Starting phenix.real_space_refine on Wed Feb 21 19:29:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7luc_23520/02_2024/7luc_23520.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7luc_23520/02_2024/7luc_23520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7luc_23520/02_2024/7luc_23520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7luc_23520/02_2024/7luc_23520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7luc_23520/02_2024/7luc_23520.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7luc_23520/02_2024/7luc_23520.pdb" } resolution = 3.21 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= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10401 atoms to isotropic. 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 111 5.16 5 C 13473 2.51 5 N 3561 2.21 5 O 4143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 66": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B GLU 472": "OE1" <-> "OE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 344": "OD1" <-> "OD2" Residue "C GLU 463": "OE1" <-> "OE2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "G ARG 45": "NH1" <-> "NH2" Residue "G ARG 46": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G GLU 105": "OE1" <-> "OE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "I ARG 45": "NH1" <-> "NH2" Residue "I ARG 46": "NH1" <-> "NH2" Residue "I ARG 77": "NH1" <-> "NH2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 16": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K GLU 105": "OE1" <-> "OE2" Residue "L GLU 16": "OE1" <-> "OE2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "M GLU 105": "OE1" <-> "OE2" Residue "N GLU 16": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "O GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21288 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3477 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 435} Chain breaks: 1 Chain: "B" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3477 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 435} Chain breaks: 1 Chain: "C" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3477 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 435} Chain breaks: 1 Chain: "D" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 925 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "E" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 879 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 925 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "G" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 879 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 925 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "I" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 879 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "J" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 121} Chain: "K" Number of atoms: 820 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 830 Chain: "L" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 121} Chain: "M" Number of atoms: 820 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 830 Chain: "N" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 121} Chain: "O" Number of atoms: 820 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 830 Time building chain proxies: 13.02, per 1000 atoms: 0.61 Number of scatterers: 21288 At special positions: 0 Unit cell: (140.563, 137.344, 152.366, 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 111 16.00 O 4143 8.00 N 3561 7.00 C 13473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 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: 8.20 Conformation dependent library (CDL) restraints added in 4.5 seconds 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 46 sheets defined 20.7% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 73 through 96 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 171 removed outlier: 3.557A pdb=" N LEU A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 203 through 210 Processing helix chain 'A' and resid 216 through 240 removed outlier: 4.397A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.553A pdb=" N LYS A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.662A pdb=" N ASN A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 509 Processing helix chain 'B' and resid 73 through 96 Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 171 removed outlier: 3.558A pdb=" N LEU B 171 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 202 Processing helix chain 'B' and resid 203 through 210 Processing helix chain 'B' and resid 216 through 240 removed outlier: 4.397A pdb=" N VAL B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 267 through 277 removed outlier: 3.552A