Starting phenix.real_space_refine on Mon Mar 25 14:29:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u65_26360/03_2024/7u65_26360.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u65_26360/03_2024/7u65_26360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u65_26360/03_2024/7u65_26360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u65_26360/03_2024/7u65_26360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u65_26360/03_2024/7u65_26360.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u65_26360/03_2024/7u65_26360.pdb" } resolution = 2.8 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= 0.005 sd= 0.051 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 22812 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 120 5.16 5 C 17154 2.51 5 N 4626 2.21 5 O 4716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 239": "OE1" <-> "OE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ASP 354": "OD1" <-> "OD2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ASP 354": "OD1" <-> "OD2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 239": "OE1" <-> "OE2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C ASP 354": "OD1" <-> "OD2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ASP 354": "OD1" <-> "OD2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 239": "OE1" <-> "OE2" Residue "E GLU 265": "OE1" <-> "OE2" Residue "E ARG 337": "NH1" <-> "NH2" Residue "E ASP 354": "OD1" <-> "OD2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 239": "OE1" <-> "OE2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F ARG 337": "NH1" <-> "NH2" Residue "F ASP 354": "OD1" <-> "OD2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "I GLU 63": "OE1" <-> "OE2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "K GLU 63": "OE1" <-> "OE2" Residue "L GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26616 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 21, 'TRANS': 459} Chain breaks: 5 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLN%COO:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 16, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 144 Chain: "G" Number of atoms: 620 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 83, 615 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 82} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 Conformer: "B" Number of residues, atoms: 83, 615 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 82} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 bond proxies already assigned to first conformer: 623 Chain: "B" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 21, 'TRANS': 459} Chain breaks: 5 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLN%COO:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 16, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 144 Chain: "C" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 21, 'TRANS': 459} Chain breaks: 5 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLN%COO:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 16, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 144 Chain: "D" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 21, 'TRANS': 459} Chain breaks: 5 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLN%COO:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 16, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 144 Chain: "E" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 21, 'TRANS': 459} Chain breaks: 5 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLN%COO:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 16, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 144 Chain: "F" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 21, 'TRANS': 459} Chain breaks: 5 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLN%COO:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 16, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 144 Chain: "H" Number of atoms: 620 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 83, 615 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 82} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 Conformer: "B" Number of residues, atoms: 83, 615 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 82} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 bond proxies already assigned to first conformer: 623 Chain: "I" Number of atoms: 620 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 83, 615 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 82} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 Conformer: "B" Number of residues, atoms: 83, 615 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 82} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 bond proxies already assigned to first conformer: 623 Chain: "J" Number of atoms: 620 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 83, 615 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 82} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 Conformer: "B" Number of residues, atoms: 83, 615 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 82} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 bond proxies already assigned to first conformer: 623 Chain: "K" Number of atoms: 620 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 83, 615 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 82} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 Conformer: "B" Number of residues, atoms: 83, 615 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 82} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 bond proxies already assigned to first conformer: 623 Chain: "L" Number of atoms: 620 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 83, 615 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 82} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 Conformer: "B" Number of residues, atoms: 83, 615 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 82} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 bond proxies already assigned to first conformer: 623 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ATHR G 36 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR G 36 " occ=0.50 residue: pdb=" N ATHR H 36 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR H 36 " occ=0.50 residue: pdb=" N ATHR I 36 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR I 36 " occ=0.50 residue: pdb=" N ATHR J 36 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR J 36 " occ=0.50 residue: pdb=" N ATHR K 36 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR K 36 " occ=0.50 residue: pdb=" N ATHR L 36 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR L 36 " occ=0.50 Time building chain proxies: 14.59, per 1000 atoms: 0.55 Number of scatterers: 26616 At special positions: 0 Unit cell: (131.412, 138.868, 135.14, 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 120 16.00 O 4716 8.00 N 4626 7.00 C 17154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.66 Conformation dependent library (CDL) restraints added in 5.5 seconds 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6528 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 12 sheets defined 66.