Starting phenix.real_space_refine on Sun Feb 25 08:12:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k38_36847/02_2024/8k38_36847.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k38_36847/02_2024/8k38_36847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k38_36847/02_2024/8k38_36847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k38_36847/02_2024/8k38_36847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k38_36847/02_2024/8k38_36847.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k38_36847/02_2024/8k38_36847.pdb" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 1.466 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 300 5.16 5 C 31284 2.51 5 N 9108 2.21 5 O 9480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 122": "OD1" <-> "OD2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A ASP 446": "OD1" <-> "OD2" Residue "A ASP 456": "OD1" <-> "OD2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 293": "OD1" <-> "OD2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 446": "OD1" <-> "OD2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ASP 122": "OD1" <-> "OD2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 446": "OD1" <-> "OD2" Residue "C GLU 463": "OE1" <-> "OE2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "D ASP 122": "OD1" <-> "OD2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 285": "OE1" <-> "OE2" Residue "D PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 456": "OD1" <-> "OD2" Residue "D GLU 460": "OE1" <-> "OE2" Residue "D ASP 484": "OD1" <-> "OD2" Residue "E TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 122": "OD1" <-> "OD2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 463": "OE1" <-> "OE2" Residue "E ASP 484": "OD1" <-> "OD2" Residue "E GLU 488": "OE1" <-> "OE2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 208": "OE1" <-> "OE2" Residue "F PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 446": "OD1" <-> "OD2" Residue "F GLU 463": "OE1" <-> "OE2" Residue "F ASP 484": "OD1" <-> "OD2" Residue "F GLU 488": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G ASP 122": "OD1" <-> "OD2" Residue "G PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G GLU 238": "OE1" <-> "OE2" Residue "G PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 285": "OE1" <-> "OE2" Residue "G TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 446": "OD1" <-> "OD2" Residue "G ASP 456": "OD1" <-> "OD2" Residue "G GLU 460": "OE1" <-> "OE2" Residue "G ASP 484": "OD1" <-> "OD2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "H ASP 122": "OD1" <-> "OD2" Residue "H GLU 129": "OE1" <-> "OE2" Residue "H GLU 208": "OE1" <-> "OE2" Residue "H PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 285": "OE1" <-> "OE2" Residue "H ASP 446": "OD1" <-> "OD2" Residue "H GLU 463": "OE1" <-> "OE2" Residue "H ASP 484": "OD1" <-> "OD2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 102": "OE1" <-> "OE2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "I ASP 122": "OD1" <-> "OD2" Residue "I TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 208": "OE1" <-> "OE2" Residue "I PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 446": "OD1" <-> "OD2" Residue "I GLU 463": "OE1" <-> "OE2" Residue "I GLU 478": "OE1" <-> "OE2" Residue "I ASP 484": "OD1" <-> "OD2" Residue "I GLU 488": "OE1" <-> "OE2" Residue "J ASP 122": "OD1" <-> "OD2" Residue "J PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 208": "OE1" <-> "OE2" Residue "J GLU 238": "OE1" <-> "OE2" Residue "J PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 285": "OE1" <-> "OE2" Residue "J ASP 446": "OD1" <-> "OD2" Residue "J ASP 456": "OD1" <-> "OD2" Residue "J GLU 460": "OE1" <-> "OE2" Residue "J ASP 484": "OD1" <-> "OD2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 122": "OD1" <-> "OD2" Residue "K GLU 129": "OE1" <-> "OE2" Residue "K GLU 208": "OE1" <-> "OE2" Residue "K PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 285": "OE1" <-> "OE2" Residue "K PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 484": "OD1" <-> "OD2" Residue "K GLU 488": "OE1" <-> "OE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L GLU 110": "OE1" <-> "OE2" Residue "L ASP 122": "OD1" <-> "OD2" Residue "L TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 208": "OE1" <-> "OE2" Residue "L PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 446": "OD1" <-> "OD2" Residue "L GLU 463": "OE1" <-> "OE2" Residue "L ASP 484": "OD1" <-> "OD2" Residue "L GLU 488": "OE1" <-> "OE2" Residue "M GLU 5": "OE1" <-> "OE2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "N ASP 42": "OD1" <-> "OD2" Residue "O GLU 5": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O ASP 42": "OD1" <-> "OD2" Residue "P GLU 5": "OE1" <-> "OE2" Residue "Q GLU 34": "OE1" <-> "OE2" Residue "Q ASP 42": "OD1" <-> "OD2" Residue "R GLU 5": "OE1" <-> "OE2" Residue "R GLU 6": "OE1" <-> "OE2" Residue "S GLU 5": "OE1" <-> "OE2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T ASP 42": "OD1" <-> "OD2" Residue "U GLU 5": "OE1" <-> "OE2" Residue "U ASP 42": "OD1" <-> "OD2" Residue "V GLU 5": "OE1" <-> "OE2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "W ASP 42": "OD1" <-> "OD2" Residue "X GLU 5": "OE1" <-> "OE2" Residue "X GLU 6": "OE1" <-> "OE2" Residue "X ASP 42": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 50172 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3675 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "B" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3675 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "C" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3675 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "D" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3675 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "E" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3675 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "F" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3675 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "G" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3675 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "H" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3675 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "I" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3675 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "J" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3675 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "K" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3675 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "L" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3675 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "M" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 506 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "N" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 506 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "O" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 506 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "P" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 506 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "Q" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 506 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "R" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 506 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "S" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 506 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "T" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 506 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "U" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 506 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "V" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 506 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "W" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 506 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "X" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 506 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Time building chain proxies: 25.31, per 1000 atoms: 0.50 Number of scatterers: 50172 At special positions: 0 Unit cell: (161.84, 161.84, 161.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 300 16.00 O 9480 8.00 N 9108 7.00 C 31284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.83 Conformation dependent library (CDL) restraints added in 10.6 seconds 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11784 Finding SS restraints... Secondary structure from input PDB file: 232 helices and 61 sheets defined 52.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.21 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 52 through 67 Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 93 through 98 removed outlier: 3.754A pdb=" N LEU A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 120 Processing helix chain 'A' and resid 133 through 148 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.948A pdb=" N TYR A 252 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 253 " --> pdb=" O VAL A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 253' Processing helix chain 'A' and resid 254 through 278 removed outlier: 3.882A pdb=" N TYR A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 350 through 367 removed outlier: 3.581A pdb=" N PHE A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 381 through 422 removed outlier: 3.817A pdb=" N TYR A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER A 405 " --> pdb=" O LYS A 401 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU A 418 " --> pdb=" O CYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 456 through 470 removed outlier: 3.516A pdb=" N GLU A 460 " --> pdb=" O ASP A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.836A pdb=" N ARG A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 504 removed outlier: 3.695A pdb=" N MET A 498 " --> pdb=" O VAL A 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 50 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.510A pdb=" N LEU B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 121 removed outlier: 3.571A pdb=" N GLU B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 149 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 249 through 253 removed outlier: 3.659A pdb=" N TYR B 252 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 253 " --> pdb=" O VAL B 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 253' Processing helix chain 'B' and resid 254 through 278 removed outlier: 3.957A pdb=" N TYR B 278 " --> pdb=" O VAL B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 350 through 367 Processing helix chain 'B' and resid 369 through 375 Processing helix chain 'B' and resid 381 through 422 removed outlier: 3.817A pdb=" N TYR B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA B 404 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 456 through 470 removed outlier: 3.575A pdb=" N GLU B 460 " --> pdb=" O ASP B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 removed outlier: 3.845A pdb=" N ARG B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 504 removed outlier: 3.678A pdb=" N MET B 498 " --> pdb=" O VAL B 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 37 removed outlier: 4.550A pdb=" N SER C 37 " --> pdb=" O GLN C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 50 Processing helix chain 'C' and resid 52 through 67 Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 93 through 98 removed outlier: 3.556A pdb=" N LEU C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 120 Processing helix chain 'C' and resid 133 through 149 Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 249 through 253 removed outlier: 3.789A pdb=" N TYR C 252 " --> pdb=" O ASN C 249 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 253 " --> pdb=" O VAL C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 253' Processing helix chain 'C' and resid 254 through 278 removed outlier: 4.028A pdb=" N TYR C 278 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 350 through 367 Processing helix chain 