pdb=" N LYS B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 376 through 384 Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.661A pdb=" N ASN B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 509 Processing helix chain 'C' and resid 73 through 96 Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 removed outlier: 3.558A pdb=" N LEU C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 202 Processing helix chain 'C' and resid 203 through 210 Processing helix chain 'C' and resid 216 through 240 removed outlier: 4.396A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 267 through 277 removed outlier: 3.553A pdb=" N LYS C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 376 through 384 Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.662A pdb=" N ASN C 476 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 509 Processing helix chain 'D' and resid 28 through 31 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.651A pdb=" N THR D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.651A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.651A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 31 removed outlier: 3.831A pdb=" N THR J 30 " --> pdb=" O ASP J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.656A pdb=" N THR J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 31 removed outlier: 3.832A pdb=" N THR L 30 " --> pdb=" O ASP L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 87 removed outlier: 3.657A pdb=" N THR L 87 " --> pdb=" O ALA L 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 31 removed outlier: 3.831A pdb=" N THR N 30 " --> pdb=" O ASP N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.657A pdb=" N THR N 87 " --> pdb=" O ALA N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.690A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 374 removed outlier: 3.599A pdb=" N SER A 348 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN A 345 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 309 removed outlier: 4.178A pdb=" N VAL A 308 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 48 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 11.429A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA A 298 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 407 Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 5.095A pdb=" N ILE A 431 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 426 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 373 through 374 Processing sheet with id=AA8, first strand: chain 'B' and resid 308 through 309 removed outlier: 4.178A pdb=" N VAL B 308 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 48 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 180 removed outlier: 11.429A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA B 298 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB2, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AB3, first strand: chain 'B' and resid 430 through 434 removed outlier: 5.095A pdb=" N ILE B 431 " --> pdb=" O ASN B 426 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN B 426 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 373 through 374 removed outlier: 3.619A pdb=" N SER C 348 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN C 345 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 308 through 309 removed outlier: 4.179A pdb=" N VAL C 308 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 48 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 180 removed outlier: 11.430A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA C 298 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 66 through 67 removed outlier: 4.256A pdb=" N GLU C 66 " --> pdb=" O VAL N 100A" (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL N 100A" --> pdb=" O GLU C 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AB9, first strand: chain 'C' and resid 404 through 407 Processing sheet with id=AC1, first strand: chain 'C' and resid 430 through 434 removed outlier: 5.096A pdb=" N ILE C 431 " --> pdb=" O ASN C 426 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN C 426 " --> pdb=" O ILE C 431 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.589A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.796A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG E 50 " --> pdb=" O HIS E 53 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.590A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 13 removed outlier: 4.796A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG G 50 " --> pdb=" O HIS G 53 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.590A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AD4, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.431A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.928A