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 24 through 41 removed outlier: 3.559A pdb=" N ASN A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.700A pdb=" N ARG A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 91 removed outlier: 3.509A pdb=" N HIS A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 125 through 141 Processing helix chain 'A' and resid 142 through 145 Processing helix chain 'A' and resid 167 through 180 removed outlier: 3.869A pdb=" N GLU A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 239 through 250 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.556A pdb=" N SER A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 277 " --> pdb=" O CYS A 273 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.620A pdb=" N SER A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 355 removed outlier: 4.155A pdb=" N VAL A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 339 " --> pdb=" O TYR A 335 " (cutoff:3.500A) Proline residue: A 346 - end of helix Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.615A pdb=" N ASP A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 415 removed outlier: 3.506A pdb=" N GLU A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 421 through 431 removed outlier: 3.639A pdb=" N LYS A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 446 Processing helix chain 'A' and resid 448 through 461 removed outlier: 3.539A pdb=" N ARG A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 487 Processing helix chain 'A' and resid 489 through 501 Processing helix chain 'G' and resid 5 through 22 Processing helix chain 'G' and resid 62 through 82 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 24 through 41 removed outlier: 3.560A pdb=" N ASN B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.699A pdb=" N ARG B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 91 removed outlier: 3.509A pdb=" N HIS B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 125 through 141 Processing helix chain 'B' and resid 142 through 145 Processing helix chain 'B' and resid 167 through 180 removed outlier: 3.869A pdb=" N GLU B 171 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 195 Processing helix chain 'B' and resid 202 through 208 Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 239 through 250 Processing helix chain 'B' and resid 260 through 283 removed outlier: 3.556A pdb=" N SER B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 277 " --> pdb=" O CYS B 273 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 299 Processing helix chain 'B' and resid 309 through 319 removed outlier: 3.619A pdb=" N SER B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 355 removed outlier: 4.155A pdb=" N VAL B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN B 339 " --> pdb=" O TYR B 335 " (cutoff:3.500A) Proline residue: B 346 - end of helix Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 373 through 390 removed outlier: 3.616A pdb=" N ASP B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 415 removed outlier: 3.506A pdb=" N GLU B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 421 through 431 removed outlier: 3.640A pdb=" N LYS B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 446 Processing helix chain 'B' and resid 448 through 461 removed outlier: 3.539A pdb=" N ARG B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 487 Processing helix chain 'B' and resid 489 through 501 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 24 through 41 removed outlier: 3.559A pdb=" N ASN C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.700A pdb=" N ARG C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 91 removed outlier: 3.510A pdb=" N HIS C 69 " --> pdb=" O THR C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 125 through 141 Processing helix chain 'C' and resid 142 through 145 Processing helix chain 'C' and resid 167 through 180 removed outlier: 3.869A pdb=" N GLU C 171 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU C 172 " --> pdb=" O PRO C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 239 through 250 Processing helix chain 'C' and resid 260 through 283 removed outlier: 3.556A pdb=" N SER C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR C 272 " --> pdb=" O ASP C 268 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 277 " --> pdb=" O CYS C 273 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 299 Processing helix chain 'C' and resid 309 through 319 removed outlier: 3.620A pdb=" N SER C 319 " --> pdb=" O ALA C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 355 removed outlier: 4.155A pdb=" N VAL C 338 " --> pdb=" O MET C 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Proline residue: C 346 - end of helix Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 373 through 390 removed outlier: 3.615A pdb=" N ASP C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 415 removed outlier: 3.506A pdb=" N GLU C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 421 through 431 removed outlier: 3.638A pdb=" N LYS C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 446 Processing helix chain 'C' and resid 448 through 461 removed outlier: 3.539A pdb=" N ARG C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 461 " --> pdb=" O GLU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 487 Processing helix chain 'C' and resid 489 through 501 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 24 through 41 removed outlier: 3.559A pdb=" N ASN D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 removed outlier: 3.699A pdb=" N ARG D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 91 removed outlier: 3.510A pdb=" N HIS D 69 " --> pdb=" O THR D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 Processing helix chain 'D' and resid 125 through 141 Processing helix chain 'D' and resid 142 through 145 Processing helix chain 'D' and resid 167 through 180 removed outlier: 3.868A pdb=" N GLU D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU D 172 " --> pdb=" O PRO D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 195 Processing helix chain 'D' and resid 202 through 208 Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 239 through 250 Processing helix chain 'D' and resid 260 through 283 removed outlier: 3.555A pdb=" N SER D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASP D 276 " --> pdb=" O TYR D 272 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D 277 " --> pdb=" O CYS D 273 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 299 Processing helix chain 'D' and resid 309 through 319 removed outlier: 3.620A pdb=" N SER D 319 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 355 removed outlier: 4.155A pdb=" N VAL D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) Proline residue: D 346 - end of helix Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 373 through 390 removed outlier: 3.616A pdb=" N ASP D 377 " --> pdb=" O SER D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 415 removed outlier: 3.506A pdb=" N GLU D 397 " --> pdb=" O HIS D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 421 through 431 removed outlier: 3.639A pdb=" N LYS D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 446 Processing helix chain 'D' and resid 448 through 461 removed outlier: 3.539A pdb=" N ARG D 452 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 487 Processing helix chain 'D' and resid 489 through 501 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.559A pdb=" N ASN E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 removed outlier: 3.699A pdb=" N ARG E 46 " --> pdb=" O SER E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 91 removed outlier: 3.509A pdb=" N HIS E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 116 Processing helix chain 'E' and resid 125 through 141 Processing helix chain 'E' and resid 142 through 145 Processing helix chain 'E' and resid 167 through 180 removed outlier: 3.869A pdb=" N GLU E 171 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU E 172 " --> pdb=" O PRO E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 195 Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 236 through 238 No H-bonds generated for 'chain 'E' and resid 236 through 238' Processing helix chain 'E' and resid 239 through 250 Processing helix chain 'E' and resid 260 through 283 removed outlier: 3.556A pdb=" N SER E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR E 272 " --> pdb=" O ASP E 268 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS E 273 " --> pdb=" O ASP E 269 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP E 276 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU E 277 " --> pdb=" O CYS E 273 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 299 Processing helix chain 'E' and resid 309 through 319 removed outlier: 3.619A pdb=" N SER E 319 " --> pdb=" O ALA E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 355 removed outlier: 4.155A pdb=" N VAL E 338 " --> pdb=" O MET E 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN E 339 " --> pdb=" O TYR E 335 " (cutoff:3.500A) Proline residue: E 346 - end of helix Processing helix chain 'E' and resid 355 through 362 Processing helix chain 'E' and resid 373 through 390 removed outlier: 3.615A pdb=" N ASP E 377 " --> pdb=" O SER E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 415 removed outlier: 3.506A pdb=" N GLU E 397 " --> pdb=" O HIS E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 419 Processing helix chain 'E' and resid 421 through 431 removed outlier: 3.638A pdb=" N LYS E 431 " --> pdb=" O GLU E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 446 Processing helix chain 'E' and resid 448 through 461 removed outlier: 3.540A pdb=" N ARG E 452 " --> pdb=" O SER E 448 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 487 Processing helix chain 'E' and resid 489 through 501 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 24 through 41 removed outlier: 3.558A pdb=" N ASN F 41 " --> pdb=" O GLY F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.699A pdb=" N ARG F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 91 removed outlier: 3.510A pdb=" N HIS F 69 " --> pdb=" O THR F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 116 Processing helix chain 'F' and resid 125 through 141 Processing helix chain 'F' and resid 142 through 145 Processing helix chain 'F' and resid 167 through 180 removed outlier: 3.869A pdb=" N GLU F 171 " --> pdb=" O GLU F 167 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU F 172 " --> pdb=" O PRO F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 195 Processing helix chain 'F' and resid 202 through 208 Processing helix chain 'F' and resid 236 through 238 No H-bonds generated for 'chain 'F' and resid 236 through 238' Processing helix chain 'F' and resid 239 through 250 Processing helix chain 'F' and resid 260 through 283 removed outlier: 3.555A pdb=" N SER F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR F 272 " --> pdb=" O ASP F 268 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS F 273 " --> pdb=" O ASP F 269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL F 274 " --> pdb=" O ILE F 270 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP F 276 " --> pdb=" O TYR F 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU F 277 " --> pdb=" O CYS F 273 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 Processing helix chain 'F' and resid 309 through 319 removed outlier: 3.620A pdb=" N SER F 319 " --> pdb=" O ALA F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 355 removed outlier: 4.155A pdb=" N VAL F 338 " --> pdb=" O MET F 334 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN F 339 " --> pdb=" O TYR F 335 " (cutoff:3.500A) Proline residue: F 346 - end of helix Processing helix chain 'F' and resid 355 through 362 Processing helix chain 'F' and resid 373 through 390 removed outlier: 3.615A pdb=" N ASP F 377 " --> pdb=" O SER F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 415 removed outlier: 3.505A pdb=" N GLU F 397 " --> pdb=" O HIS F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 419 Processing helix chain 'F' and resid 421 through 431 removed outlier: 3.639A pdb=" N LYS F 431 " --> pdb=" O GLU F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 446 Processing helix chain 'F' and resid 448 through 461 removed outlier: 3.540A pdb=" N ARG F 452 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS F 461 " --> pdb=" O GLU F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 487 Processing helix chain 'F' and resid 489 through 501 Processing helix chain 'H' and resid 5 through 22 Processing helix chain 'H' and resid 62 through 82 Processing helix chain 'I' and resid 5 through 22 Processing helix chain 'I' and resid 62 through 82 Processing helix chain 'J' and resid 5 through 22 Processing helix chain 'J' and resid 62 through 82 Processing helix chain 'K' and resid 5 through 22 Processing helix chain 'K' and resid 62 through 82 Processing helix chain 'L' and resid 5 through 22 Processing helix chain 'L' and resid 62 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 215 removed outlier: 6.561A pdb=" N ARG A 214 " --> pdb=" O GLY A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'G' and resid 25 through 33 Processing sheet with id=AA3, first strand: chain 'B' and resid 214 through 215 removed outlier: 6.561A pdb=" N ARG B 214 " --> pdb=" O GLY B 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 214 through 215 removed outlier: 6.562A pdb=" N ARG C 214 " --> pdb=" O GLY C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 214 through 215 removed outlier: 6.561A pdb=" N ARG D 214 " --> pdb=" O GLY D 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 214 through 215 removed outlier: 6.561A pdb=" N ARG E 214 " --> pdb=" O GLY E 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 214 through 215 removed outlier: 6.561A pdb=" N ARG F 214 " --> pdb=" O GLY F 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 25 through 33 Processing sheet with id=AA9, first strand: chain 'I' and resid 25 through 33 Processing sheet with id=AB1, first strand: chain 'J' and resid 25 through 33 Processing sheet with id=AB2, first strand: chain 'K' and resid 25 through 33 Processing sheet with id=AB3, first strand: chain 'L' and resid 25 through 33 1584 hydrogen bonds defined for protein. 4644 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: 7.75 Time building geometry restraints manager: 10.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4315 1.32 - 1.44: 7738 1.44 - 1.56: 15019 1.56 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 27264 Sorted by residual: bond pdb=" C ARG C 498 " pdb=" O ARG C 498 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.26e-02 6.30e+03 1.20e+01 bond pdb=" C ARG F 498 " pdb=" O ARG F 498 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.26e-02 6.30e+03 1.20e+01 bond pdb=" C ARG A 498 " pdb=" O ARG A 498 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.26e-02 6.30e+03 1.19e+01 bond pdb=" C ARG B 498 " pdb=" O ARG B 498 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.26e-02 6.30e+03 1.18e+01 bond pdb=" C ARG E 498 " pdb=" O ARG E 498 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.26e-02 6.30e+03 1.16e+01 ... (remaining 27259 not shown) Histogram of bond angle deviations from ideal: 100.64 - 107.32: 965 107.32 - 114.00: 15112 114.00 - 120.69: 11676 120.69 - 127.37: 8955 127.37 - 134.05: 354 Bond angle restraints: 37062 Sorted by residual: angle pdb=" C VAL C 429 " pdb=" CA VAL C 429 " pdb=" CB VAL C 429 " ideal model delta sigma weight residual 112.22 105.83 6.39 1.38e+00 5.25e-01 2.14e+01 angle pdb=" C VAL B 429 " pdb=" CA VAL B 429 " pdb=" CB VAL B 429 " ideal model delta sigma weight residual 112.22 105.84 6.38 1.38e+00 5.25e-01 2.14e+01 angle pdb=" C VAL A 429 " pdb=" CA VAL A 429 " pdb=" CB VAL A 429 " ideal model delta sigma weight residual 112.22 105.86 6.36 1.38e+00 5.25e-01 2.12e+01 angle pdb=" C VAL D 429 " pdb=" CA VAL D 429 " pdb=" CB VAL D 429 " ideal model delta sigma weight residual 112.22 105.86 6.36 1.38e+00 5.25e-01 2.12e+01 angle pdb=" C VAL E 429 " pdb=" CA VAL E 429 " pdb=" CB VAL E 429 " ideal model delta sigma weight residual 112.22 105.87 6.35 1.38e+00 5.25e-01 2.12e+01 ... (remaining 37057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 14736 16.82 - 33.65: 1143 33.65 - 50.47: 195 50.47 - 67.29: 42 67.29 - 84.11: 18 Dihedral angle restraints: 16134 sinusoidal: 6096 harmonic: 10038 Sorted by residual: dihedral pdb=" CA