Starting phenix.real_space_refine on Sat Feb 24 02:20:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cka_16694/02_2024/8cka_16694.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cka_16694/02_2024/8cka_16694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cka_16694/02_2024/8cka_16694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cka_16694/02_2024/8cka_16694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cka_16694/02_2024/8cka_16694.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cka_16694/02_2024/8cka_16694.pdb" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 48 5.16 5 C 25164 2.51 5 N 7158 2.21 5 O 8400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 243": "OE1" <-> "OE2" Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 552": "OE1" <-> "OE2" Residue "B GLU 604": "OE1" <-> "OE2" Residue "B PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 899": "OD1" <-> "OD2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 552": "OE1" <-> "OE2" Residue "D GLU 604": "OE1" <-> "OE2" Residue "D PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 899": "OD1" <-> "OD2" Residue "E GLU 243": "OE1" <-> "OE2" Residue "E PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 324": "OE1" <-> "OE2" Residue "E PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 552": "OE1" <-> "OE2" Residue "F GLU 604": "OE1" <-> "OE2" Residue "F PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 899": "OD1" <-> "OD2" Residue "G GLU 243": "OE1" <-> "OE2" Residue "G PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 324": "OE1" <-> "OE2" Residue "G PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 552": "OE1" <-> "OE2" Residue "H GLU 604": "OE1" <-> "OE2" Residue "H PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 899": "OD1" <-> "OD2" Residue "I GLU 243": "OE1" <-> "OE2" Residue "I PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 324": "OE1" <-> "OE2" Residue "I PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 552": "OE1" <-> "OE2" Residue "J GLU 604": "OE1" <-> "OE2" Residue "J PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 899": "OD1" <-> "OD2" Residue "K GLU 243": "OE1" <-> "OE2" Residue "K PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 324": "OE1" <-> "OE2" Residue "K PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 552": "OE1" <-> "OE2" Residue "L GLU 604": "OE1" <-> "OE2" Residue "L PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 899": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 40770 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3686 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 21, 'TRANS': 474} Chain: "B" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3109 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3686 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 21, 'TRANS': 474} Chain: "D" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3109 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3686 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 21, 'TRANS': 474} Chain: "F" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3109 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3686 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 21, 'TRANS': 474} Chain: "H" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3109 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3686 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 21, 'TRANS': 474} Chain: "J" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3109 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3686 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 21, 'TRANS': 474} Chain: "L" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3109 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 19.68, per 1000 atoms: 0.48 Number of scatterers: 40770 At special positions: 0 Unit cell: (252.252, 271.908, 126.672, 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 48 16.00 O 8400 8.00 N 7158 7.00 C 25164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 554 " - pdb=" SG CYS B 666 " distance=2.08 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 554 " - pdb=" SG CYS D 666 " distance=2.08 Simple disulfide: pdb=" SG CYS E 168 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 554 " - pdb=" SG CYS F 666 " distance=2.07 Simple disulfide: pdb=" SG CYS G 168 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 554 " - pdb=" SG CYS H 666 " distance=2.08 Simple disulfide: pdb=" SG CYS I 168 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 554 " - pdb=" SG CYS J 666 " distance=2.08 Simple disulfide: pdb=" SG CYS K 168 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 554 " - pdb=" SG CYS L 666 " distance=2.07 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: 14.50 Conformation dependent library (CDL) restraints added in 7.0 seconds 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9852 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 102 sheets defined 7.6% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.729A pdb=" N ASN A 443 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 598 through 600 No H-bonds generated for 'chain 'A' and resid 598 through 600' Processing helix chain 'B' and resid 598 through 600 No H-bonds generated for 'chain 'B' and resid 598 through 600' Processing helix chain 'B' and resid 797 through 800 Processing helix chain 'B' and resid 841 through 854 Processing helix chain 'B' and resid 856 through 861 Processing helix chain 'B' and resid 865 through 875 Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 439 through 443 removed outlier: 3.729A pdb=" N ASN C 443 " --> pdb=" O ALA C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 461 Processing helix chain 'C' and resid 598 through 600 No H-bonds generated for 'chain 'C' and resid 598 through 600' Processing helix chain 'D' and resid 598 through 600 No H-bonds generated for 'chain 'D' and resid 598 through 600' Processing helix chain 'D' and resid 797 through 800 Processing helix chain 'D' and resid 841 through 854 Processing helix chain 'D' and resid 856 through 861 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'E' and resid 234 through 237 Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 439 through 443 removed outlier: 3.729A pdb=" N ASN E 443 " --> pdb=" O ALA E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 461 Processing helix chain 'E' and resid 598 through 600 No H-bonds generated for 'chain 'E' and resid 598 through 600' Processing helix chain 'F' and resid 598 through 600 No H-bonds generated for 'chain 'F' and resid 598 through 600' Processing helix chain 'F' and resid 797 through 800 Processing helix chain 'F' and resid 841 through 854 Processing helix chain 'F' and resid 856 through 861 Processing helix chain 'F' and resid 865 through 875 Processing helix chain 'G' and resid 234 through 237 Processing helix chain 'G' and resid 309 through 311 No H-bonds generated for 'chain 'G' and resid 309 through 311' Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 439 through 443 removed outlier: 3.729A pdb=" N ASN G 443 " --> pdb=" O ALA G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 461 Processing helix chain 'G' and resid 598 through 600 No H-bonds generated for 'chain 'G' and resid 598 through 600' Processing helix chain 'H' and resid 598 through 600 No H-bonds generated for 'chain 'H' and resid 598 through 600' Processing helix chain 'H' and resid 797 through 800 Processing helix chain 'H' and resid 841 through 854 Processing helix chain 'H' and resid 856 through 861 Processing helix chain 'H' and resid 865 through 875 Processing helix chain 'I' and resid 234 through 237 Processing helix chain 'I' and resid 309 through 311 No H-bonds generated for 'chain 'I' and resid 309 through 311' Processing helix chain 'I' and resid 333 through 337 Processing helix chain 'I' and resid 439 through 443 removed outlier: 3.729A pdb=" N ASN I 443 " --> pdb=" O ALA I 440 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 461 Processing helix chain 'I' and resid 598 through 600 No H-bonds generated for 'chain 'I' and resid 598 through 600' Processing helix chain 'J' and resid 598 through 600 No H-bonds generated for 'chain 'J' and resid 598 through 600' Processing helix chain 'J' and resid 797 through 800 Processing helix chain 'J' and resid 841 through 854 Processing helix chain 'J' and resid 856 through 861 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'K' and resid 234 through 237 Processing helix chain 'K' and resid 309 through 311 No H-bonds generated for 'chain 'K' and resid 309 through 311' Processing helix chain 'K' and resid 333 through 337 Processing helix chain 'K' and resid 439 through 443 removed outlier: 3.729A pdb=" N ASN K 443 " --> pdb=" O ALA K 440 " (cutoff:3.500A) Processing helix chain 'K' and resid 450 through 461 Processing helix chain 'K' and resid 598 through 600 No H-bonds generated for 'chain 'K' and resid 598 through 600' Processing helix chain 'L' and resid 598 through 600 No H-bonds generated for 'chain 'L' and resid 598 through 600' Processing helix chain 'L' and resid 797 through 800 Processing helix chain 'L' and resid 841 through 854 Processing helix chain 'L' and resid 856 through 861 Processing helix chain 'L' and resid 865 through 875 Processing sheet with id= 1, first strand: chain 'A' and resid 136 through 140 removed outlier: 5.481A pdb=" N ILE A 138 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 158 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 146 through 148 removed outlier: 6.594A pdb=" N ALA A 147 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 230 through 232 Processing sheet with id= 4, first strand: chain 'A' and resid 252 through 260 removed outlier: 25.580A pdb=" N GLY A 268 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 19.263A pdb=" N TYR A 354 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 14.543A pdb=" N VAL A 270 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE A 272 " --> pdb=" O PRO A 356 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 315 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU A 294 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 313 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 369 through 373 Processing sheet with id= 6, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR A 391 " --> pdb=" O ARG A 525 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR A 391 " --> pdb=" O ARG A 525 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 532 