pdb=" N LEU J 18 " --> pdb=" O TRP J 82 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.689A pdb=" N ILE J 34 " --> pdb=" O MET J 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N MET J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.216A pdb=" N ALA J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL J 96 " --> pdb=" O MET J 100L" (cutoff:3.500A) removed outlier: 6.194A pdb=" N MET J 100L" --> pdb=" O VAL J 96 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.448A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.928A pdb=" N LEU L 18 " --> pdb=" O TRP L 82 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.688A pdb=" N ILE L 34 " --> pdb=" O MET L 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N MET L 50 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP L 36 " --> pdb=" O MET L 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.216A pdb=" N ALA L 102 " --> pdb=" O ARG L 94 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL L 96 " --> pdb=" O MET L 100L" (cutoff:3.500A) removed outlier: 6.194A pdb=" N MET L 100L" --> pdb=" O VAL L 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.532A pdb=" N LEU M 11 " --> pdb=" O LYS M 103 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR M 102 " --> pdb=" O TYR M 86 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU M 33 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N PHE M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.929A pdb=" N LEU N 18 " --> pdb=" O TRP N 82 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.689A pdb=" N ILE N 34 " --> pdb=" O MET N 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N MET N 50 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP N 36 " --> pdb=" O MET N 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.216A pdb=" N ALA N 102 " --> pdb=" O ARG N 94 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL N 96 " --> pdb=" O MET N 100L" (cutoff:3.500A) removed outlier: 6.194A pdb=" N MET N 100L" --> pdb=" O VAL N 96 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.264A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN O 37 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU O 46 " --> pdb=" O GLN O 37 " (cutoff:3.500A) 968 hydrogen bonds defined for protein. 2367 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: 8.26 Time building geometry restraints manager: 8.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 3496 1.26 - 1.40: 5153 1.40 - 1.54: 12807 1.54 - 1.68: 102 1.68 - 1.82: 156 Bond restraints: 21714 Sorted by residual: bond pdb=" C ASN C 345 " pdb=" O ASN C 345 " ideal model delta sigma weight residual 1.235 1.125 0.110 1.12e-02 7.97e+03 9.66e+01 bond pdb=" CA SER A 350 " pdb=" C SER A 350 " ideal model delta sigma weight residual 1.526 1.638 -0.112 1.37e-02 5.33e+03 6.63e+01 bond pdb=" C ALA C 346 " pdb=" O ALA C 346 " ideal model delta sigma weight residual 1.239 1.162 0.077 9.60e-03 1.09e+04 6.41e+01 bond pdb=" CA SER C 350 " pdb=" C SER C 350 " ideal model delta sigma weight residual 1.526 1.634 -0.108 1.37e-02 5.33e+03 6.18e+01 bond pdb=" CA SER A 350 " pdb=" CB SER A 350 " ideal model delta sigma weight residual 1.529 1.418 0.111 1.66e-02 3.63e+03 4.46e+01 ... (remaining 21709 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.37: 580 106.37 - 113.40: 11929 113.40 - 120.43: 7943 120.43 - 127.46: 8826 127.46 - 134.49: 188 Bond angle restraints: 29466 Sorted by residual: angle pdb=" N ALA C 346 " pdb=" CA ALA C 346 " pdb=" C ALA C 346 " ideal model delta sigma weight residual 108.31 122.16 -13.85 1.52e+00 4.33e-01 8.31e+01 angle pdb=" CA PRO B 215 " pdb=" N PRO B 215 " pdb=" CD PRO B 215 " ideal model delta sigma weight residual 112.00 99.34 12.66 1.40e+00 5.10e-01 8.18e+01 angle pdb=" CA PRO C 215 " pdb=" N PRO C 215 " pdb=" CD PRO C 215 " ideal model delta sigma weight residual 112.00 99.34 12.66 1.40e+00 5.10e-01 8.17e+01 angle pdb=" CA PRO A 215 " pdb=" N PRO A 215 " pdb=" CD PRO A 215 " ideal model delta sigma weight residual 112.00 99.37 12.63 1.40e+00 5.10e-01 8.14e+01 angle pdb=" N GLY C 347 " pdb=" CA GLY C 347 " pdb=" C GLY C 347 " ideal model delta sigma weight residual 113.24 122.70 -9.46 1.31e+00 5.83e-01 5.22e+01 ... (remaining 29461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 11524 17.12 - 34.24: 1151 34.24 - 51.37: 314 51.37 - 68.49: 92 68.49 - 85.61: 32 Dihedral angle restraints: 13113 sinusoidal: 5148 harmonic: 7965 Sorted by residual: dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 393 " pdb=" CB CYS B 393 " ideal model delta sinusoidal sigma weight residual 93.00 165.50 -72.50 