'C' and resid 369 through 375 Processing helix chain 'C' and resid 381 through 422 removed outlier: 3.856A pdb=" N TYR C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.515A pdb=" N TRP C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.537A pdb=" N GLU C 460 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 482 removed outlier: 3.731A pdb=" N ARG C 482 " --> pdb=" O GLU C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 504 removed outlier: 3.682A pdb=" N MET C 498 " --> pdb=" O VAL C 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 50 Processing helix chain 'D' and resid 52 through 67 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 93 through 98 removed outlier: 3.595A pdb=" N LEU D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 Processing helix chain 'D' and resid 133 through 149 Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 249 through 253 removed outlier: 3.949A pdb=" N TYR D 252 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D 253 " --> pdb=" O VAL D 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 249 through 253' Processing helix chain 'D' and resid 254 through 278 removed outlier: 3.946A pdb=" N TYR D 278 " --> pdb=" O VAL D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 350 through 367 removed outlier: 3.503A pdb=" N PHE D 354 " --> pdb=" O GLY D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 375 Processing helix chain 'D' and resid 381 through 422 removed outlier: 3.821A pdb=" N TYR D 395 " --> pdb=" O GLU D 391 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA D 404 " --> pdb=" O ARG D 400 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER D 405 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 456 through 470 Processing helix chain 'D' and resid 474 through 482 removed outlier: 3.751A pdb=" N ARG D 482 " --> pdb=" O GLU D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 504 removed outlier: 3.696A pdb=" N MET D 498 " --> pdb=" O VAL D 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 52 through 67 Processing helix chain 'E' and resid 67 through 82 Processing helix chain 'E' and resid 93 through 98 Processing helix chain 'E' and resid 100 through 120 Processing helix chain 'E' and resid 133 through 149 Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 249 through 253 removed outlier: 3.659A pdb=" N TYR E 252 " --> pdb=" O ASN E 249 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER E 253 " --> pdb=" O VAL E 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 249 through 253' Processing helix chain 'E' and resid 254 through 278 removed outlier: 3.955A pdb=" N TYR E 278 " --> pdb=" O VAL E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 Processing helix chain 'E' and resid 350 through 367 Processing helix chain 'E' and resid 369 through 375 Processing helix chain 'E' and resid 381 through 422 removed outlier: 3.820A pdb=" N TYR E 395 " --> pdb=" O GLU E 391 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA E 404 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER E 405 " --> pdb=" O LYS E 401 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 456 through 470 removed outlier: 3.654A pdb=" N GLU E 460 " --> pdb=" O ASP E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 482 removed outlier: 3.647A pdb=" N ARG E 482 " --> pdb=" O GLU E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 504 removed outlier: 3.673A pdb=" N MET E 498 " --> pdb=" O VAL E 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 37 removed outlier: 4.547A pdb=" N SER F 37 " --> pdb=" O GLN F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 50 Processing helix chain 'F' and resid 52 through 67 Processing helix chain 'F' and resid 67 through 82 Processing helix chain 'F' and resid 93 through 98 Processing helix chain 'F' and resid 100 through 120 Processing helix chain 'F' and resid 133 through 149 Processing helix chain 'F' and resid 179 through 183 Processing helix chain 'F' and resid 249 through 253 removed outlier: 3.790A pdb=" N TYR F 252 " --> pdb=" O ASN F 249 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER F 253 " --> pdb=" O VAL F 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 249 through 253' Processing helix chain 'F' and resid 254 through 278 removed outlier: 4.070A pdb=" N TYR F 278 " --> pdb=" O VAL F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 295 Processing helix chain 'F' and resid 350 through 367 Processing helix chain 'F' and resid 369 through 375 Processing helix chain 'F' and resid 381 through 422 removed outlier: 3.854A pdb=" N TYR F 395 " --> pdb=" O GLU F 391 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA F 404 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER F 405 " --> pdb=" O LYS F 401 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.512A pdb=" N TRP F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 470 removed outlier: 3.640A pdb=" N GLU F 460 " --> pdb=" O ASP F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 482 removed outlier: 3.733A pdb=" N ARG F 482 " --> pdb=" O GLU F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 504 Processing helix chain 'G' and resid 44 through 50 Processing helix chain 'G' and resid 52 through 67 Processing helix chain 'G' and resid 67 through 82 Processing helix chain 'G' and resid 93 through 98 removed outlier: 3.606A pdb=" N LEU G 97 " --> pdb=" O SER G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 120 Processing helix chain 'G' and resid 133 through 148 Processing helix chain 'G' and resid 179 through 183 Processing helix chain 'G' and resid 249 through 253 removed outlier: 3.804A pdb=" N TYR G 252 " --> pdb=" O ASN G 249 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER G 253 " --> pdb=" O VAL G 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 249 through 253' Processing helix chain 'G' and resid 254 through 278 removed outlier: 3.944A pdb=" N TYR G 278 " --> pdb=" O VAL G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 295 Processing helix chain 'G' and resid 350 through 367 removed outlier: 3.572A pdb=" N PHE G 354 " --> pdb=" O GLY G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 375 Processing helix chain 'G' and resid 381 through 422 removed outlier: 3.869A pdb=" N TYR G 395 " --> pdb=" O GLU G 391 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA G 404 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER G 405 " --> pdb=" O LYS G 401 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU G 418 " --> pdb=" O CYS G 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 443 Processing helix chain 'G' and resid 456 through 470 Processing helix chain 'G' and resid 474 through 482 removed outlier: 3.723A pdb=" N ARG G 482 " --> pdb=" O GLU G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 504 removed outlier: 3.694A pdb=" N MET G 498 " --> pdb=" O VAL G 494 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 50 Processing helix chain 'H' and resid 52 through 67 Processing helix chain 'H' and resid 67 through 82 Processing helix chain 'H' and resid 93 through 98 Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'H' and resid 133 through 149 Processing helix chain 'H' and resid 179 through 183 Processing helix chain 'H' and resid 249 through 253 removed outlier: 3.660A pdb=" N TYR H 252 " --> pdb=" O ASN H 249 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER H 253 " --> pdb=" O VAL H 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 249 through 253' Processing helix chain 'H' and resid 254 through 278 removed outlier: 3.954A pdb=" N TYR H 278 " --> pdb=" O VAL H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 295 Processing helix chain 'H' and resid 350 through 367 Processing helix chain 'H' and resid 369 through 375 Processing helix chain 'H' and resid 381 through 422 removed outlier: 3.819A pdb=" N TYR H 395 " --> pdb=" O GLU H 391 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA H 404 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER H 405 " --> pdb=" O LYS H 401 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU H 418 " --> pdb=" O CYS H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 438 through 443 Processing helix chain 'H' and resid 456 through 470 removed outlier: 3.564A pdb=" N GLU H 460 " --> pdb=" O ASP H 456 " (cutoff:3.500A) Processing helix chain 'H' and resid 474 through 482 removed outlier: 3.832A pdb=" N ARG H 482 " --> pdb=" O GLU H 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 485 through 504 removed outlier: 3.677A pdb=" N MET H 498 " --> pdb=" O VAL H 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 37 removed outlier: 4.546A pdb=" N SER I 37 " --> pdb=" O GLN I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 50 Processing helix chain 'I' and resid 52 through 67 Processing helix chain 'I' and resid 67 through 82 Processing helix chain 'I' and resid 93 through 98 Processing helix chain 'I' and resid 100 through 120 Processing helix chain 'I' and resid 133 through 149 Processing helix chain 'I' and resid 179 through 183 Processing helix chain 'I' and resid 249 through 253 removed outlier: 3.785A pdb=" N TYR I 252 " --> pdb=" O ASN I 249 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER I 253 " --> pdb=" O VAL I 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 249 through 253' Processing helix chain 'I' and resid 254 through 278 removed outlier: 4.081A pdb=" N TYR I 278 " --> pdb=" O VAL I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 295 Processing helix chain 'I' and resid 350 through 367 Processing helix chain 'I' and resid 369 through 375 Processing helix chain 'I' and resid 381 through 422 removed outlier: 3.850A pdb=" N TYR I 395 " --> pdb=" O GLU I 391 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA I 404 " --> pdb=" O ARG I 400 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER I 405 " --> pdb=" O LYS I 401 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU I 418 " --> pdb=" O CYS I 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 443 removed outlier: 3.516A pdb=" N TRP I 442 " --> pdb=" O ALA I 438 " (cutoff:3.500A) Processing helix chain 'I' and resid 456 through 470 removed outlier: 3.622A pdb=" N GLU I 460 " --> pdb=" O ASP I 456 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 482 removed outlier: 3.853A pdb=" N ARG I 482 " --> pdb=" O GLU I 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 485 through 504 removed outlier: 3.688A pdb=" N MET I 498 " --> pdb=" O VAL I 494 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 50 Processing helix chain 'J' and resid 52 through 67 Processing helix chain 'J' and resid 67 through 82 Processing helix chain 'J' and resid 93 through 98 removed outlier: 3.633A pdb=" N LEU J 97 " --> pdb=" O SER J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 120 Processing helix chain 'J' and resid 133 through 148 Processing helix chain 'J' and resid 179 through 183 Processing helix chain 'J' and resid 249 through 253 removed outlier: 3.949A pdb=" N TYR J 252 " --> pdb=" O ASN J 249 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER J 253 " --> pdb=" O VAL J 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 249 through 253' Processing helix chain 'J' and resid 254 through 278 removed outlier: 3.940A pdb=" N TYR J 278 " --> pdb=" O VAL J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 295 Processing helix chain 'J' and resid 350 through 367 removed outlier: 3.573A pdb=" N PHE J 354 " --> pdb=" O GLY J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 369 through 375 Processing helix chain 'J' and resid 381 through 422 removed outlier: 3.868A pdb=" N TYR J 395 " --> pdb=" O GLU J 391 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA J 404 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER J 405 " --> pdb=" O LYS J 401 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU J 418 " --> pdb=" O CYS J 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 438 through 443 Processing helix chain 'J' and resid 456 through 470 Processing helix chain 'J' and resid 474 through 482 removed outlier: 3.751A pdb=" N ARG J 482 " --> pdb=" O GLU J 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 485 through 504 removed outlier: 3.697A pdb=" N MET J 498 " --> pdb=" O VAL J 494 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 50 Processing helix chain 'K' and resid 52 through 67 Processing helix chain 'K' and resid 67 through 82 Processing helix chain 'K' and resid 93 through 98 Processing helix chain 'K' and resid 100 through 120 Processing helix chain 'K' and resid 133 through 149 Processing helix chain 'K' and resid 179 through 183 Processing helix chain 'K' and resid 249 through 253 removed outlier: 3.682A pdb=" N TYR K 252 " --> pdb=" O ASN K 249 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER K 253 " --> pdb=" O VAL K 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 249 through 253' Processing helix chain 'K' and resid 254 through 278 removed outlier: 3.967A pdb=" N TYR K 278 " --> pdb=" O VAL K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 295 Processing helix chain 'K' and resid 350 through 367 Processing helix chain 'K' and resid 369 through 375 Processing helix chain 'K' and resid 381 through 422 removed outlier: 3.818A pdb=" N TYR K 395 " --> pdb=" O GLU K 391 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA K 404 " --> pdb=" O ARG K 400 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER K 405 " --> pdb=" O LYS K 401 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 438 through 443 Processing helix chain 'K' and resid 456 through 470 removed outlier: 3.550A pdb=" N GLU K 460 " --> pdb=" O ASP K 456 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 482 removed outlier: 3.716A pdb=" N ARG K 482 " --> pdb=" O GLU K 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 485 through 504 removed outlier: 3.675A pdb=" N MET K 498 " --> pdb=" O VAL K 494 " (cutoff:3.500A) Processing helix chain 'L' and resid 33 through 37 removed outlier: 4.551A pdb=" N SER L 37 " --> pdb=" O GLN L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 50 Processing helix chain 'L' and resid 52 through 67 Processing helix chain 'L' and resid 67 through 82 Processing helix chain 'L' and resid 93 through 98 removed outlier: 3.535A pdb=" N LEU L 97 " --> pdb=" O SER L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 120 Processing helix chain 'L' and resid 133 through 149 Processing helix chain 'L' and resid 179 through 183 Processing helix chain 'L' and resid 249 through 253 removed outlier: 3.786A pdb=" N TYR L 252 " --> pdb=" O ASN L 249 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER L 253 " --> pdb=" O VAL L 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 249 through 253' Processing helix chain 'L' and resid 254 through 278 removed outlier: 3.931A pdb=" N TYR L 278 " --> pdb=" O VAL L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 295 Processing helix chain 'L' and resid 350 through 367 Processing helix chain 'L' and resid 369 through 375 Processing helix chain 'L' and resid 381 through 422 removed outlier: 3.877A pdb=" N TYR L 395 " --> pdb=" O GLU L 391 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA L 404 " --> pdb=" O ARG L 400 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER L 405 " --> pdb=" O LYS L 401 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU L 418 " --> pdb=" O CYS L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 438 through 443 removed outlier: 3.524A pdb=" N TRP L 442 " --> pdb=" O ALA L 438 " (cutoff:3.500A) Processing helix chain 'L' and resid 456 through 470 removed outlier: 3.621A pdb=" N GLU L 460 " --> pdb=" O ASP L 456 " (cutoff:3.500A) Processing helix chain 'L' and resid 474 through 482 removed outlier: 3.763A pdb=" N ARG L 482 " --> pdb=" O GLU L 478 " (cutoff:3.500A) Processing helix chain 'L' and resid 485 through 504 removed outlier: 3.685A pdb=" N MET L 498 " --> pdb=" O VAL L 494 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 20 removed outlier: 3.893A pdb=" N ALA M 9 " --> pdb=" O GLU M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 55 Processing helix chain 'N' and resid 5 through 20 removed outlier: 3.915A pdb=" N ALA N 9 " --> pdb=" O GLU N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 55 Processing helix chain 'O' and resid 6 through 20 removed outlier: 3.599A pdb=" N ALA O 10 " --> pdb=" O GLU O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 39 through 55 Processing helix chain 'P' and resid 5 through 20 removed outlier: 3.885A pdb=" N ALA P 9 " --> pdb=" O GLU P 5 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 55 Processing helix chain 'Q' and resid 5 through 20 removed outlier: 3.922A pdb=" N ALA Q 9 " --> pdb=" O GLU Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 55 Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 39 through 55 Processing helix chain 'S' and resid 5 through 20 removed outlier: 3.916A pdb=" N ALA S 9 " --> pdb=" O GLU S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 55 Processing helix chain 'T' and resid 5 through 20 removed outlier: 4.001A pdb=" N ALA T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 55 Processing helix chain 'U' and resid 6 through 20 Processing helix chain 'U' and resid 39 through 55 Processing helix chain 'V' and resid 5 through 20 removed outlier: 3.950A pdb=" N ALA V 9 " --> pdb=" O GLU V 5 " (cutoff:3.500A) Processing helix chain 'V' and resid 39 through 55 Processing helix chain 'W' and resid 5 through 20 removed outlier: 3.964A pdb=" N ALA W 9 " --> pdb=" O GLU W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 55 Processing helix chain 'X' and resid 6 through 20 Processing helix chain 'X' and resid 39 through 55 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 90 Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 172 removed outlier: 4.006A pdb=" N PHE A 152 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 190 removed outlier: 6.926A pdb=" N GLN A 194 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 341 removed outlier: 8.426A pdb=" N LEU B 333 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE A 282 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA6, first strand: chain 'A' and resid 332 through 333 Processing sheet with id=AA7, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AA8, first strand: chain 'B' and resid 167 through 172 removed outlier: 3.948A pdb=" N PHE B 152 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 189 through 190 removed outlier: 6.879A pdb=" N GLN B 194 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 338 through 341 removed outlier: 8.334A pdb=" N LEU C 333 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE B 282 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 322 through 324 Processing sheet with id=AB3, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AB4, first strand: chain 'C' and resid 167 through 172 removed outlier: 3.880A pdb=" N PHE C 152 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 189 through 190 removed outlier: 6.874A pdb=" N GLN C 194 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 338 through 341 removed outlier: 8.416A pdb=" N LEU D 333 " --> pdb=" O ALA C 280 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE C 282 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 322 through 324 Processing sheet with id=AB8, first strand: chain 'D' and resid 86 through 90 Processing sheet with id=AB9, first strand: chain 'D' and resid 167 through 172 removed outlier: 4.024A pdb=" N PHE D 152 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 189 through 190 removed outlier: 6.926A pdb=" N GLN D 194 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 338 through 341 removed outlier: 8.446A pdb=" N LEU E 333 " --> pdb=" O ALA D 280 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE D 282 " --> pdb=" O LEU E 333 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 322 through 324 Processing sheet with id=AC4, first strand: chain 'E' and resid 87 through 90 Processing sheet with id=AC5, first strand: chain 'E' and resid 167 through 172 removed outlier: 3.922A pdb=" N PHE E 152 " --> pdb=" O VAL E 172 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 189 through 190 removed outlier: 6.880A pdb=" N GLN E 194 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 338 through 341 removed outlier: 8.339A pdb=" N LEU F 333 " --> pdb=" O ALA E 280 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE E 282 " --> pdb=" O LEU F 333 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 322 through 324 Processing sheet with id=AC9, first strand: chain 'F' and resid 87 through 90 Processing sheet with id=AD1, first strand: chain 'F' and resid 167 through 172 removed outlier: 3.872A pdb=" N PHE F 152 " --> pdb=" O VAL F 172 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 189 through 190 removed outlier: 6.913A pdb=" N GLN F 194 " --> pdb=" O LEU F 202 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 338 through 341 removed outlier: 8.422A pdb=" N LEU G 333 " --> pdb=" O ALA F 280 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE F 282 " --> pdb=" O LEU G 333 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 322 through 324 Processing sheet with id=AD5, first strand: chain 'G' and resid 86 through 90 Processing sheet with id=AD6, first strand: chain 'G' and resid 167 through 172 removed outlier: 4.007A pdb=" N PHE G 152 " --> pdb=" O VAL G 172 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 189 through 190 removed outlier: 6.928A pdb=" N GLN G 194 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 338 through 341 removed outlier: 8.444A pdb=" N LEU H 333 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE G 282 " --> pdb=" O LEU H 333 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 322 through 324 Processing sheet with id=AE1, first strand: chain 'H' and resid 87 through 90 Processing sheet with id=AE2, first strand: chain 'H' and resid 167 through 172 removed outlier: 3.926A pdb=" N PHE H 152 " --> pdb=" O VAL H 172 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 189 through 190 removed outlier: 6.883A pdb=" N GLN H 194 " --> pdb=" O LEU H 202 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 338 through 341 removed outlier: 8.337A pdb=" N LEU I 333 " --> pdb=" O ALA H 280 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE H 282 " --> pdb=" O LEU I 333 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 322 through 324 Processing sheet with id=AE6, first strand: chain 'I' and resid 87 through 90 Processing sheet with id=AE7, first strand: chain 'I' and resid 167 through 172 removed outlier: 3.877A pdb=" N PHE I 152 " --> pdb=" O VAL I 172 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 189 through 190 removed outlier: 6.917A pdb=" N GLN I 194 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 338 through 341 removed outlier: 8.413A pdb=" N LEU J 333 " --> pdb=" O ALA I 280 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE I 282 " --> pdb=" O LEU J 333 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 322 through 324 Processing sheet with id=AF2, first strand: chain 'J' and resid 86 through 90 Processing sheet with id=AF3, first strand: chain 'J' and resid 167 through 172 removed outlier: 4.004A pdb=" N PHE J 152 " --> pdb=" O VAL J 172 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 189 through 190 removed outlier: 6.926A pdb=" N GLN J 194 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 338 through 341 removed outlier: 8.444A pdb=" N LEU K 333 " --> pdb=" O ALA J 280 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE J 282 " --> pdb=" O LEU K 333 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 322 through 324 Processing sheet with id=AF7, first strand: chain 'K' and resid 87 through 90 Processing sheet with id=AF8, first strand: chain 'K' and resid 167 through 172 removed outlier: 3.930A pdb=" N PHE K 152 " --> pdb=" O VAL K 172 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 189 through 190 removed outlier: 6.875A pdb=" N GLN K 194 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 338 through 341 removed outlier: 8.330A pdb=" N LEU L 333 " --> pdb=" O ALA K 280 