through 533 Processing sheet with id= 9, first strand: chain 'A' and resid 537 through 540 Processing sheet with id= 10, first strand: chain 'A' and resid 554 through 555 removed outlier: 4.439A pdb=" N PHE A 583 " --> pdb=" O ILE A 590 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 532 through 533 Processing sheet with id= 12, first strand: chain 'B' and resid 537 through 540 Processing sheet with id= 13, first strand: chain 'B' and resid 554 through 555 removed outlier: 4.386A pdb=" N PHE B 583 " --> pdb=" O ILE B 590 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 637 through 640 Processing sheet with id= 15, first strand: chain 'B' and resid 648 through 650 removed outlier: 6.296A pdb=" N PHE B 649 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR B 728 " --> pdb=" O TRP B 675 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP B 675 " --> pdb=" O TYR B 728 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG B 730 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU B 673 " --> pdb=" O ARG B 730 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU B 732 " --> pdb=" O THR B 671 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B 671 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 734 " --> pdb=" O TYR B 669 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 698 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP B 675 " --> pdb=" O GLN B 696 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN B 696 " --> pdb=" O TRP B 675 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 764 through 768 Processing sheet with id= 17, first strand: chain 'B' and resid 883 through 888 removed outlier: 6.619A pdb=" N ALA B 836 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER B 888 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 834 " --> pdb=" O SER B 888 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN B 927 " --> pdb=" O ARG B 839 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'C' and resid 136 through 140 removed outlier: 5.481A pdb=" N ILE C 138 " --> pdb=" O THR C 158 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR C 158 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.594A pdb=" N ALA C 147 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'C' and resid 230 through 232 Processing sheet with id= 21, first strand: chain 'C' and resid 252 through 260 removed outlier: 25.580A pdb=" N GLY C 268 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 19.263A pdb=" N TYR C 354 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 14.543A pdb=" N VAL C 270 " --> pdb=" O TYR C 354 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE C 272 " --> pdb=" O PRO C 356 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 315 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU C 294 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 313 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 369 through 373 Processing sheet with id= 23, first strand: chain 'C' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR C 391 " --> pdb=" O ARG C 525 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR C 391 " --> pdb=" O ARG C 525 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 532 through 533 Processing sheet with id= 26, first strand: chain 'C' and resid 537 through 540 Processing sheet with id= 27, first strand: chain 'C' and resid 554 through 555 removed outlier: 4.438A pdb=" N PHE C 583 " --> pdb=" O ILE C 590 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 532 through 533 Processing sheet with id= 29, first strand: chain 'D' and resid 537 through 540 Processing sheet with id= 30, first strand: chain 'D' and resid 554 through 555 removed outlier: 4.386A pdb=" N PHE D 583 " --> pdb=" O ILE D 590 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 637 through 640 Processing sheet with id= 32, first strand: chain 'D' and resid 648 through 650 removed outlier: 6.296A pdb=" N PHE D 649 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR D 728 " --> pdb=" O TRP D 675 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP D 675 " --> pdb=" O TYR D 728 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG D 730 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU D 673 " --> pdb=" O ARG D 730 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU D 732 " --> pdb=" O THR D 671 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR D 671 " --> pdb=" O LEU D 732 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL D 734 " --> pdb=" O TYR D 669 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 698 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP D 675 " --> pdb=" O GLN D 696 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN D 696 " --> pdb=" O TRP D 675 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 764 through 768 Processing sheet with id= 34, first strand: chain 'D' and resid 883 through 888 removed outlier: 6.619A pdb=" N ALA D 836 " --> pdb=" O LEU D 886 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER D 888 " --> pdb=" O VAL D 834 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL D 834 " --> pdb=" O SER D 888 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN D 927 " --> pdb=" O ARG D 839 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'E' and resid 136 through 140 removed outlier: 5.481A pdb=" N ILE E 138 " --> pdb=" O THR E 158 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR E 158 " --> pdb=" O ILE E 138 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.595A pdb=" N ALA E 147 " --> pdb=" O LYS E 219 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'E' and resid 230 through 232 Processing sheet with id= 38, first strand: chain 'E' and resid 252 through 260 removed outlier: 25.579A pdb=" N GLY E 268 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 19.263A pdb=" N TYR E 354 " --> pdb=" O GLY E 268 " (cutoff:3.500A) removed outlier: 14.543A pdb=" N VAL E 270 " --> pdb=" O TYR E 354 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE E 272 " --> pdb=" O PRO E 356 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG E 315 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU E 294 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL E 313 " --> pdb=" O LEU E 294 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'E' and resid 369 through 373 Processing sheet with id= 40, first strand: chain 'E' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR E 391 " --> pdb=" O ARG E 525 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'E' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR E 391 " --> pdb=" O ARG E 525 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'E' and resid 532 through 533 Processing sheet with id= 43, first strand: chain 'E' and resid 537 through 540 Processing sheet with id= 44, first strand: chain 'E' and resid 554 through 555 removed outlier: 4.439A pdb=" N PHE E 583 " --> pdb=" O ILE E 590 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'F' and resid 532 through 533 Processing sheet with id= 46, first strand: chain 'F' and resid 537 through 540 Processing sheet with id= 47, first strand: chain 'F' and resid 554 through 555 removed outlier: 4.386A pdb=" N PHE F 583 " --> pdb=" O ILE F 590 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'F' and resid 637 through 640 Processing sheet with id= 49, first strand: chain 'F' and resid 648 through 650 removed outlier: 6.296A pdb=" N PHE F 649 " --> pdb=" O ASN F 750 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR F 728 " --> pdb=" O TRP F 675 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP F 675 " --> pdb=" O TYR F 728 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG F 730 " --> pdb=" O LEU F 673 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU F 673 " --> pdb=" O ARG F 730 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU F 732 " --> pdb=" O THR F 671 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR F 671 " --> pdb=" O LEU F 732 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL F 734 " --> pdb=" O TYR F 669 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA F 698 " --> pdb=" O LEU F 673 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP F 675 " --> pdb=" O GLN F 696 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN F 696 " --> pdb=" O TRP F 675 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'F' and resid 764 through 768 Processing sheet with id= 51, first strand: chain 'F' and resid 883 through 888 removed outlier: 6.619A pdb=" N ALA F 836 " --> pdb=" O LEU F 886 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER F 888 " --> pdb=" O VAL F 834 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL F 834 " --> pdb=" O SER F 888 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN F 927 " --> pdb=" O ARG F 839 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'G' and resid 136 through 140 removed outlier: 5.481A pdb=" N ILE G 138 " --> pdb=" O THR G 158 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR G 158 " --> pdb=" O ILE G 138 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'G' and resid 146 through 148 removed outlier: 6.594A pdb=" N ALA G 147 " --> pdb=" O LYS G 219 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'G' and resid 230 through 232 Processing sheet with id= 55, first strand: chain 'G' and resid 252 through 260 removed outlier: 25.580A pdb=" N GLY G 268 " --> pdb=" O VAL G 352 " (cutoff:3.500A) removed outlier: 19.263A pdb=" N TYR G 354 " --> pdb=" O GLY G 268 " (cutoff:3.500A) removed outlier: 14.543A pdb=" N VAL G 270 " --> pdb=" O TYR G 354 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE G 272 " --> pdb=" O PRO G 356 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG G 315 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU G 294 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL G 313 " --> pdb=" O LEU G 294 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'G' and resid 369 through 373 Processing sheet with id= 57, first strand: chain 'G' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR G 391 " --> pdb=" O ARG G 525 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'G' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR G 391 " --> pdb=" O ARG G 525 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'G' and resid 532 through 533 Processing sheet with id= 60, first strand: chain 'G' and resid 537 through 540 Processing sheet with id= 61, first strand: chain 'G' and resid 554 through 555 removed outlier: 4.439A pdb=" N PHE G 583 " --> pdb=" O ILE