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 393 " pdb=" CB CYS A 393 " ideal model delta sinusoidal sigma weight residual 93.00 165.48 -72.48 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CB CYS C 382 " pdb=" SG CYS C 382 " pdb=" SG CYS C 393 " pdb=" CB CYS C 393 " ideal model delta sinusoidal sigma weight residual 93.00 165.46 -72.46 1 1.00e+01 1.00e-02 6.71e+01 ... (remaining 13110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 3320 0.116 - 0.232: 60 0.232 - 0.349: 6 0.349 - 0.465: 0 0.465 - 0.581: 1 Chirality restraints: 3387 Sorted by residual: chirality pdb=" CA ALA C 346 " pdb=" N ALA C 346 " pdb=" C ALA C 346 " pdb=" CB ALA C 346 " both_signs ideal model delta sigma weight residual False 2.48 1.90 0.58 2.00e-01 2.50e+01 8.44e+00 chirality pdb=" CA SER A 350 " pdb=" N SER A 350 " pdb=" C SER A 350 " pdb=" CB SER A 350 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ASN C 345 " pdb=" N ASN C 345 " pdb=" C ASN C 345 " pdb=" CB ASN C 345 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 3384 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 344 " 0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" CG ASP C 344 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASP C 344 " 0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP C 344 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 214 " -0.064 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO B 215 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 215 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 215 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 214 " 0.064 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO A 215 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " 0.048 5.00e-02 4.00e+02 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 194 2.53 - 3.12: 15620 3.12 - 3.71: 32616 3.71 - 4.31: 45981 4.31 - 4.90: 77413 Nonbonded interactions: 171824 Sorted by model distance: nonbonded pdb=" CB SER B 348 " pdb=" O LEU B 375 " model vdw 1.937 3.440 nonbonded pdb=" NZ LYS B 209 " pdb=" OD2 ASP M 50 " model vdw 1.942 2.520 nonbonded pdb=" OG1 THR C 311 " pdb=" O ASP C 344 " model vdw 1.960 2.440 nonbonded pdb=" CB SER A 348 " pdb=" O LEU A 375 " model vdw 1.998 3.440 nonbonded pdb=" NZ LYS C 209 " pdb=" OD2 ASP O 50 " model vdw 2.012 2.520 ... (remaining 171819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = (chain 'K' and (resid 1 through 71 or resid 73 through 75 or resid 77 through 10 \ 7)) selection = (chain 'M' and (resid 1 through 71 or resid 73 through 75 or resid 77 through 10 \ 7)) selection = (chain 'O' and (resid 1 through 71 or resid 73 through 75 or resid 77 through 10 \ 7)) } 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 8.890 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 61.370 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 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 : 0.004 0.112 21714 Z= 0.263 Angle : 0.730 13.854 29466 Z= 0.407 Chirality : 0.046 0.581 3387 Planarity : 0.005 0.088 3732 Dihedral : 15.744 85.612 7902 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.51 % Allowed : 14.37 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.15), residues: 2718 helix: -0.68 (0.22), residues: 426 sheet: -0.75 (0.15), residues: 1026 loop : -1.71 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 36 HIS 0.002 0.001 HIS L 32 PHE 0.010 0.001 PHE C 32 TYR 0.011 0.001 TYR I 49 ARG 0.014 0.001 ARG B 429 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 463 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.5781 (OUTLIER) cc_final: 0.5554 (mm-30) REVERT: A 191 LYS cc_start: 0.6661 (mtpt) cc_final: 0.6452 (mtmt) REVERT: A 234 THR cc_start: 0.7902 (m) cc_final: 0.7415 (p) REVERT: B 198 TYR cc_start: 0.8082 (t80) cc_final: 0.7840 (t80) REVERT: C 191 LYS cc_start: 0.6642 (mtpt) cc_final: 0.6337 (mtmt) REVERT: D 59 TYR cc_start: 0.6525 (m-10) cc_final: 0.6255 (m-80) REVERT: F 59 TYR cc_start: 0.6535 (m-10) cc_final: 0.6183 (m-80) REVERT: F 95 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6779 (t0) REVERT: H 59 TYR cc_start: 0.6558 (m-10) cc_final: 0.6239 (m-80) REVERT: H 103 TRP cc_start: 0.6988 (m-10) cc_final: 0.6660 (m-10) outliers start: 85 outliers final: 42 residues processed: 530 average time/residue: 0.3164 time to fit residues: 259.5791 Evaluate side-chains 476 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 432 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain L residue 23 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain O residue 47 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 112 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 80 optimal weight: 0.0030 chunk 127 