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE K 282 " --> pdb=" O LEU L 333 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 322 through 324 Processing sheet with id=AG3, first strand: chain 'L' and resid 87 through 90 Processing sheet with id=AG4, first strand: chain 'L' and resid 167 through 172 removed outlier: 3.881A pdb=" N PHE L 152 " --> pdb=" O VAL L 172 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 189 through 190 removed outlier: 6.909A pdb=" N GLN L 194 " --> pdb=" O LEU L 202 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 322 through 324 Processing sheet with id=AG7, first strand: chain 'M' and resid 23 through 28 removed outlier: 5.710A pdb=" N ALA M 24 " --> pdb=" O PHE M 35 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG M 32 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL N 26 " --> pdb=" O ARG M 32 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU M 34 " --> pdb=" O ALA N 24 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA N 24 " --> pdb=" O PHE N 35 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ARG N 32 " --> pdb=" O VAL O 26 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL O 26 " --> pdb=" O ARG N 32 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU N 34 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA O 24 " --> pdb=" O PHE O 35 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG O 32 " --> pdb=" O VAL P 26 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL P 26 " --> pdb=" O ARG O 32 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLU O 34 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ALA P 24 " --> pdb=" O PHE P 35 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG P 32 " --> pdb=" O VAL Q 26 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL Q 26 " --> pdb=" O ARG P 32 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU P 34 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ALA Q 24 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ARG Q 32 " --> pdb=" O VAL R 26 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL R 26 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU Q 34 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ALA R 24 " --> pdb=" O PHE R 35 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG R 32 " --> pdb=" O VAL S 26 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL S 26 " --> pdb=" O ARG R 32 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU R 34 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ALA S 24 " --> pdb=" O PHE S 35 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG S 32 " --> pdb=" O VAL T 26 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL T 26 " --> pdb=" O ARG S 32 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU S 34 " --> pdb=" O ALA T 24 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ALA T 24 " --> pdb=" O PHE T 35 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG T 32 " --> pdb=" O VAL U 26 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL U 26 " --> pdb=" O ARG T 32 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU T 34 " --> pdb=" O ALA U 24 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ALA U 24 " --> pdb=" O PHE U 35 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG U 32 " --> pdb=" O VAL V 26 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL V 26 " --> pdb=" O ARG U 32 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU U 34 " --> pdb=" O ALA V 24 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ALA V 24 " --> pdb=" O PHE V 35 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ARG V 32 " --> pdb=" O VAL W 26 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL W 26 " --> pdb=" O ARG V 32 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU V 34 " --> pdb=" O ALA W 24 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ALA W 24 " --> pdb=" O PHE W 35 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG W 32 " --> pdb=" O VAL X 26 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL X 26 " --> pdb=" O ARG W 32 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU W 34 " --> pdb=" O ALA X 24 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA X 24 " --> pdb=" O PHE X 35 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG X 32 " --> pdb=" O VAL M 26 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL M 26 " --> pdb=" O ARG X 32 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU X 34 " --> pdb=" O ALA M 24 " (cutoff:3.500A) 2677 hydrogen bonds defined for protein. 7779 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: 21.67 Time building geometry restraints manager: 19.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8497 1.31 - 1.43: 14306 1.43 - 1.56: 27873 1.56 - 1.68: 0 1.68 - 1.81: 516 Bond restraints: 51192 Sorted by residual: bond pdb=" CA GLU B 418 " pdb=" C GLU B 418 " ideal model delta sigma weight residual 1.524 1.452 0.072 1.26e-02 6.30e+03 3.28e+01 bond pdb=" CA GLU A 418 " pdb=" C GLU A 418 " ideal model delta sigma weight residual 1.524 1.458 0.066 1.26e-02 6.30e+03 2.74e+01 bond pdb=" CA GLU D 418 " pdb=" C GLU D 418 " ideal model delta sigma weight residual 1.524 1.459 0.065 1.26e-02 6.30e+03 2.66e+01 bond pdb=" CA GLU J 418 " pdb=" C GLU J 418 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.26e-02 6.30e+03 2.57e+01 bond pdb=" CA GLU G 418 " pdb=" C GLU G 418 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.26e-02 6.30e+03 2.55e+01 ... (remaining 51187 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.47: 1282 106.47 - 113.36: 26478 113.36 - 120.25: 18116 120.25 - 127.14: 22653 127.14 - 134.03: 555 Bond angle restraints: 69084 Sorted by residual: angle pdb=" N ALA B 119 " pdb=" CA ALA B 119 " pdb=" C ALA B 119 " ideal model delta sigma weight residual 111.36 119.15 -7.79 1.09e+00 8.42e-01 5.11e+01 angle pdb=" N GLU O 6 " pdb=" CA GLU O 6 " pdb=" C GLU O 6 " ideal model delta sigma weight residual 114.12 104.92 9.20 1.39e+00 5.18e-01 4.38e+01 angle pdb=" O LEU H 416 " pdb=" C LEU H 416 " pdb=" N GLU H 417 " ideal model delta sigma weight residual 122.43 115.17 7.26 1.34e+00 5.57e-01 2.93e+01 angle pdb=" N GLU P 6 " pdb=" CA GLU P 6 " pdb=" C GLU P 6 " ideal model delta sigma weight residual 112.90 105.93 6.97 1.31e+00 5.83e-01 2.83e+01 angle pdb=" N GLU M 6 " pdb=" CA GLU M 6 " pdb=" C GLU M 6 " ideal model delta sigma weight residual 112.90 106.00 6.90 1.31e+00 5.83e-01 2.78e+01 ... (remaining 69079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 27532 16.56 - 33.13: 2498 33.13 - 49.69: 434 49.69 - 66.25: 81 66.25 - 82.82: 43 Dihedral angle restraints: 30588 sinusoidal: 12240 harmonic: 18348 Sorted by residual: dihedral pdb=" C TYR J 96 " pdb=" N TYR J 96 " pdb=" CA TYR J 96 " pdb=" CB TYR J 96 " ideal model delta harmonic sigma weight residual -122.60 -113.15 -9.45 0 2.50e+00 1.60e-01 1.43e+01 dihedral pdb=" C TYR G 96 " pdb=" N TYR G 96 " pdb=" CA TYR G 96 " pdb=" CB TYR G 96 " ideal model delta harmonic sigma weight residual -122.60 -113.35 -9.25 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" CA PHE K 402 " pdb=" C PHE K 402 " pdb=" N VAL K 403 " pdb=" CA VAL K 403 " ideal model delta harmonic sigma weight residual -180.00 -162.68 -17.32 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 30585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 6763 0.065 - 0.129: 445 0.129 - 0.194: 14 0.194 - 0.259: 3 0.259 - 0.323: 11 Chirality restraints: 7236 Sorted by residual: chirality pdb=" CA GLU B 120 " pdb=" N GLU B 120 " pdb=" C GLU B 120 " pdb=" CB GLU B 120 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA THR K 167 " pdb=" N THR K 167 " pdb=" C THR K 167 " pdb=" CB THR K 167 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA THR H 167 " pdb=" N THR H 167 " pdb=" C THR H 167 " pdb=" CB THR H 167 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 7233 not shown) Planarity restraints: 9156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU H 416 " 0.023 2.00e-02 2.50e+03 4.39e-02 1.92e+01 pdb=" C LEU H 416 " -0.076 2.00e-02 2.50e+03 pdb=" O LEU H 416 " 0.027 2.00e-02 2.50e+03 pdb=" N GLU H 417 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 115 " -0.017 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C TRP A 115 " 0.056 2.00e-02 2.50e+03 pdb=" O TRP A 115 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS A 116 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 116 " 0.016 2.00e-02 2.50e+03 3.08e-02 9.51e+00 pdb=" C LYS F 116 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS F 116 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU F 117 " 0.018 2.00e-02 2.50e+03 ... (remaining 9153 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 6107 2.75 - 3.29: 46604 3.29 - 3.83: 81250 3.83 - 4.36: 94710 4.36 - 4.90: 172375 Nonbonded interactions: 401046 Sorted by model distance: nonbonded pdb=" NE2 GLN A 34 " pdb=" OE2 GLU B 256 " model vdw 2.215 2.520 nonbonded pdb=" NE2 GLN J 34 " pdb=" OE2 GLU K 256 " model vdw 2.218 2.520 nonbonded pdb=" NE2 GLN D 34 " pdb=" OE2 GLU E 256 " model vdw 2.222 2.520 nonbonded pdb=" NE2 GLN G 34 " pdb=" OE2 GLU H 256 " model vdw 2.224 2.520 nonbonded pdb=" NE2 GLN E 34 " pdb=" OE2 GLU F 256 " model vdw 2.231 2.520 ... (remaining 401041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 16.760 Check model and map are aligned: 0.740 Set scattering table: 0.440 Process input model: 128.860 Find NCS groups from input model: 3.470 Set up NCS constraints: 0.560 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 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 0.072 51192 Z= 0.230 Angle : 0.524 9.195 69084 Z= 0.319 Chirality : 0.037 0.323 7236 Planarity : 0.004 0.046 9156 Dihedral : 12.995 82.817 18804 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.12 % Allowed : 0.21 % Favored : 99.67 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.10), residues: 6300 helix: 2.70 (0.09), residues: 2976 sheet: 1.18 (0.18), residues: 636 loop : -0.66 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 94 HIS 0.003 0.001 HIS A 90 PHE 0.013 0.001 PHE K 147 TYR 0.022 0.001 TYR I 96 ARG 0.008 0.000 ARG C 501 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1168 time to evaluate : 5.654 Fit side-chains REVERT: A 162 SER cc_start: 0.8688 (p) cc_final: 0.8080 (t) REVERT: A 187 ARG cc_start: 0.7210 (mtp85) cc_final: 0.6891 (ttp80) REVERT: B 55 ARG cc_start: 0.8413 (ttp-170) cc_final: 0.8197 (ttp-170) REVERT: B 446 ASP cc_start: 0.7628 (m-30) cc_final: 0.7364 (m-30) REVERT: C 271 SER cc_start: 0.9259 (t) cc_final: 0.8978 (p) REVERT: C 446 ASP cc_start: 0.7446 (m-30) cc_final: 0.7178 (m-30) REVERT: D 162 SER cc_start: 0.8699 (p) cc_final: 0.8106 (t) REVERT: D 446 ASP cc_start: 0.7956 (m-30) cc_final: 0.7640 (m-30) REVERT: E 440 SER cc_start: 0.8210 (m) cc_final: 0.7584 (p) REVERT: F 271 SER cc_start: 0.9247 (t) cc_final: 0.9032 (p) REVERT: F 277 MET cc_start: 0.8975 (ttm) cc_final: 0.8715 (ttp) REVERT: F 446 ASP cc_start: 0.7473 (m-30) cc_final: 0.7208 (m-30) REVERT: F 460 GLU cc_start: 0.7012 (mp0) cc_final: 0.6578 (mp0) REVERT: G 162 SER cc_start: 0.8667 (p) cc_final: 0.8113 (t) REVERT: G 187 ARG cc_start: 0.7153 (mtp85) cc_final: 0.6846 (ttp80) REVERT: G 446 ASP cc_start: 0.7891 (m-30) cc_final: 0.7624 (m-30) REVERT: H 440 SER cc_start: 0.8182 (m) cc_final: 0.7520 (p) REVERT: H 446 ASP cc_start: 0.7657 (m-30) cc_final: 0.7412 (m-30) REVERT: I 271 SER cc_start: 0.9185 (t) cc_final: 0.8935 (p) REVERT: I 277 MET cc_start: 0.8949 (ttm) cc_final: 0.8656 (ttp) REVERT: I 446 ASP cc_start: 0.7457 (m-30) cc_final: 0.7200 (m-30) REVERT: J 61 ASP cc_start: 0.7612 (m-30) cc_final: 0.7399 (m-30) REVERT: J 162 SER cc_start: 0.8668 (p) cc_final: 0.8079 (t) REVERT: J 187 ARG cc_start: 0.7172 (mtp85) cc_final: 0.6896 (ttp80) REVERT: J 446 ASP cc_start: 0.7883 (m-30) cc_final: 0.7631 (m-30) REVERT: K 349 ASN cc_start: 0.7163 (p0) cc_final: 0.6909 (p0) REVERT: K 446 ASP cc_start: 0.7600 (m-30) cc_final: 0.7361 (m-30) REVERT: L 271 SER cc_start: 0.9205 (t) cc_final: 0.8919 (p) REVERT: L 446 ASP cc_start: 0.7442 (m-30) cc_final: 0.7200 (m-30) REVERT: M 32 ARG cc_start: 0.8684 (ttt90) cc_final: 0.8297 (ttt90) REVERT: M 52 VAL cc_start: 0.8523 (t) cc_final: 0.8278 (t) REVERT: P 32 ARG cc_start: 0.8683 (ttt90) cc_final: 0.8435 (ttt90) REVERT: P 52 VAL cc_start: 0.8584 (t) cc_final: 0.8367 (t) REVERT: P 56 MET cc_start: 0.7677 (ppp) cc_final: 0.6768 (ptp) REVERT: R 38 THR cc_start: 0.9157 (t) cc_final: 0.8922 (p) REVERT: S 32 ARG cc_start: 0.8687 (ttt90) cc_final: 0.8357 (ttt180) REVERT: U 38 THR cc_start: 0.9147 (t) cc_final: 0.8901 (p) REVERT: V 32 ARG cc_start: 0.8682 (ttt90) cc_final: 0.8348 (ttt180) REVERT: W 11 ARG cc_start: 0.8266 (mtt-85) cc_final: 0.7971 (mtt90) REVERT: X 38 THR cc_start: 0.9176 (t) cc_final: 0.8972 (p) outliers start: 6 outliers final: 5 residues processed: 1168 average time/residue: 0.7985 time to fit residues: 1399.4824 Evaluate side-chains 835 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 830 time to evaluate : 5.