G 590 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'H' and resid 532 through 533 Processing sheet with id= 63, first strand: chain 'H' and resid 537 through 540 Processing sheet with id= 64, first strand: chain 'H' and resid 554 through 555 removed outlier: 4.386A pdb=" N PHE H 583 " --> pdb=" O ILE H 590 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'H' and resid 637 through 640 Processing sheet with id= 66, first strand: chain 'H' and resid 648 through 650 removed outlier: 6.296A pdb=" N PHE H 649 " --> pdb=" O ASN H 750 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR H 728 " --> pdb=" O TRP H 675 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP H 675 " --> pdb=" O TYR H 728 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG H 730 " --> pdb=" O LEU H 673 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU H 673 " --> pdb=" O ARG H 730 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU H 732 " --> pdb=" O THR H 671 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR H 671 " --> pdb=" O LEU H 732 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL H 734 " --> pdb=" O TYR H 669 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA H 698 " --> pdb=" O LEU H 673 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP H 675 " --> pdb=" O GLN H 696 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN H 696 " --> pdb=" O TRP H 675 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'H' and resid 764 through 768 Processing sheet with id= 68, first strand: chain 'H' and resid 883 through 888 removed outlier: 6.619A pdb=" N ALA H 836 " --> pdb=" O LEU H 886 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER H 888 " --> pdb=" O VAL H 834 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL H 834 " --> pdb=" O SER H 888 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN H 927 " --> pdb=" O ARG H 839 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'I' and resid 136 through 140 removed outlier: 5.481A pdb=" N ILE I 138 " --> pdb=" O THR I 158 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR I 158 " --> pdb=" O ILE I 138 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'I' and resid 146 through 148 removed outlier: 6.594A pdb=" N ALA I 147 " --> pdb=" O LYS I 219 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'I' and resid 230 through 232 Processing sheet with id= 72, first strand: chain 'I' and resid 252 through 260 removed outlier: 25.580A pdb=" N GLY I 268 " --> pdb=" O VAL I 352 " (cutoff:3.500A) removed outlier: 19.263A pdb=" N TYR I 354 " --> pdb=" O GLY I 268 " (cutoff:3.500A) removed outlier: 14.543A pdb=" N VAL I 270 " --> pdb=" O TYR I 354 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE I 272 " --> pdb=" O PRO I 356 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG I 315 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU I 294 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL I 313 " --> pdb=" O LEU I 294 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'I' and resid 369 through 373 Processing sheet with id= 74, first strand: chain 'I' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR I 391 " --> pdb=" O ARG I 525 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'I' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR I 391 " --> pdb=" O ARG I 525 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'I' and resid 532 through 533 Processing sheet with id= 77, first strand: chain 'I' and resid 537 through 540 Processing sheet with id= 78, first strand: chain 'I' and resid 554 through 555 removed outlier: 4.438A pdb=" N PHE I 583 " --> pdb=" O ILE I 590 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'J' and resid 532 through 533 Processing sheet with id= 80, first strand: chain 'J' and resid 537 through 540 Processing sheet with id= 81, first strand: chain 'J' and resid 554 through 555 removed outlier: 4.386A pdb=" N PHE J 583 " --> pdb=" O ILE J 590 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'J' and resid 637 through 640 Processing sheet with id= 83, first strand: chain 'J' and resid 648 through 650 removed outlier: 6.296A pdb=" N PHE J 649 " --> pdb=" O ASN J 750 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR J 728 " --> pdb=" O TRP J 675 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP J 675 " --> pdb=" O TYR J 728 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG J 730 " --> pdb=" O LEU J 673 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU J 673 " --> pdb=" O ARG J 730 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU J 732 " --> pdb=" O THR J 671 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR J 671 " --> pdb=" O LEU J 732 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL J 734 " --> pdb=" O TYR J 669 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA J 698 " --> pdb=" O LEU J 673 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP J 675 " --> pdb=" O GLN J 696 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN J 696 " --> pdb=" O TRP J 675 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'J' and resid 764 through 768 Processing sheet with id= 85, first strand: chain 'J' and resid 883 through 888 removed outlier: 6.619A pdb=" N ALA J 836 " --> pdb=" O LEU J 886 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER J 888 " --> pdb=" O VAL J 834 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL J 834 " --> pdb=" O SER J 888 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN J 927 " --> pdb=" O ARG J 839 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'K' and resid 136 through 140 removed outlier: 5.481A pdb=" N ILE K 138 " --> pdb=" O THR K 158 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR K 158 " --> pdb=" O ILE K 138 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'K' and resid 146 through 148 removed outlier: 6.595A pdb=" N ALA K 147 " --> pdb=" O LYS K 219 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'K' and resid 230 through 232 Processing sheet with id= 89, first strand: chain 'K' and resid 252 through 260 removed outlier: 25.579A pdb=" N GLY K 268 " --> pdb=" O VAL K 352 " (cutoff:3.500A) removed outlier: 19.263A pdb=" N TYR K 354 " --> pdb=" O GLY K 268 " (cutoff:3.500A) removed outlier: 14.543A pdb=" N VAL K 270 " --> pdb=" O TYR K 354 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE K 272 " --> pdb=" O PRO K 356 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG K 315 " --> pdb=" O VAL K 292 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU K 294 " --> pdb=" O VAL K 313 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL K 313 " --> pdb=" O LEU K 294 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'K' and resid 369 through 373 Processing sheet with id= 91, first strand: chain 'K' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR K 391 " --> pdb=" O ARG K 525 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'K' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR K 391 " --> pdb=" O ARG K 525 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'K' and resid 532 through 533 Processing sheet with id= 94, first strand: chain 'K' and resid 537 through 540 Processing sheet with id= 95, first strand: chain 'K' and resid 554 through 555 removed outlier: 4.439A pdb=" N PHE K 583 " --> pdb=" O ILE K 590 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'L' and resid 532 through 533 Processing sheet with id= 97, first strand: chain 'L' and resid 537 through 540 Processing sheet with id= 98, first strand: chain 'L' and resid 554 through 555 removed outlier: 4.386A pdb=" N PHE L 583 " --> pdb=" O ILE L 590 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'L' and resid 637 through 640 Processing sheet with id=100, first strand: chain 'L' and resid 648 through 650 removed outlier: 6.296A pdb=" N PHE L 649 " --> pdb=" O ASN L 750 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR L 728 " --> pdb=" O TRP L 675 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP L 675 " --> pdb=" O TYR L 728 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG L 730 " --> pdb=" O LEU L 673 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU L 673 " --> pdb=" O ARG L 730 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU L 732 " --> pdb=" O THR L 671 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR L 671 " --> pdb=" O LEU L 732 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL L 734 " --> pdb=" O TYR L 669 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA L 698 " --> pdb=" O LEU L 673 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP L 675 " --> pdb=" O GLN L 696 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN L 696 " --> pdb=" O TRP L 675 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'L' and resid 764 through 768 Processing sheet with id=102, first strand: chain 'L' and resid 883 through 888 removed outlier: 6.619A pdb=" N ALA L 836 " --> pdb=" O LEU L 886 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER L 888 " --> pdb=" O VAL L 834 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL L 834 " --> pdb=" O SER L 888 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN L 927 " --> pdb=" O ARG L 839 " (cutoff:3.500A) 1356 hydrogen bonds defined for protein. 3384 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: 18.93 Time building geometry restraints manager: 15.