CYS E 273 " pdb=" C CYS E 273 " pdb=" N VAL E 274 " pdb=" CA VAL E 274 " ideal model delta harmonic sigma weight residual 180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA CYS C 273 " pdb=" C CYS C 273 " pdb=" N VAL C 274 " pdb=" CA VAL C 274 " ideal model delta harmonic sigma weight residual -180.00 -153.94 -26.06 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA CYS F 273 " pdb=" C CYS F 273 " pdb=" N VAL F 274 " pdb=" CA VAL F 274 " ideal model delta harmonic sigma weight residual -180.00 -153.95 -26.05 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 16131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3841 0.077 - 0.154: 245 0.154 - 0.231: 20 0.231 - 0.308: 11 0.308 - 0.385: 17 Chirality restraints: 4134 Sorted by residual: chirality pdb=" CA PHE E 127 " pdb=" N PHE E 127 " pdb=" C PHE E 127 " pdb=" CB PHE E 127 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA PHE F 127 " pdb=" N PHE F 127 " pdb=" C PHE F 127 " pdb=" CB PHE F 127 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA PHE B 127 " pdb=" N PHE B 127 " pdb=" C PHE B 127 " pdb=" CB PHE B 127 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 4131 not shown) Planarity restraints: 4716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 148 " -0.050 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO C 149 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 148 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO A 149 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 148 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO F 149 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO F 149 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 149 " 0.041 5.00e-02 4.00e+02 ... (remaining 4713 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7465 2.82 - 3.34: 24186 3.34 - 3.86: 41801 3.86 - 4.38: 46972 4.38 - 4.90: 85366 Nonbonded interactions: 205790 Sorted by model distance: nonbonded pdb=" OD1 ASN A 41 " pdb=" OE2 GLU B 72 " model vdw 2.297 3.040 nonbonded pdb=" OE2 GLU E 72 " pdb=" OD1 ASN F 41 " model vdw 2.302 3.040 nonbonded pdb=" OE2 GLU C 72 " pdb=" OD1 ASN D 41 " model vdw 2.307 3.040 nonbonded pdb=" OD1 ASN C 41 " pdb=" OE2 GLU D 72 " model vdw 2.322 3.040 nonbonded pdb=" OD1 ASN E 41 " pdb=" OE2 GLU F 72 " model vdw 2.324 3.040 ... (remaining 205785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 3 through 35 or resid 37 through 85)) selection = (chain 'H' and (resid 3 through 35 or resid 37 through 85)) selection = (chain 'I' and (resid 3 through 35 or resid 37 through 85)) selection = (chain 'J' and (resid 3 through 35 or resid 37 through 85)) selection = (chain 'K' and (resid 3 through 35 or resid 37 through 85)) selection = (chain 'L' and (resid 3 through 35 or resid 37 through 85)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.020 Extract box with map and model: 4.040 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 66.510 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 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 : 0.005 0.064 27264 Z= 0.308 Angle : 0.648 8.092 37062 Z= 0.400 Chirality : 0.048 0.385 4134 Planarity : 0.006 0.076 4716 Dihedral : 12.920 84.114 9606 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.46 % Allowed : 0.80 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.15), residues: 3318 helix: 1.68 (0.12), residues: 1998 sheet: 1.40 (0.44), residues: 156 loop : -0.90 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 217 HIS 0.004 0.001 HIS E 69 PHE 0.027 0.002 PHE B 127 TYR 0.012 0.001 TYR E 79 ARG 0.006 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 634 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7456 (m-30) cc_final: 0.7253 (m-30) REVERT: A 498 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7620 (mtm180) REVERT: B 217 TRP cc_start: 0.8620 (p-90) cc_final: 0.8207 (p90) REVERT: B 251 ASN cc_start: 0.8015 (m-40) cc_final: 0.7799 (m110) REVERT: B 440 GLU cc_start: 0.6817 (mp0) cc_final: 0.6572 (mp0) REVERT: B 491 LEU cc_start: 0.8152 (mt) cc_final: 0.7943 (mm) REVERT: B 498 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7278 (mtm180) REVERT: C 137 ARG cc_start: 0.7998 (ttm110) cc_final: 0.7792 (ttp-110) REVERT: C 217 TRP cc_start: 0.8772 (p-90) cc_final: 0.8266 (p90) REVERT: C 421 SER cc_start: 0.8384 (m) cc_final: 0.8088 (p) REVERT: C 422 LEU cc_start: 0.8503 (tp) cc_final: 0.8272 (tp) REVERT: C 469 PHE cc_start: 0.7712 (t80) cc_final: 0.7393 (t80) REVERT: C 486 SER cc_start: 0.8365 (t) cc_final: 0.8110 (p) REVERT: D 192 LEU cc_start: 0.8154 (tp) cc_final: 0.7911 (tt) REVERT: D 197 MET cc_start: 0.7708 (mmm) cc_final: 0.7461 (mmm) REVERT: D 217 TRP cc_start: 0.8708 (p-90) cc_final: 0.8345 (p90) REVERT: D 237 LEU cc_start: 0.8581 (tp) cc_final: 0.8353 (tt) REVERT: D 251 ASN cc_start: 0.8195 (m-40) cc_final: 0.7965 (m-40) REVERT: D 268 ASP cc_start: 0.6992 (t0) cc_final: 0.6662 (t0) REVERT: D 337 ARG cc_start: 0.5540 (mtt-85) cc_final: 0.5301 (mtt-85) REVERT: D 421 SER cc_start: 0.8321 (m) cc_final: 0.8087 (p) REVERT: D 469 PHE cc_start: 0.7631 (t80) cc_final: 0.7362 (t80) REVERT: E 71 MET cc_start: 0.7465 (mtp) cc_final: 0.7249 (mtp) REVERT: E 121 ASN cc_start: 0.8210 (m110) cc_final: 0.7989 (m-40) REVERT: E 154 ARG cc_start: 0.8246 (mtp180) cc_final: 0.8027 (mtm-85) REVERT: E 217 TRP cc_start: 0.8602 (p-90) cc_final: 0.8289 (p90) REVERT: E 230 MET cc_start: 0.8284 (mtp) cc_final: 0.8047 (mtp) REVERT: E 440 GLU cc_start: 0.6765 (mp0) cc_final: 0.6533 (mp0) REVERT: E 446 LYS cc_start: 0.8128 (tppp) cc_final: 0.7761 (tppp) REVERT: E 491 LEU cc_start: 0.8137 (mt) cc_final: 0.7363 (mm) REVERT: E 495 ASP cc_start: 0.6894 (m-30) cc_final: 0.6610 (m-30) REVERT: F 10 ILE cc_start: 0.8399 (mt) cc_final: 0.8141 (mp) REVERT: F 134 ASP cc_start: 0.7392 (m-30) cc_final: 0.7150 (m-30) REVERT: I 71 THR cc_start: 0.8017 (m) cc_final: 0.7796 (m) outliers start: 12 outliers final: 0 residues processed: 644 average time/residue: 1.6330 time to fit residues: 1185.6551 Evaluate side-chains 607 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 607 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 136 optimal weight: 0.0870 chunk 263 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 305 optimal weight: 7.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN A 342 ASN B 41 ASN B 53 GLN B 342 ASN B 365 ASN C 11 ASN C 41 ASN C 49 GLN C 53 GLN C 342 ASN C 365 ASN D 41 ASN D 53 GLN E 11 ASN E 41 ASN E 53 GLN E 350 GLN E 365 ASN F 11 ASN F 41 ASN F 49 GLN F 53 GLN F 342 ASN I 75 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27264 Z= 0.218 Angle : 0.517 6.324 37062 Z= 0.279 Chirality : 0.038 0.163 4134 Planarity : 0.005 0.060 4716 Dihedral : 3.768 16.555 3732 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.49 % Allowed : 7.91 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.15), residues: 3318 helix: 2.08 (0.11), residues: 2136 sheet: 1.49 (0.45), residues: 168 loop : -0.63 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 262 HIS 0.004 0.001 HIS F 126 PHE 0.017 0.002 PHE B 127 TYR 0.018 0.001 TYR D 292 ARG 0.005 0.000 ARG D 498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 601 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7455 (m-30) cc_final: 0.7163 (m-30) REVERT: A 365 ASN cc_start: 0.8369 (t0) cc_final: 0.8079 (t0) REVERT: A 415 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6643 (ttp80) REVERT: A 498 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7516 (mtm180) REVERT: B 53 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.6838 (tm130) REVERT: B 55 PHE cc_start: 0.8390 (m-80) cc_final: 0.8093 (m-80) REVERT: B 217 TRP cc_start: 0.8651 (p-90) cc_final: 0.8308 (p90) REVERT: B 251 ASN cc_start: 0.8036 (m-40) cc_final: 0.7777 (m110) REVERT: B 354 ASP cc_start: 0.6603 (t0) cc_final: 0.6363 (t0) REVERT: B 440 GLU cc_start: 0.6867 (mp0) cc_final: 0.6616 (mp0) REVERT: B 491 LEU cc_start: 0.8057 (mt) cc_final: 0.7847 (mm) REVERT: B 498 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7565 (mtm180) REVERT: C 38 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7782 (mtt90) REVERT: C 137 ARG cc_start: 0.8023 (ttm110) cc_final: 0.7763 (ttp-110) REVERT: C 459 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8121 (t) REVERT: C 469 PHE cc_start: 0.7679 (t80) cc_final: 0.7398 (t80) REVERT: C 498 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.6927 (mtm-85) REVERT: D 217 TRP cc_start: 0.8692 (p-90) cc_final: 0.8356 (p90) REVERT: D 415 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6900 (ttp80) REVERT: D 421 SER cc_start: 0.8451 (m) cc_final: 0.8196 (p) REVERT: D 469 PHE cc_start: 0.7613 (t80) cc_final: 0.7339 (t80) REVERT: D 498 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.6949 (mtm-85) REVERT: E 148 GLN cc_start: 0.7670 (pm20) cc_final: 0.7382 (pm20) REVERT: E 175 LYS cc_start: 0.8264 (mtmt) cc_final: 0.8063 (mtpt) REVERT: E 217 TRP cc_start: 0.8613 (p-90) cc_final: 0.8376 (p90) REVERT: E 440 GLU cc_start: 0.6796 (mp0) cc_final: 0.6557 (mp0) REVERT: E 446 LYS cc_start: 0.8098 (tppp) cc_final: 0.7834 (tppp) REVERT: E 491 LEU cc_start: 0.8073 (mt) cc_final: 0.7411 (mm) REVERT: E 495 ASP cc_start: 0.6969 (m-30) cc_final: 0.6611 (m-30) REVERT: F 134 ASP cc_start: 0.7429 (m-30) cc_final: 0.7112 (m-30) REVERT: F 286 PHE cc_start: 0.8159 (p90) cc_final: 0.7907 (p90) REVERT: F 415 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6699 (ttp80) REVERT: F 498 ARG cc_start: 0.7479 (mtm180) cc_final: 0.7137 (mtm180) REVERT: H 4 LEU cc_start: 0.8520 (tp) cc_final: 0.8309 (tp) REVERT: I 71 THR cc_start: 0.8106 (m) cc_final: 0.7865 (m) REVERT: K 69 MET cc_start: 0.7700 (mtp) cc_final: 0.7471 (mtm) outliers start: 39 outliers final: 24 residues processed: 607 average time/residue: 1.6505 time to fit residues: 1127.9564 Evaluate side-chains 623 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 593 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 464 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 305 optimal weight: 7.9990 chunk 330 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 303 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN A 342 ASN B 41 ASN B 53 GLN B 186 ASN B 342 ASN C 11 ASN C 41 ASN C 49 GLN C 53 GLN C 121 ASN C 126 HIS D 49 GLN D 53 GLN E 11 ASN E 41 ASN E 53 GLN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS F 342 ASN I 75 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.063 27264 Z= 0.625 Angle : 0.701 8.481 37062 Z= 0.374 Chirality : 0.050 0.235 4134 Planarity : 0.006 0.062 4716 Dihedral : 4.278 16.340 3732 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.52 % Allowed : 9.02 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.15), residues: 3318 helix: 1.59 (0.11), residues: 2142 sheet: 2.01 (0.47), residues: 162 loop : -0.83 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 262 HIS 0.008 0.002 HIS A 69 PHE 0.029 0.003 PHE A 106 TYR 0.020 0.003 TYR D 272 ARG 0.007 0.001 ARG C 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 631 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 ASN cc_start: 0.8404 (t0) cc_final: 0.8084 (t0) REVERT: A 415 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6928 (ttp80) REVERT: A 483 ASP cc_start: 0.7349 (m-30) cc_final: 0.7123 (m-30) REVERT: A 498 ARG cc_start: 0.7859 (mtm180) cc_final: 0.7564 (mtm180) REVERT: B 175 LYS cc_start: 0.8239 (mtmm) cc_final: 0.7966 (mtpt) REVERT: B 217 TRP cc_start: 0.8631 (p-90) cc_final: 0.8310 (p90) REVERT: B 232 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7877 (mtpm) REVERT: B 440 GLU cc_start: 0.6895 (mp0) cc_final: 0.6643 (mp0) REVERT: C 119 ILE cc_start: 0.7884 (tt) cc_final: 0.7681 (pt) REVERT: D 137 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7451 (ttp-170) REVERT: D 217 TRP cc_start: 0.8776 (p-90) cc_final: 0.8345 (p90) REVERT: D 415 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7225 (ttp80) REVERT: E 86 SER cc_start: 0.8435 (t) cc_final: 0.8194 (p) REVERT: E 148 GLN cc_start: 0.7664 (pm20) cc_final: 0.7212 (pm20) REVERT: E 175 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7882 (mtpt) REVERT: E 186 ASN cc_start: 0.7951 (m-40) cc_final: 0.7738 (m-40) REVERT: E 217 TRP cc_start: 0.8629 (p-90) cc_final: 0.8392 (p90) REVERT: E 440 GLU cc_start: 0.6843 (mp0) cc_final: 0.6613 (mp0) REVERT: E 446 LYS cc_start: 0.8180 (tppp) cc_final: 0.7746 (tppp) REVERT: F 10 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8138 (mp) REVERT: F 415 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6880 (ttp80) REVERT: H 4 LEU cc_start: 0.8604 (tp) cc_final: 0.8403 (tp) outliers start: 66 outliers final: 33 residues processed: 650 average time/residue: 1.6776 time to fit residues: 1226.2746 Evaluate side-chains 671 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 632 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 TRP Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 464 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.7980 chunk 229 optimal weight: 0.6980 chunk 158 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 205 optimal weight: 0.0060 chunk 306 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 290 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN B 41 ASN B 53 GLN B 342 ASN B 350 GLN C 11 ASN C 49 GLN C 53 GLN D 49 GLN D 53 GLN E 41 ASN E 53 GLN E 342 ASN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS F 342 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 27264 Z= 0.154 Angle : 0.456 5.938 37062 Z= 0.247 Chirality : 0.036 0.153 4134 Planarity : 0.004 0.050 4716 Dihedral : 3.760 15.810 3732 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.91 % Allowed : 11.12 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.15), residues: 3318 helix: 2.18 (0.11), residues: 2136 sheet: 2.30 (0.47), residues: 162 loop : -0.62 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 217 HIS 0.004 0.001 HIS F 126 PHE 0.014 0.001 PHE A 106 TYR 0.015 0.001 TYR D 292 ARG 0.008 0.000 ARG E 398 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 598 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7438 (m-30) cc_final: 0.7144 (m-30) REVERT: A 139 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.7030 (tpp-160) REVERT: A 232 LYS cc_start: 0.8256 (mtpm) cc_final: 0.8027 (mtpt) REVERT: A 365 ASN cc_start: 0.8388 (t0) cc_final: 0.8070 (t0) REVERT: A 415 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6506 (ttp80) REVERT: A 498 ARG cc_start: 0.7773 (mtm180) cc_final: 0.7449 (mtm180) REVERT: A 501 MET cc_start: 0.8135 (mmm) cc_final: 0.7932 (tpt) REVERT: B 175 LYS cc_start: 0.8352 (mtmm) cc_final: 0.8150 (mtmm) REVERT: B 217 TRP cc_start: 0.8593 (p-90) cc_final: 0.8306 (p90) REVERT: B 440 GLU cc_start: 0.6874 (mp0) cc_final: 0.6597 (mp0) REVERT: B 495 ASP cc_start: 0.7015 (m-30) cc_final: 0.6665 (m-30) REVERT: C 38 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7674 (mtt180) REVERT: C 459 VAL cc_start: 0.8283 (t) cc_final: 0.8054 (t) REVERT: C 498 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.6983 (mtm-85) REVERT: D 217 TRP cc_start: 0.8727 (p-90) cc_final: 0.8338 (p90) REVERT: D 415 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6812 (ttp80) REVERT: D 495 ASP cc_start: 0.7013 (m-30) cc_final: 0.6737 (m-30) REVERT: D 498 ARG cc_start: 0.7950 (mtm-85) cc_final: 0.6861 (mtm-85) REVERT: E 53 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.6871 (tm130) REVERT: E 148 GLN cc_start: 0.7667 (pm20) cc_final: 0.7216 (pm20) REVERT: E 175 LYS cc_start: 0.8174 (mtmt) cc_final: 0.7965 (mtpt) REVERT: E 217 TRP cc_start: 0.8582 (p-90) cc_final: 0.8372 (p90) REVERT: E 440 GLU cc_start: 0.6808 (mp0) cc_final: 0.6567 (mp0) REVERT: E 446 LYS cc_start: 0.8046 (tppp) cc_final: 0.7622 (tppp) REVERT: E 495 ASP cc_start: 0.7011 (m-30) cc_final: 0.6652 (m-30) REVERT: F 134 ASP cc_start: 0.7400 (m-30) cc_final: 0.7076 (m-30) REVERT: F 415 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6589 (ttp80) REVERT: F 498 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7160 (mtm-85) REVERT: H 4 LEU cc_start: 0.8506 (tp) cc_final: 0.8260 (tp) REVERT: J 71 THR cc_start: 0.8025 (m) cc_final: 0.7782 (m) REVERT: K 69 MET cc_start: 0.7719 (mtp) cc_final: 0.7488 (mtm) outliers start: 50 outliers final: 25 residues processed: 614 average time/residue: 1.6697 time to fit residues: 1155.2464 Evaluate side-chains 621 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 591 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 464 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 241 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 277 optimal weight: 7.9990 chunk 224 optimal weight: 0.0010 chunk 0 optimal weight: 5.9990 chunk 165 optimal weight: 0.6980 chunk 291 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN A 342 ASN B 41 ASN B 53 GLN B 342 ASN B 350 GLN C 11 ASN C 41 ASN C 49 GLN C 53 GLN C 121 ASN C 342 ASN D 41 ASN D 49 GLN D 53 GLN E 342 ASN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS F 342 ASN I 75 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 27264 Z= 0.234 Angle : 0.494 7.791 37062 Z= 0.262 Chirality : 0.038 0.168 4134 Planarity : 0.004 0.047 4716 Dihedral : 3.742 15.504 3732 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.99 % Allowed : 12.31 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.15), residues: 3318 helix: 2.28 (0.11), residues: 2136 sheet: 2.37 (0.47), residues: 162 loop : -0.54 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 135 HIS 0.004 0.001 HIS A 69 PHE 0.019 0.002 PHE A 106 TYR 0.021 0.001 TYR D 292 ARG 0.005 0.000 ARG E 398 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 601 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7451 (m-30) cc_final: 0.7220 (m-30) REVERT: A 139 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7069 (mpp-170) REVERT: A 192 LEU cc_start: 0.8128 (tp) cc_final: 0.7920 (tt) REVERT: A 365 ASN cc_start: 0.8413 (t0) cc_final: 0.8065 (t0) REVERT: A 415 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6632 (ttp80) REVERT: A 498 ARG cc_start: 0.7750 (mtm180) cc_final: 0.7491 (mtm180) REVERT: B 53 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.6703 (tm130) REVERT: B 217 TRP cc_start: 0.8629 (p-90) cc_final: 0.8327 (p90) REVERT: B 251 ASN cc_start: 0.8065 (m-40) cc_final: 0.7759 (m110) REVERT: B 440 GLU cc_start: 0.6884 (mp0) cc_final: 0.6606 (mp0) REVERT: B 495 ASP cc_start: 0.7047 (m-30) cc_final: 0.6697 (m-30) REVERT: C 38 ARG cc_start: 0.8007 (mtt90) cc_final: 0.7783 (mtt90) REVERT: C 118 ASP cc_start: 0.6896 (m-30) cc_final: 0.6657 (t0) REVERT: C 121 ASN cc_start: 0.8159 (m-40) cc_final: 0.7936 (m110) REVERT: C 415 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6993 (ttt180) REVERT: C 446 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7536 (mtpp) REVERT: C 459 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8078 (t) REVERT: D 78 ARG cc_start: 0.7812 (ttm-80) cc_final: 0.7429 (ttt-90) REVERT: D 137 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7803 (ttp80) REVERT: D 217 TRP cc_start: 0.8736 (p-90) cc_final: 0.8320 (p90) REVERT: D 415 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6982 (ttp80) REVERT: D 498 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.6847 (mtm-85) REVERT: E 148 GLN cc_start: 0.7666 (pm20) cc_final: 0.7238 (pm20) REVERT: E 175 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7914 (mtpt) REVERT: E 217 TRP cc_start: 0.8605 (p-90) cc_final: 0.8380 (p90) REVERT: E 440 GLU cc_start: 0.6804 (mp0) cc_final: 0.6565 (mp0) REVERT: E 446 LYS cc_start: 0.8111 (tppp) cc_final: 0.7680 (tppp) REVERT: E 495 ASP cc_start: 0.7044 (m-30) cc_final: 0.6693 (m-30) REVERT: F 134 ASP cc_start: 0.7405 (m-30) cc_final: 0.7131 (m-30) REVERT: F 415 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6676 (ttp80) REVERT: H 4 LEU cc_start: 0.8516 (tp) cc_final: 0.8269 (tp) REVERT: K 69 MET cc_start: 0.7730 (mtp) cc_final: 0.7485 (mtm) outliers start: 52 outliers final: 33 residues processed: 611 average time/residue: 1.6705 time to fit residues: 1147.7736 Evaluate side-chains 642 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 600 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain L residue 4 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 0.8980 chunk 292 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 325 optimal weight: 0.7980 chunk 269 optimal weight: 0.0170 chunk 150 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN A 227 HIS B 11 ASN B 41 ASN B 53 GLN B 350 GLN C 11 ASN C 41 ASN C 49 GLN D 41 ASN D 49 GLN D 50 GLN E 53 GLN E 251 ASN E 342 ASN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS F 342 ASN I 75 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27264 Z= 0.151 Angle : 0.445 7.029 37062 Z= 0.237 Chirality : 0.036 0.145 4134 Planarity : 0.004 0.045 4716 Dihedral : 3.595 16.036 3732 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.06 % Allowed : 12.61 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.16), residues: 3318 helix: 2.46 (0.11), residues: 2136 sheet: 2.52 (0.48), residues: 162 loop : -0.44 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 217 HIS 0.005 0.001 HIS F 126 PHE 0.014 0.001 PHE D 106 TYR 0.022 0.001 TYR D 292 ARG 0.005 0.000 ARG E 398 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 608 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7407 (m-30) cc_final: 0.7150 (m-30) REVERT: A 139 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.7030 (mpp-170) REVERT: A 365 ASN cc_start: 0.8378 (t0) cc_final: 0.8049 (t0) REVERT: A 415 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6493 (ttp80) REVERT: A 498 ARG cc_start: 0.7738 (mtm180) cc_final: 0.7478 (mtm180) REVERT: B 217 TRP cc_start: 0.8622 (p-90) cc_final: 0.8331 (p90) REVERT: B 251 ASN cc_start: 0.8082 (m-40) cc_final: 0.7767 (m110) REVERT: B 382 TYR cc_start: 0.7028 (m-80) cc_final: 0.6637 (m-80) REVERT: B 440 GLU cc_start: 0.6865 (mp0) cc_final: 0.6598 (mp0) REVERT: B 495 ASP cc_start: 0.7055 (m-30) cc_final: 0.6705 (m-30) REVERT: C 38 ARG cc_start: 0.7950 (mtt90) cc_final: 0.7728 (mtt90) REVERT: C 118 ASP cc_start: 0.6900 (m-30) cc_final: 0.6583 (t0) REVERT: C 121 ASN cc_start: 0.8069 (m-40) cc_final: 0.7849 (m110) REVERT: C 415 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6805 (ttt180) REVERT: C 446 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7687 (mtpp) REVERT: C 459 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7972 (t) REVERT: C 498 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7071 (mtm-85) REVERT: D 217 TRP cc_start: 0.8732 (p-90) cc_final: 0.8323 (p90) REVERT: D 415 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6759 (ttp80) REVERT: D 469 PHE cc_start: 0.7518 (t80) cc_final: 0.7051 (t80) REVERT: D 498 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.6835 (mtm-85) REVERT: E 148 GLN cc_start: 0.7647 (pm20) cc_final: 0.7255 (pm20) REVERT: E 175 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7917 (mtpt) REVERT: E 217 TRP cc_start: 0.8602 (p-90) cc_final: 0.8387 (p90) REVERT: E 440 GLU cc_start: 0.6799 (mp0) cc_final: 0.6537 (mp0) REVERT: E 446 LYS cc_start: 0.8075 (tppp) cc_final: 0.7636 (tppp) REVERT: E 495 ASP cc_start: 0.7051 (m-30) cc_final: 0.6756 (m-30) REVERT: F 10 ILE cc_start: 0.8395 (mm) cc_final: 0.8086 (mp) REVERT: F 38 ARG cc_start: 0.8044 (mtt-85) cc_final: 0.7783 (mtt90) REVERT: F 134 ASP cc_start: 0.7393 (m-30) cc_final: 0.7076 (m-30) REVERT: F 415 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6562 (ttp80) REVERT: F 498 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.7180 (mtm-85) REVERT: H 4 LEU cc_start: 0.8487 (tp) cc_final: 0.8234 (tp) REVERT: J 71 THR cc_start: 0.8079 (m) cc_final: 0.7875 (m) REVERT: K 69 MET cc_start: 0.7711 (mtp) cc_final: 0.7473 (mtm) outliers start: 54 outliers final: 