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 5 GLU Chi-restraints excluded: chain P residue 5 GLU Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain V residue 5 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 7.9990 chunk 472 optimal weight: 4.9990 chunk 262 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 319 optimal weight: 5.9990 chunk 252 optimal weight: 0.6980 chunk 489 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 297 optimal weight: 4.9990 chunk 364 optimal weight: 8.9990 chunk 566 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 GLN B 39 ASN B 289 GLN B 410 GLN C 66 ASN D 39 ASN D 289 GLN D 356 GLN E 39 ASN E 410 GLN F 39 ASN F 66 ASN G 39 ASN G 289 GLN G 356 GLN H 39 ASN H 410 GLN I 39 ASN I 66 ASN J 39 ASN J 289 GLN J 356 GLN K 39 ASN K 289 GLN L 66 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 51192 Z= 0.365 Angle : 0.543 6.650 69084 Z= 0.293 Chirality : 0.040 0.168 7236 Planarity : 0.005 0.047 9156 Dihedral : 4.407 58.991 7107 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.75 % Allowed : 8.49 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.65 (0.10), residues: 6300 helix: 2.64 (0.09), residues: 3036 sheet: 0.89 (0.19), residues: 636 loop : -0.77 (0.10), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 442 HIS 0.008 0.002 HIS H 332 PHE 0.032 0.002 PHE B 147 TYR 0.030 0.002 TYR D 96 ARG 0.007 0.001 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 841 time to evaluate : 5.710 Fit side-chains REVERT: A 187 ARG cc_start: 0.7295 (mtp85) cc_final: 0.6996 (ttp80) REVERT: B 91 ARG cc_start: 0.7018 (mmt180) cc_final: 0.6727 (mmp80) REVERT: B 446 ASP cc_start: 0.7764 (m-30) cc_final: 0.7510 (m-30) REVERT: C 62 ASP cc_start: 0.8512 (t0) cc_final: 0.8187 (t0) REVERT: C 384 THR cc_start: 0.8869 (m) cc_final: 0.8598 (p) REVERT: C 446 ASP cc_start: 0.7379 (m-30) cc_final: 0.7176 (m-30) REVERT: D 446 ASP cc_start: 0.7895 (m-30) cc_final: 0.7659 (m-30) REVERT: E 91 ARG cc_start: 0.7226 (mmt180) cc_final: 0.6879 (mmp80) REVERT: E 292 MET cc_start: 0.9166 (mtt) cc_final: 0.8765 (mmt) REVERT: E 446 ASP cc_start: 0.7735 (m-30) cc_final: 0.7525 (m-30) REVERT: F 446 ASP cc_start: 0.7443 (m-30) cc_final: 0.7242 (m-30) REVERT: F 460 GLU cc_start: 0.7272 (mp0) cc_final: 0.6569 (mp0) REVERT: G 187 ARG cc_start: 0.7322 (mtp85) cc_final: 0.6994 (ttp80) REVERT: G 446 ASP cc_start: 0.7886 (m-30) cc_final: 0.7639 (m-30) REVERT: H 91 ARG cc_start: 0.6983 (mmt180) cc_final: 0.6691 (mmp80) REVERT: H 292 MET cc_start: 0.9155 (mtt) cc_final: 0.8736 (mmt) REVERT: H 446 ASP cc_start: 0.7783 (m-30) cc_final: 0.7539 (m-30) REVERT: I 446 ASP cc_start: 0.7439 (m-30) cc_final: 0.7234 (m-30) REVERT: J 61 ASP cc_start: 0.7610 (m-30) cc_final: 0.7349 (m-30) REVERT: J 187 ARG cc_start: 0.7296 (mtp85) cc_final: 0.6892 (ttp80) REVERT: J 432 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.7096 (ttp80) REVERT: J 446 ASP cc_start: 0.7866 (m-30) cc_final: 0.7622 (m-30) REVERT: K 91 ARG cc_start: 0.6964 (mmt180) cc_final: 0.6667 (mmp80) REVERT: K 292 MET cc_start: 0.9135 (mtt) cc_final: 0.8740 (mmt) REVERT: K 446 ASP cc_start: 0.7751 (m-30) cc_final: 0.7527 (m-30) REVERT: L 446 ASP cc_start: 0.7423 (m-30) cc_final: 0.7195 (m-30) REVERT: M 32 ARG cc_start: 0.8761 (ttt90) cc_final: 0.8548 (ttt-90) REVERT: N 11 ARG cc_start: 0.8269 (mtt-85) cc_final: 0.8041 (mtt90) REVERT: O 6 GLU cc_start: 0.7671 (tt0) cc_final: 0.7031 (tt0) REVERT: O 49 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7054 (tm-30) REVERT: P 50 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8745 (mp) REVERT: Q 11 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.8022 (mtt90) REVERT: R 38 THR cc_start: 0.9212 (t) cc_final: 0.8878 (p) REVERT: R 49 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7030 (tm-30) REVERT: S 50 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8752 (mp) REVERT: T 5 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6807 (pm20) REVERT: U 38 THR cc_start: 0.9222 (t) cc_final: 0.8876 (p) REVERT: U 49 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7057 (tm-30) REVERT: W 11 ARG cc_start: 0.8416 (mtt-85) cc_final: 0.8201 (mtt90) REVERT: X 38 THR cc_start: 0.9236 (t) cc_final: 0.8914 (p) REVERT: X 49 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7129 (tm-30) REVERT: X 50 LEU cc_start: 0.8587 (tp) cc_final: 0.8278 (tt) outliers start: 90 outliers final: 76 residues processed: 903 average time/residue: 0.8182 time to fit residues: 1114.3868 Evaluate side-chains 835 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 756 time to evaluate : 6.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 410 GLN Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 410 GLN Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 182 ASN Chi-restraints excluded: chain K residue 410 GLN Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain L residue 162 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 59 ARG Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 59 ARG Chi-restraints excluded: chain V residue 38 THR Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain X residue 23 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 471 optimal weight: 2.9990 chunk 385 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 567 optimal weight: 1.9990 chunk 613 optimal weight: 2.9990 chunk 505 optimal weight: 5.9990 chunk 562 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 455 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 356 GLN B 39 ASN C 39 ASN D 39 ASN E 39 ASN E 356 GLN F 39 ASN F 410 GLN G 39 ASN H 39 ASN H 356 GLN I 39 ASN J 39 ASN K 39 ASN K 356 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 51192 Z= 0.251 Angle : 0.468 6.344 69084 Z= 0.254 Chirality : 0.037 0.167 7236 Planarity : 0.004 0.046 9156 Dihedral : 3.986 52.560 7098 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.01 % Allowed : 9.89 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.10), residues: 6300 helix: 2.73 (0.09), residues: 3024 sheet: 0.98 (0.18), residues: 660 loop : -0.78 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 447 HIS 0.006 0.001 HIS B 332 PHE 0.026 0.002 PHE B 147 TYR 0.022 0.001 TYR C 96 ARG 0.005 0.000 ARG V 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 820 time to evaluate : 6.537 Fit side-chains REVERT: A 187 ARG cc_start: 0.7329 (mtp85) cc_final: 0.7051 (ttp80) REVERT: A 252 TYR cc_start: 0.9259 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: B 91 ARG cc_start: 0.7056 (mmt180) cc_final: 0.6763 (mmp80) REVERT: B 292 MET cc_start: 0.9080 (mtt) cc_final: 0.8859 (mmt) REVERT: B 446 ASP cc_start: 0.7761 (m-30) cc_final: 0.7477 (m-30) REVERT: C 62 ASP cc_start: 0.8488 (t0) cc_final: 0.8122 (t0) REVERT: C 384 THR cc_start: 0.8773 (m) cc_final: 0.8553 (p) REVERT: C 446 ASP cc_start: 0.7522 (m-30) cc_final: 0.7308 (m-30) REVERT: D 252 TYR cc_start: 0.9252 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: D 446 ASP cc_start: 0.7748 (m-30) cc_final: 0.7485 (m-30) REVERT: E 91 ARG cc_start: 0.7018 (mmt180) cc_final: 0.6707 (mmp80) REVERT: E 292 MET cc_start: 0.9076 (mtt) cc_final: 0.8795 (mmt) REVERT: E 446 ASP cc_start: 0.7802 (m-30) cc_final: 0.7562 (m-30) REVERT: F 166 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7194 (mtp85) REVERT: F 446 ASP cc_start: 0.7664 (m-30) cc_final: 0.7437 (m-30) REVERT: G 187 ARG cc_start: 0.7326 (mtp85) cc_final: 0.7019 (ttp80) REVERT: G 252 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8233 (m-80) REVERT: G 446 ASP cc_start: 0.7763 (m-30) cc_final: 0.7494 (m-30) REVERT: H 91 ARG cc_start: 0.7014 (mmt180) cc_final: 0.6722 (mmp80) REVERT: H 292 MET cc_start: 0.9067 (mtt) cc_final: 0.8772 (mmt) REVERT: H 446 ASP cc_start: 0.7816 (m-30) cc_final: 0.7590 (m-30) REVERT: I 446 ASP cc_start: 0.7579 (m-30) cc_final: 0.7363 (m-30) REVERT: J 187 ARG cc_start: 0.7333 (mtp85) cc_final: 0.7049 (ttp80) REVERT: J 252 TYR cc_start: 0.9303 (OUTLIER) cc_final: 0.8216 (m-80) REVERT: J 446 ASP cc_start: 0.7744 (m-30) cc_final: 0.7476 (m-30) REVERT: K 91 ARG cc_start: 0.6995 (mmt180) cc_final: 0.6680 (mmp80) REVERT: K 292 MET cc_start: 0.9052 (mtt) cc_final: 0.8769 (mmt) REVERT: K 446 ASP cc_start: 0.7794 (m-30) cc_final: 0.7571 (m-30) REVERT: L 96 TYR cc_start: 0.8046 (t80) cc_final: 0.7827 (t80) REVERT: L 446 ASP cc_start: 0.7541 (m-30) cc_final: 0.7333 (m-30) REVERT: M 32 ARG cc_start: 0.8754 (ttt90) cc_final: 0.8522 (ttt-90) REVERT: N 11 ARG cc_start: 0.8337 (mtt-85) cc_final: 0.8097 (mtt90) REVERT: O 6 GLU cc_start: 0.7695 (tt0) cc_final: 0.7004 (tt0) REVERT: O 49 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7069 (tm-30) REVERT: P 50 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8760 (mp) REVERT: Q 11 ARG cc_start: 0.8327 (mtt-85) cc_final: 0.8099 (mtt90) REVERT: R 5 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6760 (pm20) REVERT: R 38 THR cc_start: 0.9225 (t) cc_final: 0.8913 (p) REVERT: R 49 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7032 (tm-30) REVERT: U 5 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.7048 (pm20) REVERT: U 38 THR cc_start: 0.9237 (t) cc_final: 0.8896 (p) REVERT: U 49 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7028 (tm-30) REVERT: W 11 ARG cc_start: 0.8410 (mtt-85) cc_final: 0.8195 (mtt90) REVERT: X 5 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6877 (pm20) REVERT: X 38 THR cc_start: 0.9226 (t) cc_final: 0.8921 (p) REVERT: X 49 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7038 (tm-30) outliers start: 103 outliers final: 88 residues processed: 876 average time/residue: 0.7959 time to fit residues: 1055.4599 Evaluate side-chains 875 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 778 time to evaluate : 5.