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11812 1.34 - 1.46: 11659 1.46 - 1.58: 17923 1.58 - 1.70: 0 1.70 - 1.83: 66 Bond restraints: 41460 Sorted by residual: bond pdb=" C CYS J 666 " pdb=" N GLY J 667 " ideal model delta sigma weight residual 1.325 1.351 -0.026 9.40e-03 1.13e+04 7.50e+00 bond pdb=" C CYS D 666 " pdb=" N GLY D 667 " ideal model delta sigma weight residual 1.325 1.351 -0.026 9.40e-03 1.13e+04 7.50e+00 bond pdb=" C CYS L 666 " pdb=" N GLY L 667 " ideal model delta sigma weight residual 1.325 1.350 -0.025 9.40e-03 1.13e+04 7.24e+00 bond pdb=" C CYS F 666 " pdb=" N GLY F 667 " ideal model delta sigma weight residual 1.325 1.350 -0.025 9.40e-03 1.13e+04 7.24e+00 bond pdb=" C CYS B 666 " pdb=" N GLY B 667 " ideal model delta sigma weight residual 1.325 1.350 -0.025 9.40e-03 1.13e+04 7.17e+00 ... (remaining 41455 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.78: 888 105.78 - 112.97: 21817 112.97 - 120.16: 14633 120.16 - 127.35: 19146 127.35 - 134.53: 126 Bond angle restraints: 56610 Sorted by residual: angle pdb=" C PHE A 428 " pdb=" CA PHE A 428 " pdb=" CB PHE A 428 " ideal model delta sigma weight residual 109.71 101.92 7.79 1.39e+00 5.18e-01 3.14e+01 angle pdb=" C PHE G 428 " pdb=" CA PHE G 428 " pdb=" CB PHE G 428 " ideal model delta sigma weight residual 109.71 101.92 7.79 1.39e+00 5.18e-01 3.14e+01 angle pdb=" C PHE K 428 " pdb=" CA PHE K 428 " pdb=" CB PHE K 428 " ideal model delta sigma weight residual 109.71 101.94 7.77 1.39e+00 5.18e-01 3.12e+01 angle pdb=" C PHE I 428 " pdb=" CA PHE I 428 " pdb=" CB PHE I 428 " ideal model delta sigma weight residual 109.71 101.94 7.77 1.39e+00 5.18e-01 3.12e+01 angle pdb=" C PHE E 428 " pdb=" CA PHE E 428 " pdb=" CB PHE E 428 " ideal model delta sigma weight residual 109.71 101.96 7.75 1.39e+00 5.18e-01 3.11e+01 ... (remaining 56605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 22142 17.67 - 35.34: 1798 35.34 - 53.01: 414 53.01 - 70.68: 78 70.68 - 88.35: 78 Dihedral angle restraints: 24510 sinusoidal: 9030 harmonic: 15480 Sorted by residual: dihedral pdb=" CD ARG H 736 " pdb=" NE ARG H 736 " pdb=" CZ ARG H 736 " pdb=" NH1 ARG H 736 " ideal model delta sinusoidal sigma weight residual 0.00 68.65 -68.65 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CD ARG B 736 " pdb=" NE ARG B 736 " pdb=" CZ ARG B 736 " pdb=" NH1 ARG B 736 " ideal model delta sinusoidal sigma weight residual 0.00 68.65 -68.65 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CD ARG F 736 " pdb=" NE ARG F 736 " pdb=" CZ ARG F 736 " pdb=" NH1 ARG F 736 " ideal model delta sinusoidal sigma weight residual 0.00 68.64 -68.64 1 1.00e+01 1.00e-02 6.10e+01 ... (remaining 24507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3797 0.060 - 0.120: 2476 0.120 - 0.180: 309 0.180 - 0.240: 18 0.240 - 0.300: 6 Chirality restraints: 6606 Sorted by residual: chirality pdb=" CA CYS J 666 " pdb=" N CYS J 666 " pdb=" C CYS J 666 " pdb=" CB CYS J 666 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA CYS D 666 " pdb=" N CYS D 666 " pdb=" C CYS D 666 " pdb=" CB CYS D 666 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA CYS L 666 " pdb=" N CYS L 666 " pdb=" C CYS L 666 " pdb=" CB CYS L 666 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 6603 not shown) Planarity restraints: 7620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 736 " -0.902 9.50e-02 1.11e+02 4.05e-01 1.10e+02 pdb=" NE ARG F 736 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG F 736 " -0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG F 736 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG F 736 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 736 " 0.902 9.50e-02 1.11e+02 4.05e-01 1.10e+02 pdb=" NE ARG L 736 " -0.074 2.00e-02 2.50e+03 pdb=" CZ ARG L 736 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG L 736 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG L 736 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 736 " -0.902 9.50e-02 1.11e+02 4.05e-01 1.10e+02 pdb=" NE ARG B 736 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG B 736 " -0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG B 736 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 736 " -0.004 2.00e-02 2.50e+03 ... (remaining 7617 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 7490 2.78 - 3.31: 38662 3.31 - 3.84: 69262 3.84 - 4.37: 85789 4.37 - 4.90: 143657 Nonbonded interactions: 344860 Sorted by model distance: nonbonded pdb=" O PRO C 415 " pdb=" OG SER C 418 " model vdw 2.250 2.440 nonbonded pdb=" O PRO I 415 " pdb=" OG SER I 418 " model vdw 2.250 2.440 nonbonded pdb=" O PRO E 415 " pdb=" OG SER E 418 " model vdw 2.250 2.440 nonbonded pdb=" O PRO K 415 " pdb=" OG SER K 418 " model vdw 2.250 2.440 nonbonded pdb=" O PRO A 415 " pdb=" OG SER A 418 " model vdw 2.250 2.440 ... (remaining 344855 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } 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: 4.120 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: 0.040 Extract box with map and model: 16.620 Check model and map are aligned: 0.560 Set scattering table: 0.370 Process input model: 102.230 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.270 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:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.007 0.039 41460 Z= 0.484 Angle : 0.948 7.792 56610 Z= 0.615 Chirality : 0.067 0.300 6606 Planarity : 0.018 0.405 7620 Dihedral : 14.995 88.346 14622 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.27 % Allowed : 15.40 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.11), residues: 5460 helix: -0.02 (0.33), residues: 288 sheet: 1.20 (0.11), residues: 1788 loop : -0.25 (0.10), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.006 TRP D 877 HIS 0.009 0.006 HIS L 693 PHE 0.026 0.006 PHE B 900 TYR 0.037 0.005 TYR J 837 ARG 0.055 0.004 ARG L 736 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 214 time to evaluate : 4.847 Fit side-chains REVERT: A 179 GLN cc_start: 0.4788 (tm-30) cc_final: 0.4549 (tm130) REVERT: B 776 MET cc_start: 0.7718 (ptt) cc_final: 0.7439 (ptt) REVERT: D 645 MET cc_start: 0.8039 (mtp) cc_final: 0.7829 (mmm) REVERT: F 947 GLN cc_start: 0.8200 (tp40) cc_final: 0.7958 (mm-40) REVERT: G 179 GLN cc_start: 0.4782 (tm-30) cc_final: 0.4543 (tm130) REVERT: H 776 MET cc_start: 0.7717 (ptt) cc_final: 0.7437 (ptt) REVERT: J 645 MET cc_start: 0.8038 (mtp) cc_final: 0.7829 (mmm) REVERT: L 947 GLN cc_start: 0.8203 (tp40) cc_final: 0.7961 (mm-40) outliers start: 12 outliers final: 0 residues processed: 226 average time/residue: 1.4153 time to fit residues: 399.9910 Evaluate side-chains 146 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 4.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 461 optimal weight: 7.9990 chunk 413 optimal weight: 5.9990 chunk 229 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 279 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 427 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 260 optimal weight: 9.9990 chunk 318 optimal weight: 9.9990 chunk 495 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 499 ASN B 569 ASN B 780 ASN B 846 ASN B 876 ASN C 380 ASN C 422 GLN C 499 ASN D 569 ASN D 780 ASN D 846 ASN D 876 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 499 ASN F 569 ASN F 780 ASN F 846 ASN F 876 ASN G 422 GLN G 499 ASN H 569 ASN H 780 ASN H 846 ASN H 876 ASN I 380 ASN I 422 GLN I 499 ASN J 569 ASN J 780 ASN J 846 ASN J 876 ASN ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 GLN K 499 ASN L 569 ASN L 780 ASN L 846 ASN L 876 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 41460 Z= 0.401 Angle : 0.657 8.524 56610 Z= 0.355 Chirality : 0.050 0.220 6606 Planarity : 0.005 0.047 7620 Dihedral : 5.440 34.377 5898 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.90 % Rotamer: Outliers : 3.32 % Allowed : 13.67 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 5460 helix: -0.63 (0.30), residues: 288 sheet: 1.00 (0.11), residues: 1836 loop : -0.60 (0.10), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP F 675 HIS 0.007 0.004 HIS B 693 PHE 0.026 0.003 PHE H 840 TYR 0.021 0.003 TYR H 837 ARG 0.007 0.001 ARG E 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 144 time to evaluate : 4.141 Fit side-chains REVERT: B 686 THR cc_start: 0.7360 (t) cc_final: 0.7058 (p) REVERT: B 776 MET cc_start: 0.7751 (ptt) cc_final: 0.7499 (ptt) REVERT: C 250 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: D 839 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7612 (ttt180) REVERT: D 890 ASP cc_start: 0.6038 (m-30) cc_final: 0.5196 (m-30) REVERT: F 686 THR cc_start: 0.7644 (t) cc_final: 0.7242 (p) REVERT: F 839 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8114 (ttp-170) REVERT: H 686 THR cc_start: 0.7357 (t) cc_final: 0.7056 (p) REVERT: H 776 MET cc_start: 0.7750 (ptt) cc_final: 0.7498 (ptt) REVERT: I 250 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: J 839 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7610 (ttt180) REVERT: J 890 ASP cc_start: 0.6034 (m-30) cc_final: 0.5193 (m-30) REVERT: L 686 THR cc_start: 0.7643 (t) cc_final: 0.7241 (p) REVERT: L 839 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8112 (ttp-170) outliers start: 146 outliers final: 76 residues processed: 288 average time/residue: 1.3196 time to fit residues: 482.6095 Evaluate side-chains 208 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 126 time to evaluate : 4.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 635 ASP Chi-restraints excluded: chain D residue 686 THR Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 795 THR Chi-restraints excluded: chain F residue 839 ARG Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 471 GLU Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 561 ILE Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 753 ILE Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 795 THR Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 891 THR Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 558 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 635 ASP Chi-restraints excluded: chain J residue 686 THR Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 795 THR Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 422 GLN Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain K residue 597 THR Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 790 VAL Chi-restraints excluded: chain L residue 795 THR Chi-restraints excluded: chain L residue 839 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 275 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 412 optimal weight: 5.9990 chunk 337 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 496 optimal weight: 0.9980 chunk 536 optimal weight: 7.9990 chunk 442 optimal weight: 10.0000 chunk 492 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 398 optimal weight: 8.