_start: 0.7810 (tpp80) cc_final: 0.7594 (tpp80) REVERT: B 91 GLN cc_start: 0.7590 (tp-100) cc_final: 0.7155 (tp-100) REVERT: B 438 SER cc_start: 0.8952 (m) cc_final: 0.8684 (p) REVERT: D 57 MET cc_start: 0.8735 (mmm) cc_final: 0.8286 (mmm) REVERT: D 80 GLN cc_start: 0.8615 (mp10) cc_final: 0.8045 (mp10) REVERT: D 460 VAL cc_start: 0.8694 (p) cc_final: 0.8283 (t) REVERT: D 504 LEU cc_start: 0.6133 (mt) cc_final: 0.5925 (mt) REVERT: d 65 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7874 (mmtt) REVERT: E 79 MET cc_start: 0.8137 (tpp) cc_final: 0.7398 (tpt) REVERT: E 133 ASP cc_start: 0.7593 (t0) cc_final: 0.7303 (t0) REVERT: E 472 MET cc_start: 0.6704 (mmm) cc_final: 0.6305 (mmm) REVERT: E 512 LYS cc_start: 0.8114 (mttt) cc_final: 0.7695 (mtpp) REVERT: E 524 MET cc_start: 0.8326 (tpp) cc_final: 0.7955 (tpp) REVERT: e 442 GLU cc_start: 0.6988 (tt0) cc_final: 0.6751 (tt0) REVERT: e 533 LYS cc_start: 0.6862 (tptt) cc_final: 0.6359 (tptm) REVERT: g 87 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8005 (tm-30) REVERT: G 38 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7334 (tmm-80) REVERT: h 387 ARG cc_start: 0.6867 (ptm-80) cc_final: 0.6618 (ptm160) REVERT: h 394 MET cc_start: 0.8045 (mmp) cc_final: 0.7759 (mmp) REVERT: H 45 MET cc_start: 0.7003 (ttm) cc_final: 0.6765 (ttt) REVERT: H 106 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7770 (ttpt) REVERT: H 521 LYS cc_start: 0.8451 (tttt) cc_final: 0.7689 (tmtt) REVERT: Q 14 MET cc_start: 0.4053 (ppp) cc_final: 0.3061 (ptp) REVERT: Q 41 GLN cc_start: 0.8313 (tp40) cc_final: 0.7855 (tp40) REVERT: Q 78 VAL cc_start: 0.8604 (t) cc_final: 0.8304 (m) REVERT: Q 79 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8356 (mp10) REVERT: Q 90 SER cc_start: 0.9413 (OUTLIER) cc_final: 0.9110 (p) REVERT: Q 116 GLU cc_start: 0.6982 (tp30) cc_final: 0.6342 (tp30) REVERT: Q 120 ARG cc_start: 0.8017 (mmt90) cc_final: 0.7787 (mmt-90) REVERT: q 385 MET cc_start: 0.4019 (mtt) cc_final: 0.3678 (ttt) REVERT: q 523 GLN cc_start: 0.8391 (tp40) cc_final: 0.7683 (tp40) REVERT: q 524 ILE cc_start: 0.9036 (mp) cc_final: 0.8800 (mm) REVERT: q 526 MET cc_start: 0.6370 (mtm) cc_final: 0.6071 (mpp) REVERT: Z 59 ASP cc_start: 0.7406 (t0) cc_final: 0.6585 (t0) REVERT: Z 483 THR cc_start: 0.7577 (p) cc_final: 0.7270 (p) REVERT: z 44 MET cc_start: 0.8058 (mtt) cc_final: 0.7694 (mmt) REVERT: z 46 MET cc_start: 0.8917 (tpp) cc_final: 0.8488 (tpp) REVERT: z 526 MET cc_start: 0.2189 (mmm) cc_final: 0.1622 (mmm) outliers start: 77 outliers final: 62 residues processed: 793 average time/residue: 0.4671 time to fit residues: 593.2371 Evaluate side-chains 750 residues out of total 3640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 685 time to evaluate : 3.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 105 ASP Chi-restraints excluded: chain a residue 490 LEU Chi-restraints excluded: chain a residue 499 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 391 HIS Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 460 VAL Chi-restraints excluded: chain d residue 468 ASN Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain g residue 64 ASN Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 523 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 420 LEU Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain h residue 508 GLU Chi-restraints excluded: chain h residue 518 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 133 GLU Chi-restraints excluded: chain q residue 383 ASN Chi-restraints excluded: chain q residue 517 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 453 GLN Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 36 THR Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 497 ASN Chi-restraints excluded: chain z residue 522 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 277 optimal weight: 0.7980 chunk 372 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 322 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 97 optimal weight: 8.9990 chunk 350 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 359 optimal weight: 0.0040 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 0.0270 overall best weight: 0.6252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN D 494 ASN d 62 GLN ** d 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 468 ASN E 493 HIS g 116 GLN g 472 GLN ** Z 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 453 GLN ** z 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.128292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.114178 restraints weight = 74527.002| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 3.31 r_work: 0.3617 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.7529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34273 Z= 0.176 Angle : 0.651 14.735 46321 Z= 0.316 Chirality : 0.041 0.241 5617 Planarity : 0.004 0.040 5931 Dihedral : 4.603 99.956 4773 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.12 % Allowed : 23.52 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.13), residues: 4407 helix: 1.74 (0.10), residues: 2797 sheet: 0.36 (0.34), residues: 223 loop : -0.53 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 435 HIS 0.013 0.001 HIS b 391 PHE 0.031 0.001 PHE z 133 TYR 0.021 0.001 TYR h 419 ARG 0.012 0.000 ARG a 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11013.85 seconds wall clock time: 197 minutes 28.50 seconds (11848.50 seconds total)