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 410 GLN Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 252 TYR Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 384 THR Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain J residue 252 TYR Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 287 ASP Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 287 ASP Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 410 GLN Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain L residue 162 SER Chi-restraints excluded: chain L residue 271 SER Chi-restraints excluded: chain L residue 384 THR Chi-restraints excluded: chain N residue 5 GLU Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain Q residue 5 GLU Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain R residue 5 GLU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 59 ARG Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 51 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 5.9990 chunk 426 optimal weight: 4.9990 chunk 294 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 270 optimal weight: 0.9990 chunk 381 optimal weight: 8.9990 chunk 569 optimal weight: 7.9990 chunk 603 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 chunk 539 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 66 ASN B 39 ASN C 39 ASN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 HIS D 39 ASN E 39 ASN F 39 ASN F 332 HIS G 39 ASN H 39 ASN I 39 ASN I 332 HIS J 39 ASN K 39 ASN L 332 HIS O 15 HIS R 15 HIS U 15 HIS X 15 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 51192 Z= 0.453 Angle : 0.570 7.042 69084 Z= 0.308 Chirality : 0.041 0.169 7236 Planarity : 0.005 0.050 9156 Dihedral : 4.325 47.059 7098 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.71 % Allowed : 11.84 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.25 (0.10), residues: 6300 helix: 2.28 (0.09), residues: 3060 sheet: 0.58 (0.19), residues: 684 loop : -0.95 (0.11), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 94 HIS 0.010 0.002 HIS K 332 PHE 0.028 0.002 PHE H 147 TYR 0.025 0.002 TYR C 96 ARG 0.006 0.001 ARG S 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 772 time to evaluate : 6.220 Fit side-chains REVERT: A 187 ARG cc_start: 0.7316 (mtp85) cc_final: 0.7061 (ttp80) REVERT: A 252 TYR cc_start: 0.9229 (OUTLIER) cc_final: 0.8376 (m-10) REVERT: B 292 MET cc_start: 0.9094 (mtt) cc_final: 0.8866 (mmt) REVERT: B 446 ASP cc_start: 0.7787 (m-30) cc_final: 0.7410 (m-30) REVERT: C 62 ASP cc_start: 0.8551 (t0) cc_final: 0.8057 (t0) REVERT: C 287 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7269 (m-30) REVERT: C 446 ASP cc_start: 0.7639 (m-30) cc_final: 0.7427 (m-30) REVERT: D 91 ARG cc_start: 0.6879 (mmt180) cc_final: 0.6589 (mmt-90) REVERT: D 252 TYR cc_start: 0.9226 (OUTLIER) cc_final: 0.8370 (m-10) REVERT: D 446 ASP cc_start: 0.7715 (m-30) cc_final: 0.7443 (m-30) REVERT: E 292 MET cc_start: 0.9101 (mtt) cc_final: 0.8832 (mmt) REVERT: E 446 ASP cc_start: 0.7832 (m-30) cc_final: 0.7539 (m-30) REVERT: F 166 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7269 (mtp85) REVERT: F 287 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7099 (m-30) REVERT: F 446 ASP cc_start: 0.7677 (m-30) cc_final: 0.7467 (m-30) REVERT: G 91 ARG cc_start: 0.6880 (mmt180) cc_final: 0.6586 (mmt-90) REVERT: G 187 ARG cc_start: 0.7385 (mtp85) cc_final: 0.7117 (ttp80) REVERT: G 252 TYR cc_start: 0.9231 (OUTLIER) cc_final: 0.8543 (m-10) REVERT: G 446 ASP cc_start: 0.7747 (m-30) cc_final: 0.7479 (m-30) REVERT: H 292 MET cc_start: 0.9096 (mtt) cc_final: 0.8738 (mmt) REVERT: H 446 ASP cc_start: 0.7822 (m-30) cc_final: 0.7451 (m-30) REVERT: I 287 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7077 (m-30) REVERT: I 446 ASP cc_start: 0.7679 (m-30) cc_final: 0.7454 (m-30) REVERT: J 91 ARG cc_start: 0.6885 (mmt180) cc_final: 0.6593 (mmt-90) REVERT: J 187 ARG cc_start: 0.7336 (mtp85) cc_final: 0.7073 (ttp80) REVERT: J 252 TYR cc_start: 0.9259 (OUTLIER) cc_final: 0.8499 (m-10) REVERT: J 446 ASP cc_start: 0.7730 (m-30) cc_final: 0.7468 (m-30) REVERT: K 292 MET cc_start: 0.9079 (mtt) cc_final: 0.8774 (mmt) REVERT: K 446 ASP cc_start: 0.7809 (m-30) cc_final: 0.7440 (m-30) REVERT: L 287 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7119 (m-30) REVERT: L 446 ASP cc_start: 0.7657 (m-30) cc_final: 0.7441 (m-30) REVERT: M 59 ARG cc_start: 0.8391 (mtp85) cc_final: 0.8159 (mtp85) REVERT: N 59 ARG cc_start: 0.8432 (mtp85) cc_final: 0.8175 (mtp85) REVERT: O 6 GLU cc_start: 0.7575 (tt0) cc_final: 0.7062 (tt0) REVERT: O 49 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7070 (tm-30) REVERT: P 59 ARG cc_start: 0.8431 (mtp85) cc_final: 0.8180 (mtp85) REVERT: R 5 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6734 (pm20) REVERT: R 38 THR cc_start: 0.9170 (t) cc_final: 0.8901 (p) REVERT: R 49 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7058 (tm-30) REVERT: T 59 ARG cc_start: 0.8442 (mtp85) cc_final: 0.8200 (mtp85) REVERT: U 5 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: U 38 THR cc_start: 0.9157 (t) cc_final: 0.8881 (p) REVERT: U 49 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7066 (tm-30) REVERT: W 59 ARG cc_start: 0.8436 (mtp85) cc_final: 0.8208 (mtp85) REVERT: X 5 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6955 (pm20) REVERT: X 38 THR cc_start: 0.9165 (t) cc_final: 0.8908 (p) REVERT: X 49 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7052 (tm-30) outliers start: 139 outliers final: 106 residues processed: 874 average time/residue: 0.7971 time to fit residues: 1052.3089 Evaluate side-chains 864 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 746 time to evaluate : 5.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 249 ASN Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 410 GLN Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 249 ASN Chi-restraints excluded: chain G residue 252 TYR Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 410 GLN Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 384 THR Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain J residue 249 ASN Chi-restraints excluded: chain J residue 252 TYR Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 287 ASP Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 161 SER Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 287 ASP Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 410 GLN Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain K residue 427 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain L residue 162 SER Chi-restraints excluded: chain L residue 271 SER Chi-restraints excluded: chain L residue 287 ASP Chi-restraints excluded: chain L residue 384 THR Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain P residue 58 GLN Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 51 GLU Chi-restraints excluded: chain R residue 5 GLU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 39 SER Chi-restraints excluded: chain R residue 59 ARG Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 39 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 0.7980 chunk 342 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 449 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 514 optimal weight: 7.9990 chunk 416 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 307 optimal weight: 0.9990 chunk 541 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN B 39 ASN B 356 GLN B 407 GLN B 410 GLN C 66 ASN C 410 GLN D 39 ASN E 39 ASN E 410 GLN F 39 ASN F 66 ASN H 39 ASN I 39 ASN I 66 ASN I 410 GLN J 39 ASN K 39 ASN K 410 GLN L 66 ASN L 410 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 51192 Z= 0.168 Angle : 0.437 6.222 69084 Z= 0.239 Chirality : 0.036 0.158 7236 Planarity : 0.003 0.045 9156 Dihedral : 3.939 44.060 7098 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.83 % Allowed : 12.91 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.60 (0.10), residues: 6300 helix: 2.67 (0.09), residues: 3036 sheet: 0.72 (0.19), residues: 684 loop : -0.87 (0.11), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 94 HIS 0.004 0.001 HIS B 332 PHE 0.023 0.001 PHE K 147 TYR 0.024 0.001 TYR D 96 ARG 0.006 0.000 ARG C 501 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 797 time to evaluate : 5.266 Fit side-chains REVERT: A 187 ARG cc_start: 0.7318 (mtp85) cc_final: 0.6922 (ttp80) REVERT: A 252 TYR cc_start: 0.9288 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: B 446 ASP cc_start: 0.7749 (m-30) cc_final: 0.7378 (m-30) REVERT: C 62 ASP cc_start: 0.8459 (t0) cc_final: 0.8055 (t0) REVERT: C 446 ASP cc_start: 0.7585 (m-30) cc_final: 0.7357 (m-30) REVERT: D 252 TYR cc_start: 0.9285 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: D 446 ASP cc_start: 0.7811 (m-30) cc_final: 0.7549 (m-30) REVERT: E 446 ASP cc_start: 0.7800 (m-30) cc_final: 0.7510 (m-30) REVERT: F 166 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7188 (mtp85) REVERT: F 446 ASP cc_start: 0.7639 (m-30) cc_final: 0.7399 (m-30) REVERT: G 252 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.8513 (m-80) REVERT: G 446 ASP cc_start: 0.7845 (m-30) cc_final: 0.7608 (m-30) REVERT: H 91 ARG cc_start: 0.7008 (mmt180) cc_final: 0.6720 (mmp80) REVERT: H 446 ASP cc_start: 0.7812 (m-30) cc_final: 0.7506 (m-30) REVERT: I 446 ASP cc_start: 0.7637 (m-30) cc_final: 0.7397 (m-30) REVERT: J 187 ARG cc_start: 0.7343 (mtp85) cc_final: 0.6948 (ttp80) REVERT: J 252 TYR cc_start: 0.9205 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: J 446 ASP cc_start: 0.7831 (m-30) cc_final: 0.7596 (m-30) REVERT: K 292 MET cc_start: 0.8984 (mtt) cc_final: 0.8756 (mmt) REVERT: K 446 ASP cc_start: 0.7773 (m-30) cc_final: 0.7409 (m-30) REVERT: L 446 ASP cc_start: 0.7616 (m-30) cc_final: 0.7383 (m-30) REVERT: M 59 ARG cc_start: 0.8383 (mtp85) cc_final: 0.8146 (mtp85) REVERT: O 6 GLU cc_start: 0.7662 (tt0) cc_final: 0.6995 (tt0) REVERT: P 59 ARG cc_start: 0.8405 (mtp85) cc_final: 0.8174 (mtp85) REVERT: R 5 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6726 (pm20) REVERT: R 38 THR cc_start: 0.9136 (t) cc_final: 0.8896 (p) REVERT: T 52 VAL cc_start: 0.8737 (t) cc_final: 0.8520 (t) REVERT: U 5 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6808 (pm20) REVERT: U 38 THR cc_start: 0.9121 (t) cc_final: 0.8880 (p) REVERT: U 49 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7116 (tm-30) REVERT: W 52 VAL cc_start: 0.8727 (t) cc_final: 0.8512 (t) REVERT: W 59 ARG cc_start: 0.8412 (mtp85) cc_final: 0.8195 (mtp85) REVERT: X 5 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6716 (pm20) REVERT: X 38 THR cc_start: 0.9150 (t) cc_final: 0.8947 (p) outliers start: 94 outliers final: 79 residues processed: 850 average time/residue: 0.7716 time to fit residues: 994.2461 Evaluate side-chains 853 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 766 time to evaluate : 5.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 410 GLN Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 252 TYR Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 410 GLN Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 348 ASP Chi-restraints excluded: chain I residue 356 GLN Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 384 THR Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain J residue 252 TYR Chi-restraints excluded: chain J residue 287 ASP Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 287 ASP Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 410 GLN Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain K residue 427 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain L residue 162 SER Chi-restraints excluded: chain L residue 249 ASN Chi-restraints excluded: chain L residue 356 GLN Chi-restraints excluded: chain L residue 384 THR Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 51 GLU Chi-restraints excluded: chain R residue 5 GLU Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 51 GLU Chi-restraints excluded: chain X residue 5 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 0.8980 chunk 543 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 354 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 603 optimal weight: 5.9990 chunk 501 optimal weight: 0.7980 chunk 279 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 316 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN B 39 ASN D 39 ASN E 39 ASN F 39 ASN G 39 ASN H 39 ASN I 39 ASN J 39 ASN K 39 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 51192 Z= 0.206 Angle : 0.446 6.410 69084 Z= 0.242 Chirality : 0.036 0.159 7236 Planarity : 0.004 0.046 9156 Dihedral : 3.872 41.952 7098 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.43 % Allowed : 12.95 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.59 (0.10), residues: 6300 helix: 2.64 (0.09), residues: 3060 sheet: 0.69 (0.19), residues: 684 loop : -0.89 (0.11), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 94 HIS 0.004 0.001 HIS E 332 PHE 0.025 0.001 PHE K 147 TYR 0.030 0.001 TYR D 96 ARG 0.006 0.000 ARG K 501 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 776 time to evaluate : 5.626 Fit side-chains REVERT: A 187 ARG cc_start: 0.7316 (mtp85) cc_final: 0.6920 (ttp80) REVERT: A 252 TYR cc_start: 0.9287 (OUTLIER) cc_final: 0.8423 (m-80) REVERT: B 339 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9247 (tp) REVERT: B 446 ASP cc_start: 0.7750 (m-30) cc_final: 0.7382 (m-30) REVERT: C 62 ASP cc_start: 0.8432 (t0) cc_final: 0.8050 (t0) REVERT: C 287 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7047 (m-30) REVERT: C 446 ASP cc_start: 0.7669 (m-30) cc_final: 0.7356 (m-30) REVERT: D 252 TYR cc_start: 0.9298 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: D 446 ASP