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN B 383 ASN B 454 ASN B 494 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN H 108 GLN I 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN K 70 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN L 95 GLN M 34 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN O 37 GLN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5982 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21714 Z= 0.220 Angle : 0.609 11.435 29466 Z= 0.313 Chirality : 0.044 0.232 3387 Planarity : 0.004 0.060 3732 Dihedral : 6.554 71.424 3008 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.13 % Allowed : 18.71 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.16), residues: 2718 helix: 0.39 (0.24), residues: 429 sheet: -0.23 (0.16), residues: 984 loop : -1.17 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 341 HIS 0.006 0.001 HIS C 317 PHE 0.042 0.002 PHE A 505 TYR 0.022 0.002 TYR E 87 ARG 0.002 0.000 ARG O 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 447 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.5607 (OUTLIER) cc_final: 0.5325 (mm-30) REVERT: A 234 THR cc_start: 0.8163 (m) cc_final: 0.7700 (p) REVERT: A 331 ASN cc_start: 0.4524 (OUTLIER) cc_final: 0.4290 (p0) REVERT: A 365 VAL cc_start: 0.5282 (OUTLIER) cc_final: 0.4503 (p) REVERT: B 60 GLU cc_start: 0.6093 (mt-10) cc_final: 0.5801 (mt-10) REVERT: B 331 ASN cc_start: 0.4837 (OUTLIER) cc_final: 0.4584 (p0) REVERT: B 361 GLN cc_start: 0.6337 (tm-30) cc_final: 0.5853 (tm-30) REVERT: B 365 VAL cc_start: 0.4966 (OUTLIER) cc_final: 0.4317 (p) REVERT: C 191 LYS cc_start: 0.6637 (mtpt) cc_final: 0.6300 (mtmt) REVERT: C 343 CYS cc_start: 0.4807 (OUTLIER) cc_final: 0.4554 (m) REVERT: D 29 PHE cc_start: 0.6707 (t80) cc_final: 0.6439 (t80) REVERT: D 59 TYR cc_start: 0.6605 (m-10) cc_final: 0.6279 (m-80) REVERT: F 59 TYR cc_start: 0.6579 (m-10) cc_final: 0.6256 (m-80) REVERT: F 95 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.7039 (t0) REVERT: H 59 TYR cc_start: 0.6488 (m-10) cc_final: 0.6181 (m-80) REVERT: H 103 TRP cc_start: 0.7088 (m-10) cc_final: 0.6858 (m-10) outliers start: 100 outliers final: 64 residues processed: 508 average time/residue: 0.3192 time to fit residues: 252.6969 Evaluate side-chains 495 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 424 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 23 LYS Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain O residue 53 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 242 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 216 optimal weight: 0.6980 chunk 240 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 194 optimal weight: 0.0030 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21714 Z= 0.213 Angle : 0.591 11.074 29466 Z= 0.302 Chirality : 0.044 0.192 3387 Planarity : 0.004 0.060 3732 Dihedral : 5.936 60.727 2987 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.67 % Allowed : 21.60 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2718 helix: 0.78 (0.24), residues: 426 sheet: -0.00 (0.17), residues: 987 loop : -0.99 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 341 HIS 0.003 0.001 HIS C 317 PHE 0.041 0.002 PHE A 505 TYR 0.019 0.002 TYR G 49 ARG 0.003 0.000 ARG M 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 441 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 VAL cc_start: 0.5143 (OUTLIER) cc_final: 0.4359 (p) REVERT: B 60 GLU cc_start: 0.6150 (mt-10) cc_final: 0.5871 (mt-10) REVERT: B 361 GLN cc_start: 0.6205 (tm-30) cc_final: 0.5973 (tm-30) REVERT: C 191 LYS cc_start: 0.6655 (mtpt) cc_final: 0.6180 (mtpt) REVERT: C 365 VAL cc_start: 0.5303 (OUTLIER) cc_final: 0.4371 (p) REVERT: D 29 PHE cc_start: 0.6711 (t80) cc_final: 0.6430 (t80) REVERT: D 59 TYR cc_start: 0.6640 (m-10) cc_final: 0.6284 (m-80) REVERT: F 59 TYR cc_start: 0.6587 (m-10) cc_final: 0.6266 (m-80) REVERT: F 95 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.7064 (t0) REVERT: H 59 TYR cc_start: 0.6508 (m-10) cc_final: 0.6203 (m-80) outliers start: 113 outliers final: 78 residues processed: 511 average time/residue: 0.3098 time to fit residues: 245.3136 Evaluate side-chains 497 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 416 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain L residue 23 LYS Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 0.6980 chunk 182 optimal weight: 0.4980 chunk 126 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 243 optimal weight: 0.9990 chunk 258 optimal weight: 0.0470 chunk 127 optimal weight: 0.0770 chunk 231 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 ASN A 383 ASN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 383 ASN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21714 