30 residues processed: 624 average time/residue: 1.6738 time to fit residues: 1177.3323 Evaluate side-chains 639 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 602 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain L residue 4 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 273 optimal weight: 0.5980 chunk 181 optimal weight: 5.9990 chunk 323 optimal weight: 30.0000 chunk 202 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN A 227 HIS A 342 ASN B 11 ASN B 41 ASN B 49 GLN B 50 GLN B 350 GLN C 11 ASN C 41 ASN C 49 GLN D 41 ASN D 49 GLN D 50 GLN E 50 GLN E 53 GLN E 186 ASN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS F 342 ASN I 75 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 27264 Z= 0.364 Angle : 0.564 8.993 37062 Z= 0.297 Chirality : 0.042 0.192 4134 Planarity : 0.005 0.048 4716 Dihedral : 3.866 15.315 3732 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.68 % Allowed : 12.19 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.15), residues: 3318 helix: 2.21 (0.11), residues: 2136 sheet: 2.49 (0.47), residues: 162 loop : -0.49 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 135 HIS 0.006 0.001 HIS A 69 PHE 0.022 0.002 PHE A 106 TYR 0.021 0.002 TYR D 292 ARG 0.004 0.000 ARG E 398 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 623 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7074 (mpp-170) REVERT: A 415 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6910 (ttp80) REVERT: A 471 LEU cc_start: 0.7854 (mt) cc_final: 0.7606 (mt) REVERT: A 498 ARG cc_start: 0.7767 (mtm180) cc_final: 0.7516 (mtm180) REVERT: B 71 MET cc_start: 0.7168 (mmm) cc_final: 0.6866 (mpp) REVERT: B 217 TRP cc_start: 0.8651 (p-90) cc_final: 0.8327 (p90) REVERT: B 251 ASN cc_start: 0.8093 (m-40) cc_final: 0.7764 (m110) REVERT: B 277 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7631 (mp) REVERT: B 440 GLU cc_start: 0.6890 (mp0) cc_final: 0.6652 (mp0) REVERT: B 495 ASP cc_start: 0.7078 (m-30) cc_final: 0.6697 (m-30) REVERT: C 38 ARG cc_start: 0.8043 (mtt90) cc_final: 0.7830 (mtt90) REVERT: C 118 ASP cc_start: 0.6881 (m-30) cc_final: 0.6587 (t0) REVERT: C 119 ILE cc_start: 0.7859 (tt) cc_final: 0.7644 (pt) REVERT: C 121 ASN cc_start: 0.8131 (m-40) cc_final: 0.7859 (m110) REVERT: C 446 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7530 (mtpp) REVERT: C 459 VAL cc_start: 0.8301 (OUTLIER) cc_final: 0.8058 (t) REVERT: C 498 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.6984 (mtm-85) REVERT: D 78 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7369 (ttt-90) REVERT: D 265 GLU cc_start: 0.7395 (tt0) cc_final: 0.7178 (tt0) REVERT: D 415 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7094 (ttp80) REVERT: E 71 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.7044 (mtp) REVERT: E 116 MET cc_start: 0.8603 (ptm) cc_final: 0.8365 (ptt) REVERT: E 148 GLN cc_start: 0.7691 (pm20) cc_final: 0.7270 (pm20) REVERT: E 175 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7897 (mtpt) REVERT: E 217 TRP cc_start: 0.8609 (p-90) cc_final: 0.8373 (p90) REVERT: E 440 GLU cc_start: 0.6815 (mp0) cc_final: 0.6579 (mp0) REVERT: E 446 LYS cc_start: 0.8145 (tppp) cc_final: 0.7691 (tppp) REVERT: E 495 ASP cc_start: 0.7064 (m-30) cc_final: 0.6782 (m-30) REVERT: F 134 ASP cc_start: 0.7404 (m-30) cc_final: 0.7181 (m-30) REVERT: F 415 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6756 (ttp80) REVERT: H 4 LEU cc_start: 0.8526 (tp) cc_final: 0.8285 (tp) outliers start: 70 outliers final: 41 residues processed: 636 average time/residue: 1.7162 time to fit residues: 1238.2266 Evaluate side-chains 672 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 623 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 TRP Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain L residue 4 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 205 optimal weight: 0.5980 chunk 220 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 254 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN B 41 ASN B 49 GLN B 350 GLN C 11 ASN C 41 ASN D 49 GLN D 50 GLN D 126 HIS E 53 GLN E 251 ASN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS I 75 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27264 Z= 0.221 Angle : 0.495 7.873 37062 Z= 0.263 Chirality : 0.038 0.167 4134 Planarity : 0.004 0.048 4716 Dihedral : 3.742 15.351 3732 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.03 % Allowed : 13.49 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.29 (0.15), residues: 3318 helix: 2.33 (0.11), residues: 2136 sheet: 2.57 (0.48), residues: 162 loop : -0.45 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 217 HIS 0.005 0.001 HIS A 69 PHE 0.019 0.002 PHE A 106 TYR 0.030 0.001 TYR D 292 ARG 0.007 0.000 ARG E 398 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 605 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.7079 (mpp-170) REVERT: A 192 LEU cc_start: 0.8214 (tt) cc_final: 0.8013 (tp) REVERT: A 365 ASN cc_start: 0.8372 (t0) cc_final: 0.8069 (t0) REVERT: A 415 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6831 (ttp80) REVERT: A 498 ARG cc_start: 0.7754 (mtm180) cc_final: 0.7501 (mtm180) REVERT: B 71 MET cc_start: 0.7054 (mmm) cc_final: 0.6772 (mpp) REVERT: B 217 TRP cc_start: 0.8639 (p-90) cc_final: 0.8329 (p90) REVERT: B 251 ASN cc_start: 0.8083 (m-40) cc_final: 0.7770 (m110) REVERT: B 277 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7548 (mp) REVERT: B 440 GLU cc_start: 0.6875 (mp0) cc_final: 0.6632 (mp0) REVERT: B 495 ASP cc_start: 0.7059 (m-30) cc_final: 0.6684 (m-30) REVERT: C 38 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7792 (mtt90) REVERT: C 118 ASP cc_start: 0.6860 (m-30) cc_final: 0.6577 (t0) REVERT: C 121 ASN cc_start: 0.8085 (m-40) cc_final: 0.7823 (m110) REVERT: C 446 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7663 (mtpp) REVERT: C 459 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7994 (t) REVERT: C 498 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.6997 (mtm-85) REVERT: D 137 ARG cc_start: 0.8192 (tpp80) cc_final: 0.7543 (ttp-170) REVERT: D 265 GLU cc_start: 0.7310 (tt0) cc_final: 0.7056 (tt0) REVERT: D 415 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6973 (ttp80) REVERT: D 469 PHE cc_start: 0.7516 (t80) cc_final: 0.7031 (t80) REVERT: D 498 ARG cc_start: 0.8039 (mtm-85) cc_final: 0.6894 (mtm-85) REVERT: E 71 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6881 (mtp) REVERT: E 148 GLN cc_start: 0.7648 (pm20) cc_final: 0.7260 (pm20) REVERT: E 175 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7910 (mtpt) REVERT: E 217 TRP cc_start: 0.8613 (p-90) cc_final: 0.8388 (p90) REVERT: E 239 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.7002 (mm-30) REVERT: E 440 GLU cc_start: 0.6808 (mp0) cc_final: 0.6569 (mp0) REVERT: E 446 LYS cc_start: 0.8112 (tppp) cc_final: 0.7679 (tppp) REVERT: E 495 ASP cc_start: 0.7053 (m-30) cc_final: 0.6789 (m-30) REVERT: F 38 ARG cc_start: 0.8069 (mtt-85) cc_final: 0.7754 (mtt90) REVERT: F 134 ASP cc_start: 0.7397 (m-30) cc_final: 0.7150 (m-30) REVERT: F 415 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6678 (ttp80) REVERT: F 498 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7209 (mtm-85) REVERT: H 4 LEU cc_start: 0.8512 (tp) cc_final: 0.8257 (tp) outliers start: 53 outliers final: 37 residues processed: 617 average time/residue: 1.7330 time to fit residues: 1201.0238 Evaluate side-chains 652 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 606 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 TRP Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain L residue 4 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 301 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 272 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 300 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN A 227 HIS B 11 ASN B 41 ASN B 49 GLN B 53 GLN B 350 GLN C 11 ASN C 41 ASN D 41 ASN