cc_start: 0.7856 (m-30) cc_final: 0.7485 (m-30) REVERT: E 339 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9235 (tp) REVERT: E 446 ASP cc_start: 0.7809 (m-30) cc_final: 0.7519 (m-30) REVERT: F 166 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7188 (mtp85) REVERT: F 446 ASP cc_start: 0.7712 (m-30) cc_final: 0.7403 (m-30) REVERT: F 460 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: G 252 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.8426 (m-80) REVERT: G 446 ASP cc_start: 0.7846 (m-30) cc_final: 0.7615 (m-30) REVERT: H 91 ARG cc_start: 0.7007 (mmt180) cc_final: 0.6721 (mmp80) REVERT: H 339 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9239 (tp) REVERT: H 446 ASP cc_start: 0.7790 (m-30) cc_final: 0.7432 (m-30) REVERT: I 446 ASP cc_start: 0.7715 (m-30) cc_final: 0.7396 (m-30) REVERT: J 187 ARG cc_start: 0.7342 (mtp85) cc_final: 0.6954 (ttp80) REVERT: J 252 TYR cc_start: 0.9253 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: J 446 ASP cc_start: 0.7831 (m-30) cc_final: 0.7608 (m-30) REVERT: K 91 ARG cc_start: 0.6963 (mmt180) cc_final: 0.6657 (mmp80) REVERT: K 292 MET cc_start: 0.8988 (mtt) cc_final: 0.8753 (mmt) REVERT: K 339 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9242 (tp) REVERT: K 446 ASP cc_start: 0.7766 (m-30) cc_final: 0.7415 (m-30) REVERT: L 446 ASP cc_start: 0.7698 (m-30) cc_final: 0.7386 (m-30) REVERT: M 59 ARG cc_start: 0.8389 (mtp85) cc_final: 0.8159 (mtp85) REVERT: O 6 GLU cc_start: 0.7657 (tt0) cc_final: 0.6991 (tt0) REVERT: P 59 ARG cc_start: 0.8412 (mtp85) cc_final: 0.8165 (mtp85) REVERT: R 5 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6926 (pm20) REVERT: R 38 THR cc_start: 0.9121 (t) cc_final: 0.8889 (p) REVERT: T 5 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: T 52 VAL cc_start: 0.8735 (t) cc_final: 0.8530 (t) REVERT: U 5 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6921 (pm20) REVERT: U 38 THR cc_start: 0.9108 (t) cc_final: 0.8873 (p) REVERT: W 52 VAL cc_start: 0.8736 (t) cc_final: 0.8524 (t) REVERT: X 5 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6788 (pm20) REVERT: X 38 THR cc_start: 0.9138 (t) cc_final: 0.8936 (p) outliers start: 125 outliers final: 99 residues processed: 859 average time/residue: 0.7582 time to fit residues: 997.1770 Evaluate side-chains 869 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 755 time to evaluate : 5.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 252 TYR Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 410 GLN Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 348 ASP Chi-restraints excluded: chain I residue 356 GLN Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 384 THR Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 252 TYR Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 287 ASP Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 287 ASP Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain K residue 427 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain L residue 162 SER Chi-restraints excluded: chain L residue 249 ASN Chi-restraints excluded: chain L residue 271 SER Chi-restraints excluded: chain L residue 356 GLN Chi-restraints excluded: chain L residue 384 THR Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 51 GLU Chi-restraints excluded: chain R residue 5 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 51 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 33 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 343 optimal weight: 0.8980 chunk 440 optimal weight: 0.7980 chunk 341 optimal weight: 2.9990 chunk 508 optimal weight: 4.9990 chunk 337 optimal weight: 0.6980 chunk 601 optimal weight: 3.9990 chunk 376 optimal weight: 8.9990 chunk 366 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 ASN D 39 ASN E 39 ASN E 410 GLN F 39 ASN H 39 ASN I 39 ASN J 39 ASN K 39 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 51192 Z= 0.218 Angle : 0.446 6.413 69084 Z= 0.242 Chirality : 0.036 0.175 7236 Planarity : 0.004 0.046 9156 Dihedral : 3.785 39.371 7095 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.53 % Allowed : 13.06 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.59 (0.10), residues: 6300 helix: 2.65 (0.09), residues: 3060 sheet: 0.66 (0.19), residues: 684 loop : -0.89 (0.11), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 94 HIS 0.004 0.001 HIS B 332 PHE 0.024 0.001 PHE H 147 TYR 0.026 0.001 TYR D 96 ARG 0.007 0.000 ARG K 501 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 769 time to evaluate : 5.272 Fit side-chains REVERT: A 105 ARG cc_start: 0.7723 (mmt180) cc_final: 0.7432 (mmt90) REVERT: A 187 ARG cc_start: 0.7431 (mtp85) cc_final: 0.7012 (ttp80) REVERT: A 252 TYR cc_start: 0.9288 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: B 339 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9253 (tp) REVERT: B 446 ASP cc_start: 0.7746 (m-30) cc_final: 0.7379 (m-30) REVERT: C 62 ASP cc_start: 0.8432 (t0) cc_final: 0.8003 (t0) REVERT: C 287 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7052 (m-30) REVERT: C 446 ASP cc_start: 0.7665 (m-30) cc_final: 0.7350 (m-30) REVERT: D 91 ARG cc_start: 0.6871 (mmt180) cc_final: 0.6593 (mmt-90) REVERT: D 252 TYR cc_start: 0.9297 (OUTLIER) cc_final: 0.8481 (m-80) REVERT: D 446 ASP cc_start: 0.7758 (m-30) cc_final: 0.7402 (m-30) REVERT: E 446 ASP cc_start: 0.7808 (m-30) cc_final: 0.7511 (m-30) REVERT: F 166 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7182 (mtp85) REVERT: F 446 ASP cc_start: 0.7709 (m-30) cc_final: 0.7388 (m-30) REVERT: F 460 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: G 252 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.8510 (m-80) REVERT: G 446 ASP cc_start: 0.7791 (m-30) cc_final: 0.7464 (m-30) REVERT: H 91 ARG cc_start: 0.7015 (mmt180) cc_final: 0.6725 (mmp80) REVERT: H 339 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9231 (tp) REVERT: H 446 ASP cc_start: 0.7790 (m-30) cc_final: 0.7430 (m-30) REVERT: I 446 ASP cc_start: 0.7711 (m-30) cc_final: 0.7386 (m-30) REVERT: J 105 ARG cc_start: 0.7740 (mmt180) cc_final: 0.7449 (mmt90) REVERT: J 187 ARG cc_start: 0.7424 (mtp85) cc_final: 0.7042 (ttp80) REVERT: J 252 TYR cc_start: 0.9314 (OUTLIER) cc_final: 0.8502 (m-80) REVERT: J 446 ASP cc_start: 0.7789 (m-30) cc_final: 0.7469 (m-30) REVERT: K 91 ARG cc_start: 0.6966 (mmt180) cc_final: 0.6656 (mmp80) REVERT: K 292 MET cc_start: 0.8980 (mtt) cc_final: 0.8748 (mmt) REVERT: K 339 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9239 (tp) REVERT: K 446 ASP cc_start: 0.7767 (m-30) cc_final: 0.7414 (m-30) REVERT: L 446 ASP cc_start: 0.7700 (m-30) cc_final: 0.7382 (m-30) REVERT: M 59 ARG cc_start: 0.8398 (mtp85) cc_final: 0.8178 (mtp85) REVERT: O 6 GLU cc_start: 0.7650 (tt0) cc_final: 0.6999 (tt0) REVERT: P 59 ARG cc_start: 0.8423 (mtp85) cc_final: 0.8189 (mtp85) REVERT: R 5 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: R 38 THR cc_start: 0.9117 (t) cc_final: 0.8915 (p) REVERT: T 5 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: T 52 VAL cc_start: 0.8735 (t) cc_final: 0.8522 (t) REVERT: U 5 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: X 5 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6788 (pm20) outliers start: 130 outliers final: 106 residues processed: 851 average time/residue: 0.7507 time to fit residues: 979.9382 Evaluate side-chains 874 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 754 time to evaluate : 5.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 410 GLN Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 252 TYR Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain G residue 337 ASP Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 410 GLN Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 348 ASP Chi-restraints excluded: chain I residue 356 GLN Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 384 THR Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 252 TYR Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 287 ASP Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 161 SER Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 287 ASP Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 348 ASP Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain K residue 427 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain L residue 162 SER Chi-restraints excluded: chain L residue 249 ASN Chi-restraints excluded: chain L residue 271 SER Chi-restraints excluded: chain L residue 356 GLN Chi-restraints excluded: chain L residue 384 THR Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain R residue 5 GLU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 51 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 33 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 0.9990 chunk 240 optimal weight: 4.9990 chunk 359 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 382 optimal weight: 0.9980 chunk 409 optimal weight: 0.1980 chunk 297 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 472 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN B 39 ASN ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 410 GLN F 39 ASN G 39 ASN H 39 ASN I 39 ASN K 39 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 51192 Z= 0.133 Angle : 0.414 6.223 69084 Z= 0.226 Chirality : 0.035 0.157 7236 Planarity : 0.003 0.044 9156 Dihedral : 3.618 35.782 7095 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.99 % Allowed : 14.04 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.74 (0.10), residues: 6300 helix: 2.78 (0.09), residues: 3060 sheet: 0.74 (0.19), residues: 684 loop : -0.82 (0.11), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 94 HIS 0.003 0.001 HIS P 15 PHE 0.023 0.001 PHE E 147 TYR 0.024 0.001 TYR D 96 ARG 0.006 0.000 ARG F 501 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 792 time to evaluate : 5.769 Fit side-chains REVERT: A 105 ARG cc_start: 0.7629 (mmt180) cc_final: 0.7334 (mmt90) REVERT: A 187 ARG cc_start: 0.7420 (mtp85) cc_final: 0.7022 (ttp80) REVERT: A 252 TYR cc_start: 0.9287 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: B 446 ASP cc_start: 0.7734 (m-30) cc_final: 0.7371 (m-30) REVERT: C 62 ASP cc_start: 0.8399 (t0) cc_final: 0.8081 (t0) REVERT: C 446 ASP cc_start: 0.7646 (m-30) cc_final: 0.7337 (m-30) REVERT: D 252 TYR cc_start: 0.9285 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: D 446 ASP cc_start: 0.7745 (m-30) cc_final: 0.7389 (m-30) REVERT: E 91 ARG cc_start: 0.6971 (mmt180) cc_final: 0.6669 (mmp80) REVERT: E 446 ASP cc_start: 0.7789 (m-30) cc_final: 0.7507 (m-30) REVERT: F 166 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7141 (mtp85) REVERT: F 446 ASP cc_start: 0.7683 (m-30) cc_final: 0.7365 (m-30) REVERT: F 460 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: G 252 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: G 446 ASP cc_start: 0.7773 (m-30) cc_final: 0.7433 (m-30) REVERT: H 91 ARG cc_start: 0.6998 (mmt180) cc_final: 0.6719 (mmp80) REVERT: H 208 GLU cc_start: 0.7353 (tp30) cc_final: 0.7121 (tp30) REVERT: H 256 GLU cc_start: 0.7679 (tt0) cc_final: 0.7475 (tt0) REVERT: H 446 ASP cc_start: 0.7777 (m-30) cc_final: 0.7421 (m-30) REVERT: I 446 ASP cc_start: 0.7685 (m-30) cc_final: 0.7363 (m-30) REVERT: J 105 ARG cc_start: 0.7647 (mmt180) cc_final: 0.7348 (mmt90) REVERT: J 187 ARG cc_start: 0.7412 (mtp85) cc_final: 0.7020 (ttp80) REVERT: J 252 TYR cc_start: 0.9330 (OUTLIER) cc_final: 0.8433 (m-80) REVERT: J 446 ASP cc_start: 0.7768 (m-30) cc_final: 0.7443 (m-30) REVERT: K 91 ARG cc_start: 0.6951 (mmt180) cc_final: 0.6651 (mmp80) REVERT: K 292 MET cc_start: 0.8946 (mtt) cc_final: 0.8714 (mmt) REVERT: K 339 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9201 (tp) REVERT: K 446 ASP cc_start: 0.7747 (m-30) cc_final: 0.7399 (m-30) REVERT: L 446 ASP cc_start: 0.7686 (m-30) cc_final: 0.7372 (m-30) REVERT: M 59 ARG cc_start: 0.8393 (mtp85) cc_final: 0.8175 (mtp85) REVERT: P 59 ARG cc_start: 0.8411 (mtp85) cc_final: 0.8194 (mtp85) REVERT: R 5 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6880 (pm20) REVERT: R 38 THR cc_start: 0.9117 (t) cc_final: 0.8882 (p) REVERT: U 5 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6931 (pm20) REVERT: V 34 GLU cc_start: 0.7685 (tt0) cc_final: 0.7451 (tt0) REVERT: X 5 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6870 (pm20) outliers start: 102 outliers final: 84 residues processed: 853 average time/residue: 0.7600 time to fit residues: 993.2828 Evaluate side-chains 856 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 762 time to evaluate : 7.