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 380 ASN A 422 GLN B 598 ASN C 422 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 599 GLN F 598 ASN F 646 GLN F 719 GLN G 305 ASN G 422 GLN H 598 ASN I 422 GLN ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 GLN K 599 GLN L 598 ASN L 646 GLN L 719 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 41460 Z= 0.418 Angle : 0.656 9.952 56610 Z= 0.352 Chirality : 0.050 0.174 6606 Planarity : 0.005 0.053 7620 Dihedral : 5.564 38.022 5898 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.47 % Allowed : 13.62 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.10), residues: 5460 helix: -0.65 (0.29), residues: 288 sheet: 0.92 (0.11), residues: 1836 loop : -0.82 (0.10), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP F 675 HIS 0.008 0.004 HIS H 693 PHE 0.024 0.003 PHE B 840 TYR 0.020 0.003 TYR F 837 ARG 0.007 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 140 time to evaluate : 4.434 Fit side-chains REVERT: A 226 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8523 (mtp180) REVERT: A 291 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: B 776 MET cc_start: 0.7679 (ptt) cc_final: 0.7407 (ptt) REVERT: B 839 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8235 (ttp-170) REVERT: B 890 ASP cc_start: 0.6382 (m-30) cc_final: 0.5877 (m-30) REVERT: D 839 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7626 (ttt180) REVERT: D 890 ASP cc_start: 0.6197 (m-30) cc_final: 0.5521 (m-30) REVERT: D 945 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8664 (t) REVERT: E 554 CYS cc_start: 0.6789 (t) cc_final: 0.6004 (m) REVERT: F 645 MET cc_start: 0.7840 (mtm) cc_final: 0.7631 (mtp) REVERT: F 686 THR cc_start: 0.7731 (t) cc_final: 0.7342 (p) REVERT: F 839 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8187 (ttp-170) REVERT: F 890 ASP cc_start: 0.6674 (m-30) cc_final: 0.6102 (m-30) REVERT: G 226 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8522 (mtp180) REVERT: G 291 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: H 776 MET cc_start: 0.7679 (ptt) cc_final: 0.7408 (ptt) REVERT: H 839 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8234 (ttp-170) REVERT: H 890 ASP cc_start: 0.6384 (m-30) cc_final: 0.5881 (m-30) REVERT: J 839 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7622 (ttt180) REVERT: J 890 ASP cc_start: 0.6192 (m-30) cc_final: 0.5516 (m-30) REVERT: J 945 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8666 (t) REVERT: K 554 CYS cc_start: 0.6783 (t) cc_final: 0.5998 (m) REVERT: L 645 MET cc_start: 0.7843 (mtm) cc_final: 0.7634 (mtp) REVERT: L 686 THR cc_start: 0.7731 (t) cc_final: 0.7342 (p) REVERT: L 839 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8184 (ttp-170) REVERT: L 890 ASP cc_start: 0.6670 (m-30) cc_final: 0.6097 (m-30) outliers start: 153 outliers final: 91 residues processed: 285 average time/residue: 1.2466 time to fit residues: 455.3962 Evaluate side-chains 232 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 129 time to evaluate : 4.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 635 ASP Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 839 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 635 ASP Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain D residue 891 THR Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 795 THR Chi-restraints excluded: chain F residue 839 ARG Chi-restraints excluded: chain F residue 945 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain G residue 305 ASN Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 471 GLU Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 518 SER Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 561 ILE Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 635 ASP Chi-restraints excluded: chain H residue 753 ILE Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 795 THR Chi-restraints excluded: chain H residue 839 ARG Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 891 THR Chi-restraints excluded: chain H residue 945 THR Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 634 THR Chi-restraints excluded: chain J residue 635 ASP Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain J residue 795 THR Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain J residue 891 THR Chi-restraints excluded: chain J residue 945 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 625 THR Chi-restraints excluded: chain L residue 635 ASP Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 790 VAL Chi-restraints excluded: chain L residue 795 THR Chi-restraints excluded: chain L residue 839 ARG Chi-restraints excluded: chain L residue 945 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 490 optimal weight: 7.9990 chunk 373 optimal weight: 0.1980 chunk 257 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 chunk 333 optimal weight: 6.9990 chunk 498 optimal weight: 5.9990 chunk 527 optimal weight: 8.9990 chunk 260 optimal weight: 5.9990 chunk 472 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 422 GLN C 422 GLN E 422 GLN E 599 GLN G 305 ASN G 380 ASN G 422 GLN I 422 GLN ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 GLN K 599 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 41460 Z= 0.278 Angle : 0.571 7.851 56610 Z= 0.308 Chirality : 0.046 0.168 6606 Planarity : 0.004 0.053 7620 Dihedral : 5.304 38.522 5898 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.02 % Allowed : 14.60 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.11), residues: 5460 helix: -0.24 (0.31), residues: 288 sheet: 0.98 (0.11), residues: 1836 loop : -0.77 (0.10), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 675 HIS 0.006 0.003 HIS H 693 PHE 0.018 0.002 PHE B 840 TYR 0.013 0.002 TYR A 502 ARG 0.004 0.001 ARG E 315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 147 time to evaluate : 4.360 Fit side-chains REVERT: B 776 MET cc_start: 0.7628 (ptt) cc_final: 0.7388 (ptt) REVERT: B 839 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8189 (ttp-170) REVERT: B 890 ASP cc_start: 0.6708 (m-30) cc_final: 0.6404 (m-30) REVERT: C 226 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8569 (mtp180) REVERT: D 635 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8097 (m-30) REVERT: D 839 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7549 (ttt180) REVERT: D 890 ASP cc_start: 0.6109 (m-30) cc_final: 0.5472 (m-30) REVERT: E 554 CYS cc_start: 0.6857 (t) cc_final: 0.6100 (m) REVERT: E 555 LEU cc_start: 0.8143 (tt) cc_final: 0.7928 (tt) REVERT: F 645 MET cc_start: 0.7889 (mtm) cc_final: 0.7675 (mtp) REVERT: F 686 THR cc_start: 0.7744 (t) cc_final: 0.7393 (p) REVERT: F 839 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8185 (ttp-170) REVERT: F 890 ASP cc_start: 0.6635 (m-30) cc_final: 0.6171 (m-30) REVERT: H 776 MET cc_start: 0.7630 (ptt) cc_final: 0.7386 (ptt) REVERT: H 839 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8193 (ttp-170) REVERT: H 890 ASP cc_start: 0.6711 (m-30) cc_final: 0.6407 (m-30) REVERT: I 226 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8568 (mtp180) REVERT: J 635 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: J 839 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7547 (ttt180) REVERT: J 890 ASP cc_start: 0.6105 (m-30) cc_final: 0.5471 (m-30) REVERT: K 554 CYS cc_start: 0.6847 (t) cc_final: 0.6091 (m) REVERT: K 555 LEU cc_start: 0.8143 (tt) cc_final: 0.7925 (tt) REVERT: L 645 MET cc_start: 0.7891 (mtm) cc_final: 0.7677 (mtp) REVERT: L 686 THR cc_start: 0.7744 (t) cc_final: 0.7393 (p) REVERT: L 839 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8182 (ttp-170) REVERT: L 890 ASP cc_start: 0.6631 (m-30) cc_final: 0.6229 (m-30) outliers start: 133 outliers final: 89 residues processed: 268 average time/residue: 1.2648 time to fit residues: 432.4086 Evaluate side-chains 231 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 132 time to evaluate : 4.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 839 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 635 ASP Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain D residue 891 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 628 LYS Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 839 ARG Chi-restraints excluded: chain F residue 945 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 471 GLU Chi-restraints excluded: chain G residue 518 SER Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 561 ILE Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 753 ILE Chi-restraints excluded: chain H residue 795 THR Chi-restraints excluded: chain H residue 839 ARG Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 226 ARG Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 558 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 634 THR Chi-restraints excluded: chain J residue 635 ASP Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain J residue 891 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 422 GLN Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain K residue 597 THR Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 625 THR Chi-restraints excluded: chain L residue 628 LYS Chi-restraints excluded: chain L residue 635 ASP Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 790 VAL Chi-restraints excluded: chain L residue 839 ARG Chi-restraints excluded: chain L residue 945 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 439 optimal weight: 9.9990 chunk 299 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 392 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 450 optimal weight: 10.0000 chunk 364 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 269 optimal weight: 9.9990 chunk 473 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 422 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 599 GLN G 305 ASN G 422 GLN ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 GLN ** I 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 GLN K 599 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 41460 Z= 0.603 Angle : 0.754 8.555 56610 Z= 0.407 Chirality : 0.054 0.177 6606 Planarity : 0.006 0.056 7620 Dihedral : 6.013 45.580 5898 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.42 % Favored : 94.54 % Rotamer: Outliers : 4.09 % Allowed : 14.83 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.10), residues: 5460 helix: -1.23 (0.28), residues: 324 sheet: 0.66 (0.11), residues: 1848 loop : -1.21 (0.10), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP L 675 HIS 0.010 0.005 HIS H 693 PHE 0.026 0.004 PHE B 840 TYR 0.024 0.003 TYR F 837 ARG 0.009 0.001 ARG G 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 126 time to evaluate : 4.153 Fit side-chains REVERT: A 448 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6714 (tt0) REVERT: B 686 THR cc_start: 0.7529 (OUTLIER) cc_final: 0.6921 (p) REVERT: B 776 MET cc_start: 0.7708 (ptt) cc_final: 0.7452 (ptt) REVERT: B 860 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8258 (mtp180) REVERT: C 226 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8628 (mtp180) REVERT: D 663 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7000 (t70) REVERT: D 839 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7653 (ttt180) REVERT: D 890 ASP cc_start: 0.6680 (m-30) cc_final: 0.6047 (m-30) REVERT: D 945 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8656 (t) REVERT: E 226 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8470 (mtp180) REVERT: E 554 CYS cc_start: 0.6935 (t) cc_final: 0.6199 (m) REVERT: E 555 LEU cc_start: 0.8186 (tt) cc_final: 0.7978 (tt) REVERT: F 645 MET cc_start: 0.7936 (mtm) cc_final: 0.7718 (mtp) REVERT: F 686 THR cc_start: 0.7805 (t) cc_final: 0.7353 (p) REVERT: F 839 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8266 (ttp-170) REVERT: F 890 ASP cc_start: 0.6845 (m-30) cc_final: 0.6381 (m-30) REVERT: G 448 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6711 (tt0) REVERT: H 686 THR cc_start: 0.7527 (OUTLIER) cc_final: 0.6921 (p) REVERT: H 776 MET cc_start: 0.7709 (ptt) cc_final: 0.7452 (ptt) REVERT: H 860 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8260 (mtp180) REVERT: I 226 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8627 (mtp180) REVERT: J 663 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6999 (t70) REVERT: J 839 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7655 (ttt180) REVERT: J 890 ASP cc_start: 0.6676 (m-30) cc_final: 0.6044 (m-30) REVERT: J 945 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8658 (t) REVERT: K 226 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8471 (mtp180) REVERT: K 554 CYS cc_start: 0.6931 (t) cc_final: 0.6194 (m) REVERT: K 555 LEU cc_start: 0.8186 (tt) cc_final: 0.7974 (tt) REVERT: L 645 MET cc_start: 0.7938 (mtm) cc_final: 0.7719 (mtp) REVERT: L 686 THR cc_start: 0.7806 (t) cc_final: 0.7353 (p) REVERT: L 839 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8265 (ttp-170) REVERT: L 890 ASP cc_start: 0.6839 (m-30) cc_final: 0.6374 (m-30) outliers start: 180 outliers final: 126 residues processed: 286 average time/residue: 1.1889 time to fit residues: 439.8294 Evaluate side-chains 262 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 118 time to evaluate : 4.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 635 ASP Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 635 ASP Chi-restraints excluded: chain D residue 663 ASP Chi-restraints excluded: chain D residue 677 THR Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain D residue 891 THR Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain F residue 533 ILE Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 628 LYS Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 795 THR Chi-restraints excluded: chain F residue 839 ARG Chi-restraints excluded: chain F residue 945 THR Chi-restraints excluded: chain F residue 948 LYS Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain G residue 305 ASN Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 471 GLU Chi-restraints excluded: chain G residue 479 SER Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 518 SER Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 561 ILE Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 606 THR Chi-restraints excluded: chain H residue 625 THR Chi-restraints excluded: chain H residue 635 ASP Chi-restraints excluded: chain H residue 686 THR Chi-restraints excluded: chain H residue 732 LEU Chi-restraints excluded: chain H residue 743 SER Chi-restraints excluded: chain H residue 753 ILE Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 795 THR Chi-restraints excluded: chain H residue 860 ARG Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 945 THR Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 226 ARG Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 518 SER Chi-restraints excluded: chain I residue 534 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 558 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain J residue 532 THR Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 634 THR Chi-restraints excluded: chain J residue 635 ASP Chi-restraints excluded: chain J residue 663 ASP Chi-restraints excluded: chain J residue 677 THR Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 795 THR Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain J residue 891 THR Chi-restraints excluded: chain J residue 945 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 226 ARG Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain L residue 533 ILE Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 625 THR Chi-restraints excluded: chain L residue 628 LYS Chi-restraints excluded: chain L residue 635 ASP Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 790 VAL Chi-restraints excluded: chain L residue 795 THR Chi-restraints excluded: chain L residue 839 ARG Chi-restraints excluded: chain L residue 945 THR Chi-restraints excluded: chain L residue 948 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 177 optimal weight: 5.9990 chunk 475 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 309 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 528 optimal weight: 0.8980 chunk 438 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 277 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN A 422 GLN A 528 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 599 GLN ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 305 ASN G 422 GLN G 528 ASN ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 GLN K 599 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 41460 Z= 0.217 Angle : 0.553 9.557 56610 Z= 0.297 Chirality : 0.045 0.185 6606 Planarity : 0.004 0.053 7620 Dihedral : 5.338 41.147 5898 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.45 % Allowed : 15.96 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.11), residues: 5460 helix: -0.56 (0.29), residues: 324 sheet: 0.89 (0.11), residues: 1848 loop : -0.92 (0.10), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 675 HIS 0.005 0.003 HIS H 693 PHE 0.014 0.002 PHE B 840 TYR 0.012 0.001 TYR E 502 ARG 0.003 0.000 ARG E 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 133 time to evaluate : 4.545 Fit side-chains REVERT: A 448 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6698 (tt0) REVERT: B 776 MET cc_start: 0.7613 (ptt) cc_final: 0.7395 (ptt) REVERT: B 839 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8121 (ttp-170) REVERT: D 635 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8119 (m-30) REVERT: D 839 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7812 (ttt180) REVERT: D 890 ASP cc_start: 0.6435 (m-30) cc_final: 0.5791 (m-30) REVERT: D 945 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8646 (t) REVERT: D 948 LYS cc_start: 0.6141 (OUTLIER) cc_final: 0.5671 (mttp) REVERT: E 554 CYS cc_start: 0.6924 (t) cc_final: 0.6189 (m) REVERT: F 645 MET cc_start: 0.7981 (mtm) cc_final: 0.7765 (mtp) REVERT: F 686 THR cc_start: 0.7796 (t) cc_final: 0.7432 (p) REVERT: F 890 ASP cc_start: 0.6472 (m-30) cc_final: 0.6054 (m-30) REVERT: G 448 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6694 (tt0) REVERT: H 776 MET cc_start: 0.7614 (ptt) cc_final: 0.7396 (ptt) REVERT: H 839 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8125 (ttp-170) REVERT: J 635 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: J 839 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7473 (ttt180) REVERT: J 890 ASP cc_start: 0.6432 (m-30) cc_final: 0.5789 (m-30) REVERT: J 945 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8647 (t) REVERT: J 948 LYS cc_start: 0.6141 (OUTLIER) cc_final: 0.5668 (mttp) REVERT: K 554 CYS cc_start: 0.6921 (t) cc_final: 0.6186 (m) REVERT: L 645 MET cc_start: 0.7980 (mtm) cc_final: 0.7766 (mtp) REVERT: L 686 THR cc_start: 0.7797 (t) cc_final: 0.7421 (p) REVERT: L 890 ASP cc_start: 0.6503 (m-30) cc_final: 0.6116 (m-30) outliers start: 152 outliers final: 98 residues processed: 273 average time/residue: 1.3155 time to fit residues: 456.5511 Evaluate side-chains 234 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 124 time to evaluate : 4.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 635 ASP Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 839 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 635 ASP Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain D residue 891 THR Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain D residue 948 LYS Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 628 LYS Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 795 THR Chi-restraints excluded: chain F residue 945 THR Chi-restraints excluded: chain F residue 948 LYS Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 471 GLU Chi-restraints excluded: chain G residue 479 SER Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain G residue 621 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 606 THR Chi-restraints excluded: chain H residue 635 ASP Chi-restraints excluded: chain H residue 677 THR Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 839 ARG Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 188 ASP Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 518 SER Chi-restraints excluded: chain I residue 534 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 558 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 634 THR Chi-restraints excluded: chain J residue 635 ASP Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain J residue 783 SER Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 795 THR Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain J residue 891 THR Chi-restraints excluded: chain J residue 945 THR Chi-restraints excluded: chain J residue 948 LYS Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 625 THR Chi-restraints excluded: chain L residue 628 LYS Chi-restraints excluded: chain L residue 635 ASP Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 795 THR Chi-restraints excluded: chain L residue 945 THR Chi-restraints excluded: chain L residue 948 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 509 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 300 optimal weight: 0.8980 chunk 385 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 444 optimal weight: 10.0000 chunk 294 optimal weight: 2.9990 chunk 526 optimal weight: 8.9990 chunk 329 optimal weight: 9.9990 chunk 320 optimal weight: 7.9990 chunk 242 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN A 422 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 599 GLN ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 GLN K 599 GLN ** L 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 41460 Z= 0.175 Angle : 0.512 7.363 56610 Z= 0.274 Chirality : 0.044 0.160 6606 Planarity : 0.004 0.051 7620 Dihedral : 4.920 35.594 5898 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.82 % Allowed : 16.62 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.11), residues: 