Z= 0.185 Angle : 0.577 10.841 29466 Z= 0.292 Chirality : 0.043 0.171 3387 Planarity : 0.004 0.058 3732 Dihedral : 5.334 57.098 2974 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.29 % Allowed : 21.44 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2718 helix: 1.04 (0.25), residues: 423 sheet: 0.11 (0.17), residues: 984 loop : -0.86 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 341 HIS 0.003 0.001 HIS C 317 PHE 0.040 0.002 PHE A 505 TYR 0.016 0.001 TYR E 49 ARG 0.004 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 412 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 VAL cc_start: 0.5077 (OUTLIER) cc_final: 0.4196 (p) REVERT: B 361 GLN cc_start: 0.6270 (tm-30) cc_final: 0.6013 (tm-30) REVERT: C 85 LYS cc_start: 0.7324 (mtmt) cc_final: 0.7084 (mtpt) REVERT: C 191 LYS cc_start: 0.6620 (mtpt) cc_final: 0.6082 (mtpt) REVERT: C 354 GLN cc_start: 0.6228 (OUTLIER) cc_final: 0.5895 (mm110) REVERT: C 365 VAL cc_start: 0.5335 (OUTLIER) cc_final: 0.4440 (p) REVERT: D 29 PHE cc_start: 0.6750 (t80) cc_final: 0.6420 (t80) REVERT: D 59 TYR cc_start: 0.6650 (m-10) cc_final: 0.6296 (m-80) REVERT: F 59 TYR cc_start: 0.6582 (m-10) cc_final: 0.6256 (m-80) REVERT: H 59 TYR cc_start: 0.6498 (m-10) cc_final: 0.6194 (m-80) outliers start: 128 outliers final: 96 residues processed: 493 average time/residue: 0.3221 time to fit residues: 249.9404 Evaluate side-chains 501 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 402 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 106 optimal weight: 0.0870 chunk 220 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 231 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 224 GLN ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21714 Z= 0.216 Angle : 0.585 10.498 29466 Z= 0.299 Chirality : 0.044 0.162 3387 Planarity : 0.004 0.057 3732 Dihedral : 5.072 57.362 2964 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.25 % Allowed : 22.06 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.16), residues: 2718 helix: 1.15 (0.25), residues: 426 sheet: -0.01 (0.16), residues: 1026 loop : -0.76 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 341 HIS 0.004 0.001 HIS E 53 PHE 0.039 0.002 PHE A 505 TYR 0.018 0.002 TYR G 49 ARG 0.006 0.000 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 415 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 GLN cc_start: 0.5985 (OUTLIER) cc_final: 0.5684 (mm-40) REVERT: B 361 GLN cc_start: 0.6380 (tm-30) cc_final: 0.6137 (tm-30) REVERT: C 191 LYS cc_start: 0.6640 (mtpt) cc_final: 0.6168 (mtpt) REVERT: C 354 GLN cc_start: 0.6264 (OUTLIER) cc_final: 0.5947 (mm110) REVERT: D 29 PHE cc_start: 0.6773 (t80) cc_final: 0.6484 (t80) REVERT: D 59 TYR cc_start: 0.6666 (m-10) cc_final: 0.6307 (m-80) REVERT: F 59 TYR cc_start: 0.6589 (m-10) cc_final: 0.6255 (m-80) REVERT: H 59 TYR cc_start: 0.6503 (m-10) cc_final: 0.6193 (m-80) outliers start: 127 outliers final: 100 residues processed: 496 average time/residue: 0.3211 time to fit residues: 249.8165 Evaluate side-chains 507 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 405 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 3.9990 chunk 232 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 chunk 214 optimal weight: 0.3980 chunk 119 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 HIS ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21714 Z= 0.241 Angle : 0.609 10.056 29466 Z= 0.312 Chirality : 0.044 0.256 3387 Planarity : 0.004 0.056 3732 Dihedral : 5.054 48.453 2961 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.20 % Allowed : 22.55 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.16), residues: 2718 helix: 1.19 (0.25), residues: 423 sheet: 0.15 (0.17), residues: 990 loop : -0.80 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 341 HIS 0.006 0.001 HIS E 53 PHE 0.035 0.002 PHE A 505 TYR 0.020 0.002 TYR E 49 ARG 0.015 0.000 ARG L 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 415 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 VAL cc_start: 0.7915 (m) cc_final: 0.6827 (p) REVERT: A 361 GLN cc_start: 0.6177 (tm-30) cc_final: 0.5975 (tm-30) REVERT: B 289 MET cc_start: 0.7140 (tpt) cc_final: 0.6835 (tpt) REVERT: B 354 GLN cc_start: 0.6317 (OUTLIER) cc_final: 0.5974 (mm-40) REVERT: B 361 GLN cc_start: 0.6438 (tm-30) cc_final: 0.6226 (tm-30) REVERT: C 191 LYS cc_start: 0.6661 (mtpt) cc_final: 0.6100 (mtpt) REVERT: C 354 GLN cc_start: 0.6316 (OUTLIER) cc_final: 0.5989 (mm110) REVERT: D 59 TYR cc_start: 0.6650 (m-10) cc_final: 0.6289 (m-80) REVERT: F 59 TYR cc_start: 0.6579 (m-10) cc_final: 0.6273 (m-80) REVERT: G 17 GLN cc_start: 0.6014 (OUTLIER) cc_final: 0.5625 (mp10) REVERT: H 59 TYR cc_start: 0.6475 (m-10) cc_final: 0.6179 (m-80) outliers start: 126 outliers final: 104 residues processed: 497 average time/residue: 0.3052 time to fit residues: 238.4953 Evaluate side-chains 515 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 408 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 217 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 156 optimal weight: 0.1980 chunk 118 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN A 494 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 HIS ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 ASN L 66 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21714 Z= 0.223 Angle : 0.603 9.973 29466 Z= 0.308 Chirality : 0.044 0.207 3387 Planarity : 0.004 0.056 3732 Dihedral : 5.031 50.826 2959 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.53 % Allowed : 22.64 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2718 helix: 1.25 (0.25), residues: 423 sheet: 0.13 (0.16), residues: 1017 loop : -0.80 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 341 HIS 0.005 0.001 HIS E 53 PHE 0.033 0.002 PHE J 29 TYR 0.023 0.002 TYR B 441 ARG 0.007 0.000 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 413 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 VAL cc_start: 0.8017 (m) cc_final: 0.6937 (p) REVERT: A 361 GLN cc_start: 0.6217 (tm-30) cc_final: 0.5943 (tm-30) REVERT: B 354 GLN cc_start: 0.6279 (OUTLIER) cc_final: 0.5916 (mm-40) REVERT: B 361 GLN cc_start: 0.6464 (tm-30) cc_final: 0.6154 (tm-30) REVERT: C 191 LYS cc_start: 0.6619 (mtpt) cc_final: 0.6264 (mtmt) REVERT: C 354 GLN cc_start: 0.6301 (OUTLIER) cc_final: 0.5962 (mm110) REVERT: D 59 TYR cc_start: 0.6640 (m-10) cc_final: 0.6281 (m-80) REVERT: F 59 TYR cc_start: 0.6562 (m-10) cc_final: 0.6259 (m-80) REVERT: G 17 GLN cc_start: 0.6136 (OUTLIER) cc_final: 0.5719 (mp10) REVERT: H 59 TYR cc_start: 0.6492 (m-10) cc_final: 0.6207 (m-80) outliers start: 134 outliers final: 110 residues processed: 498 average time/residue: 0.3054 time to fit residues: 239.3572 Evaluate side-chains 520 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 407 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 417 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 426 ASN Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 107 THR Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 0.0010 chunk 102 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 175 optimal weight: 0.0670 chunk 127 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 202 optimal weight: 0.0020 overall best weight: 0.3132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN C 94 GLN ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 HIS ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21714 Z= 0.170 Angle : 0.587 9.981 29466 Z= 0.299 Chirality : 0.044 0.188 3387 Planarity : 0.004 0.055 3732 Dihedral : 4.888 50.216 2959 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.46 % Allowed : 23.79 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2718 helix: 1.72 (0.26), residues: 402 sheet: 0.07 (0.16), residues: 1023 loop : -0.68 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 341 HIS 0.004 0.001 HIS E 53 PHE 0.030 0.001 PHE A 505 TYR 0.021 0.001 TYR B 441 ARG 0.006 0.000 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 398 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7874 (mt) REVERT: A 301 VAL cc_start: 0.7989 (m) cc_final: 0.6916 (p) REVERT: A 361 GLN cc_start: 0.6186 (tm-30) cc_final: 0.5928 (tm-30) REVERT: B 264 MET cc_start: 0.6414 (mtp) cc_final: 0.6070 (mtt) REVERT: B 289 MET cc_start: 0.7116 (tpt) cc_final: 0.6822 (tpt) REVERT: C 80 LYS cc_start: 0.7226 (ttpt) cc_final: 0.7025 (ttmt) REVERT: C 191 LYS cc_start: 0.6536 (mtpt) cc_final: 0.6165 (mtmt) REVERT: C 354 GLN cc_start: 0.6196 (OUTLIER) cc_final: 0.5815 (mm110) REVERT: D 59 TYR cc_start: 0.6649 (m-10) cc_final: 0.6289 (m-80) REVERT: F 59 TYR cc_start: 0.6549 (m-10) cc_final: 0.6231 (m-80) REVERT: G 17 GLN cc_start: 0.5928 (OUTLIER) cc_final: 0.5528 (mp10) REVERT: H 59 TYR cc_start: 0.6451 (m-10) cc_final: 0.6182 (m-80) outliers start: 108 outliers final: 93 residues processed: 465 average time/residue: 0.3086 time to fit residues: 225.9691 Evaluate side-chains 487 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 391 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 107 THR Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 0.9980 chunk 246 optimal weight: 0.5980 chunk 224 optimal weight: 0.7980 chunk 239 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 188 optimal weight: 0.2980 chunk 73 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 HIS ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21714 Z= 0.221 Angle : 0.611 9.322 