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 410 GLN Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 252 TYR Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 410 GLN Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 348 ASP Chi-restraints excluded: chain I residue 356 GLN Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 384 THR Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 252 TYR Chi-restraints excluded: chain J residue 287 ASP Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 287 ASP Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain K residue 427 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain L residue 162 SER Chi-restraints excluded: chain L residue 249 ASN Chi-restraints excluded: chain L residue 356 GLN Chi-restraints excluded: chain L residue 384 THR Chi-restraints excluded: chain N residue 5 GLU Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain Q residue 5 GLU Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 51 GLU Chi-restraints excluded: chain R residue 5 GLU Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 51 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 33 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 4.9990 chunk 576 optimal weight: 3.9990 chunk 525 optimal weight: 2.9990 chunk 560 optimal weight: 0.9980 chunk 337 optimal weight: 0.0870 chunk 244 optimal weight: 0.4980 chunk 440 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 506 optimal weight: 0.3980 chunk 530 optimal weight: 5.9990 chunk 558 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN B 39 ASN B 410 GLN D 39 ASN D 66 ASN E 39 ASN F 39 ASN F 332 HIS G 39 ASN G 66 ASN H 39 ASN I 39 ASN I 332 HIS J 39 ASN J 66 ASN K 39 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 51192 Z= 0.118 Angle : 0.402 6.136 69084 Z= 0.218 Chirality : 0.035 0.174 7236 Planarity : 0.003 0.043 9156 Dihedral : 3.435 17.526 7092 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.73 % Allowed : 14.23 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.86 (0.10), residues: 6300 helix: 2.87 (0.09), residues: 3060 sheet: 0.80 (0.19), residues: 684 loop : -0.74 (0.11), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 94 HIS 0.002 0.001 HIS G 235 PHE 0.023 0.001 PHE E 147 TYR 0.023 0.001 TYR D 96 ARG 0.008 0.000 ARG H 501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 784 time to evaluate : 6.208 Fit side-chains REVERT: A 105 ARG cc_start: 0.7609 (mmt180) cc_final: 0.7318 (mmt90) REVERT: A 187 ARG cc_start: 0.7419 (mtp85) cc_final: 0.7050 (ttp80) REVERT: A 252 TYR cc_start: 0.9270 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: B 446 ASP cc_start: 0.7732 (m-30) cc_final: 0.7362 (m-30) REVERT: C 62 ASP cc_start: 0.8393 (t0) cc_final: 0.8134 (t0) REVERT: C 258 MET cc_start: 0.9106 (mtp) cc_final: 0.8680 (mtp) REVERT: C 446 ASP cc_start: 0.7628 (m-30) cc_final: 0.7315 (m-30) REVERT: D 252 TYR cc_start: 0.9285 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: D 446 ASP cc_start: 0.7730 (m-30) cc_final: 0.7380 (m-30) REVERT: E 91 ARG cc_start: 0.6912 (mmt180) cc_final: 0.6621 (mmp80) REVERT: E 446 ASP cc_start: 0.7775 (m-30) cc_final: 0.7494 (m-30) REVERT: F 258 MET cc_start: 0.9110 (mtp) cc_final: 0.8672 (mtp) REVERT: F 446 ASP cc_start: 0.7668 (m-30) cc_final: 0.7353 (m-30) REVERT: F 460 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: G 252 TYR cc_start: 0.9030 (OUTLIER) cc_final: 0.8300 (m-80) REVERT: G 446 ASP cc_start: 0.7759 (m-30) cc_final: 0.7446 (m-30) REVERT: H 91 ARG cc_start: 0.6990 (mmt180) cc_final: 0.6715 (mmp80) REVERT: H 446 ASP cc_start: 0.7766 (m-30) cc_final: 0.7405 (m-30) REVERT: I 446 ASP cc_start: 0.7662 (m-30) cc_final: 0.7345 (m-30) REVERT: J 105 ARG cc_start: 0.7629 (mmt180) cc_final: 0.7329 (mmt90) REVERT: J 187 ARG cc_start: 0.7416 (mtp85) cc_final: 0.7050 (ttp80) REVERT: J 446 ASP cc_start: 0.7767 (m-30) cc_final: 0.7432 (m-30) REVERT: K 91 ARG cc_start: 0.6943 (mmt180) cc_final: 0.6661 (mmp80) REVERT: K 292 MET cc_start: 0.8926 (mtt) cc_final: 0.8685 (mmt) REVERT: K 339 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9165 (tp) REVERT: K 446 ASP cc_start: 0.7734 (m-30) cc_final: 0.7390 (m-30) REVERT: L 446 ASP cc_start: 0.7665 (m-30) cc_final: 0.7348 (m-30) REVERT: M 59 ARG cc_start: 0.8396 (mtp85) cc_final: 0.8172 (mtp85) REVERT: P 59 ARG cc_start: 0.8413 (mtp85) cc_final: 0.8194 (mtp85) REVERT: R 5 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6814 (pm20) REVERT: R 38 THR cc_start: 0.9089 (t) cc_final: 0.8848 (p) REVERT: S 34 GLU cc_start: 0.7778 (tt0) cc_final: 0.7410 (tt0) REVERT: U 5 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: V 34 GLU cc_start: 0.7671 (tt0) cc_final: 0.7441 (tt0) REVERT: X 5 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6789 (pm20) outliers start: 89 outliers final: 74 residues processed: 833 average time/residue: 0.7772 time to fit residues: 985.9364 Evaluate side-chains 842 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 760 time to evaluate : 5.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 410 GLN Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 252 TYR Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 410 GLN Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 384 THR Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 287 ASP Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 287 ASP Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain K residue 427 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain L residue 249 ASN Chi-restraints excluded: chain L residue 384 THR Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain Q residue 5 GLU Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 51 GLU Chi-restraints excluded: chain R residue 5 GLU Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 51 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 33 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 5.9990 chunk 592 optimal weight: 8.9990 chunk 361 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 chunk 411 optimal weight: 0.9990 chunk 621 optimal weight: 4.9990 chunk 572 optimal weight: 0.2980 chunk 495 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 382 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 ASN E 39 ASN E 410 GLN F 39 ASN H 39 ASN I 39 ASN K 39 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 51192 Z= 0.284 Angle : 0.480 6.543 69084 Z= 0.258 Chirality : 0.038 0.159 7236 Planarity : 0.004 0.046 9156 Dihedral : 3.728 14.946 7092 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.97 % Allowed : 14.02 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.65 (0.10), residues: 6300 helix: 2.69 (0.09), residues: 3060 sheet: 0.67 (0.19), residues: 684 loop : -0.83 (0.11), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 94 HIS 0.005 0.001 HIS K 332 PHE 0.024 0.002 PHE E 147 TYR 0.024 0.002 TYR C 96 ARG 0.008 0.001 ARG B 501 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12600 Ramachandran restraints generated. 6300 Oldfield, 0 Emsley, 6300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 761 time to evaluate : 6.143 Fit side-chains REVERT: A 105 ARG cc_start: 0.7755 (mmt180) cc_final: 0.7469 (mmt90) REVERT: A 187 ARG cc_start: 0.7435 (mtp85) cc_final: 0.7026 (ttp80) REVERT: A 252 TYR cc_start: 0.9351 (OUTLIER) cc_final: 0.8466 (m-80) REVERT: B 446 ASP cc_start: 0.7765 (m-30) cc_final: 0.7392 (m-30) REVERT: C 62 ASP cc_start: 0.8508 (t0) cc_final: 0.8130 (t0) REVERT: C 446 ASP cc_start: 0.7664 (m-30) cc_final: 0.7357 (m-30) REVERT: D 105 ARG cc_start: 0.7714 (mmt180) cc_final: 0.7440 (mmt90) REVERT: D 252 TYR cc_start: 0.9339 (OUTLIER) cc_final: 0.8487 (m-80) REVERT: D 446 ASP cc_start: 0.7759 (m-30) cc_final: 0.7409 (m-30) REVERT: E 91 ARG cc_start: 0.6978 (mmt180) cc_final: 0.6669 (mmp80) REVERT: E 446 ASP cc_start: 0.7805 (m-30) cc_final: 0.7527 (m-30) REVERT: F 446 ASP cc_start: 0.7695 (m-30) cc_final: 0.7380 (m-30) REVERT: F 460 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: G 252 TYR cc_start: 0.9177 (OUTLIER) cc_final: 0.8537 (m-80) REVERT: G 446 ASP cc_start: 0.7783 (m-30) cc_final: 0.7448 (m-30) REVERT: H 91 ARG cc_start: 0.7019 (mmt180) cc_final: 0.6721 (mmp80) REVERT: H 446 ASP cc_start: 0.7795 (m-30) cc_final: 0.7438 (m-30) REVERT: I 446 ASP cc_start: 0.7691 (m-30) cc_final: 0.7374 (m-30) REVERT: J 105 ARG cc_start: 0.7745 (mmt180) cc_final: 0.7455 (mmt90) REVERT: J 187 ARG cc_start: 0.7433 (mtp85) cc_final: 0.7029 (ttp80) REVERT: J 446 ASP cc_start: 0.7771 (m-30) cc_final: 0.7446 (m-30) REVERT: K 91 ARG cc_start: 0.7012 (mmt180) cc_final: 0.6703 (mmp80) REVERT: K 292 MET cc_start: 0.9003 (mtt) cc_final: 0.8670 (mmt) REVERT: K 339 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9252 (tp) REVERT: K 446 ASP cc_start: 0.7768 (m-30) cc_final: 0.7415 (m-30) REVERT: L 446 ASP cc_start: 0.7706 (m-30) cc_final: 0.7396 (m-30) REVERT: P 59 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8243 (mtp85) REVERT: R 5 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: R 38 THR cc_start: 0.9087 (t) cc_final: 0.8846 (p) REVERT: U 5 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: X 5 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6937 (pm20) outliers start: 101 outliers final: 85 residues processed: 826 average time/residue: 0.7891 time to fit residues: 998.6863 Evaluate side-chains 853 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 760 time to evaluate : 5.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 410 GLN Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 252 TYR Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain G residue 337 ASP Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 410 GLN Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 384 THR Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 287 ASP Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 287 ASP Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain K residue 427 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain L residue 249 ASN Chi-restraints excluded: chain L residue 271 SER Chi-restraints excluded: chain L residue 348 ASP Chi-restraints excluded: chain L residue 384 THR Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 51 GLU Chi-restraints excluded: chain R residue 5 GLU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 33 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 0.8980 chunk 527 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 456 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 495 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 509 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 ASN E 39 ASN F 39 ASN H 39 ASN I 39 ASN K 39 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.094987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.076601 restraints weight = 72203.066| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 1.54 r_work: 0.2543 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2430 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 51192 Z= 0.316 Angle : 0.488 6.626 69084 Z= 0.263 Chirality : 0.038 0.159 7236 Planarity : 0.004 0.047 9156 Dihedral : 3.815 14.898 7092 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.06 % Allowed : 13.92 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.52 (0.10), residues: 6300 helix: 2.56 (0.09), residues: 3060 sheet: 0.64 (0.19), residues: 684 loop : -0.87 (0.11), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 94 HIS 0.005 0.001 HIS I 332 PHE 0.025 0.002 PHE E 147 TYR 0.024 0.002 TYR C 96 ARG 0.008 0.001 ARG K 501 =============================================================================== Job complete usr+sys time: 15907.81 seconds wall clock time: 285 minutes 28.41 seconds (17128.41 seconds total)