5460 helix: -0.27 (0.30), residues: 324 sheet: 1.03 (0.11), residues: 1854 loop : -0.74 (0.10), residues: 3282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 675 HIS 0.004 0.002 HIS B 693 PHE 0.012 0.002 PHE K 336 TYR 0.009 0.001 TYR G 502 ARG 0.003 0.000 ARG F 553 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 136 time to evaluate : 4.478 Fit side-chains REVERT: A 226 ARG cc_start: 0.8933 (mtm180) cc_final: 0.8707 (mtm180) REVERT: A 448 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6671 (tt0) REVERT: B 776 MET cc_start: 0.7599 (ptt) cc_final: 0.7376 (ptt) REVERT: B 839 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8090 (ttp-170) REVERT: D 890 ASP cc_start: 0.6003 (m-30) cc_final: 0.5347 (m-30) REVERT: D 945 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8678 (t) REVERT: D 948 LYS cc_start: 0.6067 (OUTLIER) cc_final: 0.5527 (mttp) REVERT: E 226 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8425 (mtp85) REVERT: E 251 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8275 (m110) REVERT: E 554 CYS cc_start: 0.6852 (t) cc_final: 0.6054 (m) REVERT: F 686 THR cc_start: 0.7663 (t) cc_final: 0.7328 (p) REVERT: F 890 ASP cc_start: 0.6354 (m-30) cc_final: 0.5834 (m-30) REVERT: G 226 ARG cc_start: 0.8934 (mtm180) cc_final: 0.8707 (mtm180) REVERT: G 448 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6617 (tt0) REVERT: H 776 MET cc_start: 0.7598 (ptt) cc_final: 0.7333 (ptt) REVERT: H 839 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8092 (ttp-170) REVERT: J 890 ASP cc_start: 0.6000 (m-30) cc_final: 0.5344 (m-30) REVERT: J 945 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8679 (t) REVERT: J 948 LYS cc_start: 0.6070 (OUTLIER) cc_final: 0.5526 (mttp) REVERT: K 226 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8425 (mtp85) REVERT: K 251 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8274 (m110) REVERT: K 554 CYS cc_start: 0.6848 (t) cc_final: 0.6050 (m) REVERT: L 686 THR cc_start: 0.7663 (t) cc_final: 0.7330 (p) REVERT: L 890 ASP cc_start: 0.6350 (m-30) cc_final: 0.5827 (m-30) outliers start: 124 outliers final: 90 residues processed: 250 average time/residue: 1.2305 time to fit residues: 396.0162 Evaluate side-chains 226 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 124 time to evaluate : 4.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 635 ASP Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 839 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain D residue 948 LYS Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 628 LYS Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 795 THR Chi-restraints excluded: chain F residue 945 THR Chi-restraints excluded: chain F residue 948 LYS Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 471 GLU Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain G residue 621 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 635 ASP Chi-restraints excluded: chain H residue 677 THR Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 795 THR Chi-restraints excluded: chain H residue 839 ARG Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 945 THR Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 518 SER Chi-restraints excluded: chain I residue 534 THR Chi-restraints excluded: chain I residue 558 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 795 THR Chi-restraints excluded: chain J residue 945 THR Chi-restraints excluded: chain J residue 948 LYS Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 226 ARG Chi-restraints excluded: chain K residue 251 ASN Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 606 THR Chi-restraints excluded: chain L residue 625 THR Chi-restraints excluded: chain L residue 628 LYS Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 795 THR Chi-restraints excluded: chain L residue 945 THR Chi-restraints excluded: chain L residue 948 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 325 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 314 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 334 optimal weight: 4.9990 chunk 358 optimal weight: 9.9990 chunk 260 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 413 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 599 GLN ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 305 ASN G 422 GLN ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 GLN K 599 GLN L 646 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 41460 Z= 0.405 Angle : 0.639 7.778 56610 Z= 0.344 Chirality : 0.049 0.168 6606 Planarity : 0.005 0.055 7620 Dihedral : 5.542 40.469 5898 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.41 % Allowed : 15.99 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.11), residues: 5460 helix: -0.66 (0.29), residues: 324 sheet: 0.83 (0.11), residues: 1848 loop : -0.98 (0.10), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 675 HIS 0.007 0.004 HIS B 693 PHE 0.024 0.003 PHE B 840 TYR 0.018 0.002 TYR G 502 ARG 0.006 0.001 ARG G 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 131 time to evaluate : 4.826 Fit side-chains REVERT: A 448 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6601 (tt0) REVERT: A 554 CYS cc_start: 0.7446 (t) cc_final: 0.6625 (m) REVERT: B 776 MET cc_start: 0.7622 (ptt) cc_final: 0.7382 (ptt) REVERT: B 839 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8173 (ttp80) REVERT: B 860 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8293 (mtp180) REVERT: D 635 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8152 (m-30) REVERT: D 839 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7598 (ttt180) REVERT: D 890 ASP cc_start: 0.6431 (m-30) cc_final: 0.5772 (m-30) REVERT: D 945 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8638 (t) REVERT: D 948 LYS cc_start: 0.6170 (OUTLIER) cc_final: 0.5700 (mttp) REVERT: E 226 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8425 (mtp85) REVERT: E 554 CYS cc_start: 0.7012 (t) cc_final: 0.6241 (m) REVERT: F 686 THR cc_start: 0.7751 (t) cc_final: 0.7396 (p) REVERT: F 890 ASP cc_start: 0.6775 (m-30) cc_final: 0.6381 (m-30) REVERT: G 448 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6593 (tt0) REVERT: G 554 CYS cc_start: 0.7446 (t) cc_final: 0.6626 (m) REVERT: H 776 MET cc_start: 0.7620 (ptt) cc_final: 0.7380 (ptt) REVERT: H 839 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8156 (ttp80) REVERT: H 860 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8246 (mtp180) REVERT: J 635 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8151 (m-30) REVERT: J 839 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7590 (ttt180) REVERT: J 890 ASP cc_start: 0.6430 (m-30) cc_final: 0.5771 (m-30) REVERT: J 945 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8637 (t) REVERT: J 948 LYS cc_start: 0.6166 (OUTLIER) cc_final: 0.5695 (mttp) REVERT: K 226 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8426 (mtp85) REVERT: K 554 CYS cc_start: 0.7011 (t) cc_final: 0.6239 (m) REVERT: L 686 THR cc_start: 0.7775 (t) cc_final: 0.7392 (p) REVERT: L 890 ASP cc_start: 0.6772 (m-30) cc_final: 0.6378 (m-30) outliers start: 150 outliers final: 119 residues processed: 273 average time/residue: 1.2688 time to fit residues: 443.6106 Evaluate side-chains 263 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 128 time to evaluate : 4.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 635 ASP Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 839 ARG Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 635 ASP Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain D residue 948 LYS Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 628 LYS Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 795 THR Chi-restraints excluded: chain F residue 945 THR Chi-restraints excluded: chain F residue 948 LYS Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 305 ASN Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 471 GLU Chi-restraints excluded: chain G residue 479 SER Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 518 SER Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain G residue 621 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 635 ASP Chi-restraints excluded: chain H residue 677 THR Chi-restraints excluded: chain H residue 753 ILE Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 795 THR Chi-restraints excluded: chain H residue 839 ARG Chi-restraints excluded: chain H residue 860 ARG Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 945 THR Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 518 SER Chi-restraints excluded: chain I residue 534 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 558 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain J residue 532 THR Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 635 ASP Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain J residue 783 SER Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 795 THR Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain J residue 945 THR Chi-restraints excluded: chain J residue 948 LYS Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 226 ARG Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 625 THR Chi-restraints excluded: chain L residue 628 LYS Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 790 VAL Chi-restraints excluded: chain L residue 795 THR Chi-restraints excluded: chain L residue 945 THR Chi-restraints excluded: chain L residue 948 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 478 optimal weight: 0.8980 chunk 504 optimal weight: 7.9990 chunk 459 optimal weight: 50.0000 chunk 490 optimal weight: 8.9990 chunk 295 optimal weight: 5.9990 chunk 213 optimal weight: 9.9990 chunk 385 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 443 optimal weight: 8.9990 chunk 463 optimal weight: 40.0000 chunk 488 optimal weight: 1.