29466 Z= 0.313 Chirality : 0.044 0.199 3387 Planarity : 0.004 0.054 3732 Dihedral : 4.989 53.824 2959 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.67 % Allowed : 23.92 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2718 helix: 1.34 (0.25), residues: 423 sheet: 0.12 (0.16), residues: 1035 loop : -0.76 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 341 HIS 0.005 0.001 HIS E 53 PHE 0.033 0.002 PHE J 29 TYR 0.021 0.002 TYR I 49 ARG 0.007 0.000 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 396 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7854 (mt) REVERT: A 301 VAL cc_start: 0.8004 (m) cc_final: 0.6901 (p) REVERT: A 457 TYR cc_start: 0.6271 (m-80) cc_final: 0.5923 (m-80) REVERT: B 264 MET cc_start: 0.6509 (mtp) cc_final: 0.6117 (mtt) REVERT: B 289 MET cc_start: 0.7154 (tpt) cc_final: 0.6789 (tpt) REVERT: C 191 LYS cc_start: 0.6560 (mtpt) cc_final: 0.5889 (mtpt) REVERT: C 354 GLN cc_start: 0.6227 (OUTLIER) cc_final: 0.5933 (mm-40) REVERT: D 59 TYR cc_start: 0.6605 (m-10) cc_final: 0.6232 (m-80) REVERT: F 59 TYR cc_start: 0.6536 (m-10) cc_final: 0.6231 (m-80) REVERT: G 17 GLN cc_start: 0.6064 (OUTLIER) cc_final: 0.5599 (mp10) REVERT: H 59 TYR cc_start: 0.6508 (m-10) cc_final: 0.6232 (m-80) REVERT: I 51 ILE cc_start: 0.4781 (OUTLIER) cc_final: 0.4452 (mt) outliers start: 113 outliers final: 98 residues processed: 469 average time/residue: 0.3148 time to fit residues: 232.4013 Evaluate side-chains 496 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 394 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 107 THR Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 0.6980 chunk 253 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 266 optimal weight: 0.0030 chunk 244 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 129 optimal weight: 0.0020 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS I 42 HIS ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21714 Z= 0.197 Angle : 0.611 9.277 29466 Z= 0.314 Chirality : 0.044 0.182 3387 Planarity : 0.004 0.054 3732 Dihedral : 4.949 54.134 2957 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.13 % Allowed : 24.95 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2718 helix: 1.63 (0.26), residues: 405 sheet: 0.13 (0.16), residues: 1035 loop : -0.70 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 341 HIS 0.005 0.001 HIS E 53 PHE 0.044 0.002 PHE B 505 TYR 0.020 0.002 TYR I 49 ARG 0.006 0.000 ARG J 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 398 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7846 (mt) REVERT: A 301 VAL cc_start: 0.7993 (m) cc_final: 0.6902 (p) REVERT: A 457 TYR cc_start: 0.6249 (m-80) cc_final: 0.5920 (m-80) REVERT: B 264 MET cc_start: 0.6480 (mtp) cc_final: 0.6128 (mtt) REVERT: B 289 MET cc_start: 0.7118 (tpt) cc_final: 0.6812 (tpt) REVERT: C 30 GLU cc_start: 0.5615 (tm-30) cc_final: 0.5318 (tm-30) REVERT: C 191 LYS cc_start: 0.6560 (mtpt) cc_final: 0.5968 (mtpt) REVERT: C 354 GLN cc_start: 0.6201 (OUTLIER) cc_final: 0.5999 (mm-40) REVERT: D 59 TYR cc_start: 0.6599 (m-10) cc_final: 0.6236 (m-80) REVERT: F 59 TYR cc_start: 0.6523 (m-10) cc_final: 0.6209 (m-80) REVERT: G 17 GLN cc_start: 0.6034 (OUTLIER) cc_final: 0.5567 (mp10) REVERT: H 59 TYR cc_start: 0.6558 (m-10) cc_final: 0.6295 (m-80) outliers start: 100 outliers final: 92 residues processed: 462 average time/residue: 0.3221 time to fit residues: 236.9438 Evaluate side-chains 490 residues out of total 2421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 395 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 107 THR Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 0.9980 chunk 225 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 217 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS G 42 HIS I 42 HIS ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.165067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.148635 restraints weight = 33258.747| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.29 r_work: 0.3863 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21714 Z= 0.215 Angle : 0.621 9.104 29466 Z= 0.319 Chirality : 0.044 0.184 3387 Planarity : 0.004 0.054 3732 Dihedral : 4.971 55.846 2957 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.50 % Allowed : 24.87 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2718 helix: 1.59 (0.26), residues: 405 sheet: 0.13 (0.16), residues: 1035 loop : -0.69 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 341 HIS 0.005 0.001 HIS E 42 PHE 0.054 0.002 PHE A 505 TYR 0.021 0.002 TYR I 49 ARG 0.006 0.000 ARG J 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5588.53 seconds wall clock time: 101 minutes 57.24 seconds (6117.24 seconds total)