D 49 GLN D 126 HIS E 11 ASN E 50 GLN E 53 GLN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS I 75 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 27264 Z= 0.424 Angle : 0.599 9.683 37062 Z= 0.316 Chirality : 0.043 0.203 4134 Planarity : 0.005 0.049 4716 Dihedral : 4.013 19.023 3732 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.18 % Allowed : 13.38 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.15), residues: 3318 helix: 2.05 (0.11), residues: 2130 sheet: 2.51 (0.47), residues: 162 loop : -0.54 (0.21), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 217 HIS 0.007 0.001 HIS A 69 PHE 0.023 0.002 PHE A 106 TYR 0.018 0.002 TYR D 476 ARG 0.008 0.001 ARG E 398 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 619 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7133 (mpp-170) REVERT: A 415 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6928 (ttp80) REVERT: A 498 ARG cc_start: 0.7756 (mtm180) cc_final: 0.7516 (mtm180) REVERT: B 217 TRP cc_start: 0.8639 (p-90) cc_final: 0.8326 (p90) REVERT: B 251 ASN cc_start: 0.8067 (m-40) cc_final: 0.7731 (m110) REVERT: B 277 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7682 (mp) REVERT: B 440 GLU cc_start: 0.6868 (mp0) cc_final: 0.6637 (mp0) REVERT: B 495 ASP cc_start: 0.7063 (m-30) cc_final: 0.6689 (m-30) REVERT: C 82 LYS cc_start: 0.7981 (mttm) cc_final: 0.7746 (mttp) REVERT: C 118 ASP cc_start: 0.6855 (m-30) cc_final: 0.6521 (t0) REVERT: C 121 ASN cc_start: 0.8143 (m-40) cc_final: 0.7911 (m110) REVERT: C 265 GLU cc_start: 0.7396 (tt0) cc_final: 0.7190 (tt0) REVERT: C 446 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7692 (mtpp) REVERT: C 459 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.8064 (t) REVERT: D 265 GLU cc_start: 0.7408 (tt0) cc_final: 0.7026 (tt0) REVERT: D 415 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7153 (ttp80) REVERT: E 71 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7085 (mtp) REVERT: E 116 MET cc_start: 0.8628 (ptm) cc_final: 0.8426 (ptt) REVERT: E 148 GLN cc_start: 0.7663 (pm20) cc_final: 0.7249 (pm20) REVERT: E 175 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7881 (mtpt) REVERT: E 217 TRP cc_start: 0.8638 (p-90) cc_final: 0.8404 (p90) REVERT: E 440 GLU cc_start: 0.6819 (mp0) cc_final: 0.6582 (mp0) REVERT: E 446 LYS cc_start: 0.8171 (tppp) cc_final: 0.7713 (tppp) REVERT: E 495 ASP cc_start: 0.7072 (m-30) cc_final: 0.6800 (m-30) REVERT: F 415 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6795 (ttp80) REVERT: F 498 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7250 (mtm-85) REVERT: H 4 LEU cc_start: 0.8523 (tp) cc_final: 0.8299 (tp) outliers start: 57 outliers final: 38 residues processed: 632 average time/residue: 1.7134 time to fit residues: 1221.1191 Evaluate side-chains 664 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 618 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 TRP Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain L residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 0.8980 chunk 319 optimal weight: 4.9990 chunk 194 optimal weight: 0.0270 chunk 151 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 334 optimal weight: 0.9990 chunk 308 optimal weight: 9.9990 chunk 266 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 205 optimal weight: 0.0040 chunk 163 optimal weight: 0.8980 overall best weight: 0.5650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN A 133 ASN ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 49 GLN B 53 GLN B 350 GLN C 11 ASN C 41 ASN D 49 GLN D 53 GLN D 126 HIS D 355 ASN ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 53 GLN E 251 ASN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27264 Z= 0.144 Angle : 0.463 8.313 37062 Z= 0.246 Chirality : 0.036 0.148 4134 Planarity : 0.004 0.047 4716 Dihedral : 3.653 15.711 3732 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.76 % Allowed : 13.88 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.15), residues: 3318 helix: 2.37 (0.11), residues: 2142 sheet: 2.62 (0.47), residues: 162 loop : -0.32 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 217 HIS 0.005 0.001 HIS F 126 PHE 0.014 0.001 PHE D 106 TYR 0.019 0.001 TYR D 292 ARG 0.006 0.000 ARG D 498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 599 time to evaluate : 3.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8311 (mm) cc_final: 0.8009 (mp) REVERT: A 415 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6500 (ttp80) REVERT: A 498 ARG cc_start: 0.7729 (mtm180) cc_final: 0.7470 (mtm180) REVERT: B 217 TRP cc_start: 0.8642 (p-90) cc_final: 0.8334 (p90) REVERT: B 251 ASN cc_start: 0.8079 (m-40) cc_final: 0.7736 (m110) REVERT: B 382 TYR cc_start: 0.7071 (m-80) cc_final: 0.6698 (m-80) REVERT: B 440 GLU cc_start: 0.6862 (mp0) cc_final: 0.6630 (mp0) REVERT: B 498 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7718 (mtm110) REVERT: C 118 ASP cc_start: 0.6920 (m-30) cc_final: 0.6564 (t0) REVERT: C 121 ASN cc_start: 0.8142 (m-40) cc_final: 0.7851 (m110) REVERT: C 459 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7912 (t) REVERT: C 498 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7060 (mtm-85) REVERT: D 415 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6748 (ttp80) REVERT: D 469 PHE cc_start: 0.7388 (t80) cc_final: 0.6876 (t80) REVERT: D 498 ARG cc_start: 0.7988 (mtm-85) cc_final: 0.6908 (mtm-85) REVERT: E 148 GLN cc_start: 0.7622 (pm20) cc_final: 0.7253 (pm20) REVERT: E 175 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7903 (mtpt) REVERT: E 217 TRP cc_start: 0.8605 (p-90) cc_final: 0.8395 (p90) REVERT: E 440 GLU cc_start: 0.6811 (mp0) cc_final: 0.6583 (mp0) REVERT: E 446 LYS cc_start: 0.8034 (tppp) cc_final: 0.7627 (tppp) REVERT: E 495 ASP cc_start: 0.7051 (m-30) cc_final: 0.6782 (m-30) REVERT: F 10 ILE cc_start: 0.8396 (mm) cc_final: 0.8091 (mp) REVERT: F 38 ARG cc_start: 0.8036 (mtt-85) cc_final: 0.7729 (mtt90) REVERT: F 134 ASP cc_start: 0.7346 (m-30) cc_final: 0.7138 (m-30) REVERT: F 415 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6583 (ttp80) REVERT: F 498 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7217 (mtm-85) REVERT: H 4 LEU cc_start: 0.8478 (tp) cc_final: 0.8203 (tp) outliers start: 46 outliers final: 25 residues processed: 611 average time/residue: 1.6833 time to fit residues: 1157.2764 Evaluate side-chains 621 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 592 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain L residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.4980 chunk 283 optimal weight: 0.0070 chunk 81 optimal weight: 0.9990 chunk 245 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 274 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN A 133 ASN ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN B 41 ASN B 49 GLN B 53 GLN B 350 GLN C 11 ASN C 41 ASN C 49 GLN D 41 ASN D 49 GLN E 11 ASN E 49 GLN E 53 GLN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS I 75 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.141836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119459 restraints weight = 33514.858| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.69 r_work: 0.3351 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27264 Z= 0.201 Angle : 0.485 8.554 37062 Z= 0.256 Chirality : 0.037 0.160 4134 Planarity : 0.004 0.047 4716 Dihedral : 3.651 16.386 3732 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.49 % Allowed : 14.41 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.16), residues: 3318 helix: 2.41 (0.11), residues: 2142 sheet: 2.60 (0.47), residues: 162 loop : -0.29 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 217 HIS 0.006 0.001 HIS F 126 PHE 0.018 0.001 PHE A 106 TYR 0.016 0.001 TYR D 292 ARG 0.007 0.000 ARG E 398 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15041.15 seconds wall clock time: 262 minutes 19.92 seconds (15739.92 seconds total)