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 599 GLN F 646 GLN ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 GLN K 599 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 41460 Z= 0.297 Angle : 0.584 7.567 56610 Z= 0.314 Chirality : 0.047 0.166 6606 Planarity : 0.004 0.052 7620 Dihedral : 5.389 39.364 5898 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.13 % Allowed : 16.19 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.11), residues: 5460 helix: -0.57 (0.29), residues: 324 sheet: 0.85 (0.11), residues: 1848 loop : -0.93 (0.10), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 675 HIS 0.006 0.003 HIS B 693 PHE 0.019 0.002 PHE H 840 TYR 0.014 0.002 TYR E 502 ARG 0.005 0.000 ARG E 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 130 time to evaluate : 4.961 Fit side-chains REVERT: A 448 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6677 (tt0) REVERT: A 554 CYS cc_start: 0.7449 (t) cc_final: 0.6674 (m) REVERT: B 776 MET cc_start: 0.7614 (ptt) cc_final: 0.7384 (ptt) REVERT: B 839 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8164 (ttp-170) REVERT: D 839 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7715 (ttt180) REVERT: D 890 ASP cc_start: 0.6418 (m-30) cc_final: 0.5776 (m-30) REVERT: D 945 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8626 (t) REVERT: D 948 LYS cc_start: 0.6173 (OUTLIER) cc_final: 0.5680 (mttp) REVERT: E 134 PHE cc_start: 0.4582 (p90) cc_final: 0.3955 (p90) REVERT: E 226 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8427 (mtp85) REVERT: E 554 CYS cc_start: 0.7006 (t) cc_final: 0.6233 (m) REVERT: F 686 THR cc_start: 0.7753 (t) cc_final: 0.7420 (p) REVERT: F 890 ASP cc_start: 0.6801 (m-30) cc_final: 0.6390 (m-30) REVERT: G 448 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6672 (tt0) REVERT: G 554 CYS cc_start: 0.7453 (t) cc_final: 0.6676 (m) REVERT: H 776 MET cc_start: 0.7615 (ptt) cc_final: 0.7384 (ptt) REVERT: H 839 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8172 (ttp-170) REVERT: J 839 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7747 (ttt180) REVERT: J 890 ASP cc_start: 0.6416 (m-30) cc_final: 0.5774 (m-30) REVERT: J 945 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8626 (t) REVERT: J 948 LYS cc_start: 0.6171 (OUTLIER) cc_final: 0.5674 (mttp) REVERT: K 134 PHE cc_start: 0.4586 (p90) cc_final: 0.3921 (p90) REVERT: K 226 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8426 (mtp85) REVERT: K 554 CYS cc_start: 0.7002 (t) cc_final: 0.6226 (m) REVERT: L 686 THR cc_start: 0.7756 (t) cc_final: 0.7420 (p) REVERT: L 890 ASP cc_start: 0.6798 (m-30) cc_final: 0.6410 (m-30) outliers start: 138 outliers final: 120 residues processed: 260 average time/residue: 1.2836 time to fit residues: 426.8963 Evaluate side-chains 260 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 128 time to evaluate : 4.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 635 ASP Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 839 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain D residue 948 LYS Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 628 LYS Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 795 THR Chi-restraints excluded: chain F residue 945 THR Chi-restraints excluded: chain F residue 948 LYS Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 471 GLU Chi-restraints excluded: chain G residue 479 SER Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 518 SER Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 625 THR Chi-restraints excluded: chain H residue 635 ASP Chi-restraints excluded: chain H residue 677 THR Chi-restraints excluded: chain H residue 753 ILE Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 795 THR Chi-restraints excluded: chain H residue 839 ARG Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 945 THR Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 188 ASP Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 518 SER Chi-restraints excluded: chain I residue 534 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 558 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain J residue 783 SER Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 795 THR Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain J residue 945 THR Chi-restraints excluded: chain J residue 948 LYS Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 226 ARG Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 625 THR Chi-restraints excluded: chain L residue 628 LYS Chi-restraints excluded: chain L residue 635 ASP Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 790 VAL Chi-restraints excluded: chain L residue 795 THR Chi-restraints excluded: chain L residue 945 THR Chi-restraints excluded: chain L residue 948 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 322 optimal weight: 6.9990 chunk 518 optimal weight: 4.9990 chunk 316 optimal weight: 9.9990 chunk 246 optimal weight: 8.9990 chunk 360 optimal weight: 2.9990 chunk 543 optimal weight: 9.9990 chunk 500 optimal weight: 10.0000 chunk 433 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 334 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 599 GLN ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 GLN K 599 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 41460 Z= 0.345 Angle : 0.605 7.656 56610 Z= 0.325 Chirality : 0.047 0.166 6606 Planarity : 0.005 0.051 7620 Dihedral : 5.447 39.616 5898 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.32 % Allowed : 16.10 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.11), residues: 5460 helix: -0.65 (0.29), residues: 324 sheet: 0.80 (0.11), residues: 1848 loop : -0.98 (0.10), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 675 HIS 0.007 0.003 HIS H 693 PHE 0.021 0.003 PHE B 840 TYR 0.015 0.002 TYR E 502 ARG 0.005 0.001 ARG A 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 129 time to evaluate : 4.632 Fit side-chains REVERT: A 448 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6608 (tt0) REVERT: A 554 CYS cc_start: 0.7443 (t) cc_final: 0.6671 (m) REVERT: B 776 MET cc_start: 0.7619 (ptt) cc_final: 0.7386 (ptt) REVERT: B 839 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8189 (ttp-170) REVERT: D 839 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7794 (ttt180) REVERT: D 890 ASP cc_start: 0.6433 (m-30) cc_final: 0.5788 (m-30) REVERT: D 945 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8628 (t) REVERT: D 948 LYS cc_start: 0.6185 (OUTLIER) cc_final: 0.5675 (mttp) REVERT: E 134 PHE cc_start: 0.4577 (p90) cc_final: 0.3950 (p90) REVERT: E 226 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8437 (mtp85) REVERT: E 554 CYS cc_start: 0.7015 (t) cc_final: 0.6247 (m) REVERT: F 686 THR cc_start: 0.7775 (t) cc_final: 0.7408 (p) REVERT: F 890 ASP cc_start: 0.6814 (m-30) cc_final: 0.6403 (m-30) REVERT: G 448 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6601 (tt0) REVERT: G 554 CYS cc_start: 0.7447 (t) cc_final: 0.6674 (m) REVERT: H 776 MET cc_start: 0.7619 (ptt) cc_final: 0.7387 (ptt) REVERT: H 839 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8122 (ttp80) REVERT: J 839 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7808 (ttt180) REVERT: J 890 ASP cc_start: 0.6430 (m-30) cc_final: 0.5787 (m-30) REVERT: J 945 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8637 (t) REVERT: J 948 LYS cc_start: 0.6185 (OUTLIER) cc_final: 0.5671 (mttp) REVERT: K 134 PHE cc_start: 0.4576 (p90) cc_final: 0.3962 (p90) REVERT: K 226 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8437 (mtp85) REVERT: K 554 CYS cc_start: 0.7012 (t) cc_final: 0.6243 (m) REVERT: L 686 THR cc_start: 0.7776 (t) cc_final: 0.7408 (p) REVERT: L 890 ASP cc_start: 0.6810 (m-30) cc_final: 0.6399 (m-30) outliers start: 146 outliers final: 123 residues processed: 267 average time/residue: 1.2381 time to fit residues: 426.2819 Evaluate side-chains 263 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 128 time to evaluate : 4.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 635 ASP Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 839 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain D residue 948 LYS Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 628 LYS Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 795 THR Chi-restraints excluded: chain F residue 945 THR Chi-restraints excluded: chain F residue 948 LYS Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 471 GLU Chi-restraints excluded: chain G residue 479 SER Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 518 SER Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 625 THR Chi-restraints excluded: chain H residue 635 ASP Chi-restraints excluded: chain H residue 677 THR Chi-restraints excluded: chain H residue 753 ILE Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 795 THR Chi-restraints excluded: chain H residue 839 ARG Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 945 THR Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 188 ASP Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 518 SER Chi-restraints excluded: chain I residue 534 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 558 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 634 THR Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain J residue 783 SER Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 795 THR Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain J residue 945 THR Chi-restraints excluded: chain J residue 948 LYS Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 226 ARG Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 625 THR Chi-restraints excluded: chain L residue 628 LYS Chi-restraints excluded: chain L residue 635 ASP Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 790 VAL Chi-restraints excluded: chain L residue 795 THR Chi-restraints excluded: chain L residue 945 THR Chi-restraints excluded: chain L residue 948 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 344 optimal weight: 2.9990 chunk 461 optimal weight: 50.0000 chunk 132 optimal weight: 2.9990 chunk 399 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 433 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 445 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 599 GLN ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 GLN K 599 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.114023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.088949 restraints weight = 67367.866| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.82 r_work: 0.3316 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 41460 Z= 0.319 Angle : 0.594 7.625 56610 Z= 0.318 Chirality : 0.047 0.167 6606 Planarity : 0.004 0.051 7620 Dihedral : 5.427 39.447 5898 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.38 % Allowed : 16.03 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.11), residues: 5460 helix: -0.61 (0.29), residues: 324 sheet: 0.81 (0.11), residues: 1848 loop : -0.96 (0.10), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 675 HIS 0.006 0.003 HIS H 693 PHE 0.020 0.002 PHE H 840 TYR 0.015 0.002 TYR E 502 ARG 0.005 0.001 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11644.35 seconds wall clock time: 209 minutes 46.93 seconds (12586.93 seconds total)