Starting phenix.real_space_refine (version: dev) on Thu Dec 22 14:38:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u65_26360/12_2022/7u65_26360.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u65_26360/12_2022/7u65_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_26360/12_2022/7u65_26360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u65_26360/12_2022/7u65_26360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u65_26360/12_2022/7u65_26360.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u65_26360/12_2022/7u65_26360.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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 Convert atoms to be neutral 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 15.04, per 1000 atoms: 0.57 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: 10.21 Conformation dependent library (CDL) restraints added in 4.4 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: 1.18 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: 8.20 Time building geometry restraints manager: 10.96 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 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. 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.300 Construct map_model_manager: 0.030 Extract box with map and model: 4.930 Check model and map are aligned: 0.430 Convert atoms to be neutral: 0.210 Process input model: 64.200 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 % 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 *********************** 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 : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 644 average time/residue: 1.5061 time to fit residues: 1104.2304 Evaluate side-chains 606 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 606 time to evaluate : 3.087 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3886 ------------------------------------------------------------------------------- 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: 1.9990 chunk 136 optimal weight: 0.5980 chunk 263 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 305 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.7723 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 27264 Z= 0.232 Angle : 0.527 10.585 37062 Z= 0.284 Chirality : 0.038 0.162 4134 Planarity : 0.005 0.061 4716 Dihedral : 3.788 16.575 3732 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.15), residues: 3318 helix: 2.06 (0.11), residues: 2136 sheet: 1.48 (0.45), residues: 168 loop : -0.63 (0.21), residues: 1014 *********************** 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 644 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 601 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 25 residues processed: 607 average time/residue: 1.5510 time to fit residues: 1072.5109 Evaluate side-chains 618 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 593 time to evaluate : 2.954 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 1 residues processed: 24 average time/residue: 0.6540 time to fit residues: 24.9710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 305 optimal weight: 7.9990 chunk 330 optimal weight: 9.9990 chunk 272 optimal weight: 4.9990 chunk 303 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 11 ASN B 41 ASN B 186 ASN C 11 ASN C 41 ASN C 49 GLN C 53 GLN C 121 ASN D 53 GLN E 11 ASN E 41 ASN 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.057 27264 Z= 0.572 Angle : 0.684 12.316 37062 Z= 0.365 Chirality : 0.048 0.229 4134 Planarity : 0.006 0.062 4716 Dihedral : 4.267 16.371 3732 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 2.56 % 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: 1.38 (0.15), residues: 3318 helix: 1.63 (0.11), residues: 2142 sheet: 2.01 (0.47), residues: 162 loop : -0.79 (0.21), residues: 1014 *********************** 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 700 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 633 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 31 residues processed: 652 average time/residue: 1.5326 time to fit residues: 1135.1093 Evaluate side-chains 661 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 630 time to evaluate : 3.229 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 4 residues processed: 27 average time/residue: 0.5026 time to fit residues: 23.1985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.9990 chunk 229 optimal weight: 0.6980 chunk 158 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 306 optimal weight: 8.9990 chunk 324 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 chunk 290 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 27264 Z= 0.170 Angle : 0.475 11.674 37062 Z= 0.255 Chirality : 0.037 0.154 4134 Planarity : 0.005 0.050 4716 Dihedral : 3.804 15.843 3732 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 1.72 % 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: 2.02 (0.15), residues: 3318 helix: 2.15 (0.11), residues: 2136 sheet: 2.28 (0.47), residues: 162 loop : -0.60 (0.21), residues: 1020 *********************** 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 640 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 595 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 20 residues processed: 609 average time/residue: 1.6057 time to fit residues: 1110.5815 Evaluate side-chains 615 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 595 time to evaluate : 3.223 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 6 residues processed: 14 average time/residue: 1.1225 time to fit residues: 23.0729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 1.9990 chunk 184 optimal weight: 0.0010 chunk 4 optimal weight: 0.5980 chunk 241 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 277 optimal weight: 0.6980 chunk 224 optimal weight: 0.0570 chunk 0 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 291 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.4706 ------------------------------------------------------------------------------- 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 B 41 ASN B 53 GLN B 342 ASN B 350 GLN C 11 ASN C 41 ASN C 49 GLN C 121 ASN D 41 ASN D 49 GLN D 53 GLN E 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 27264 Z= 0.132 Angle : 0.437 11.362 37062 Z= 0.230 Chirality : 0.035 0.136 4134 Planarity : 0.004 0.044 4716 Dihedral : 3.522 16.250 3732 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 1.64 % 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: 2.46 (0.15), residues: 3318 helix: 2.45 (0.11), residues: 2136 sheet: 2.80 (0.47), residues: 156 loop : -0.37 (0.21), residues: 1026 *********************** 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 654 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 611 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 17 residues processed: 625 average time/residue: 1.4983 time to fit residues: 1067.1927 Evaluate side-chains 620 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 603 time to evaluate : 3.229 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 4 residues processed: 13 average time/residue: 0.8848 time to fit residues: 18.8535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 3.9990 chunk 292 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 80 optimal weight: 0.0050 chunk 325 optimal weight: 9.9990 chunk 269 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- 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 342 ASN B 41 ASN B 49 GLN B 342 ASN B 350 GLN C 11 ASN C 41 ASN C 49 GLN C 121 ASN C 342 ASN D 41 ASN D 49 GLN E 49 GLN E 50 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: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 27264 Z= 0.257 Angle : 0.519 12.278 37062 Z= 0.272 Chirality : 0.039 0.172 4134 Planarity : 0.005 0.047 4716 Dihedral : 3.706 16.200 3732 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.15), residues: 3318 helix: 2.38 (0.11), residues: 2136 sheet: 2.84 (0.47), residues: 156 loop : -0.35 (0.21), residues: 1026 *********************** 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 670 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 617 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 26 residues processed: 630 average time/residue: 1.5625 time to fit residues: 1120.7656 Evaluate side-chains 635 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 609 time to evaluate : 3.014 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 5 residues processed: 21 average time/residue: 0.5793 time to fit residues: 20.7748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 273 optimal weight: 0.9980 chunk 181 optimal weight: 7.9990 chunk 323 optimal weight: 20.0000 chunk 202 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN B 41 ASN B 49 GLN B 50 GLN B 53 GLN B 350 GLN C 11 ASN C 41 ASN C 49 GLN C 121 ASN D 41 ASN D 126 HIS E 49 GLN E 50 GLN E 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: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 27264 Z= 0.282 Angle : 0.529 12.652 37062 Z= 0.278 Chirality : 0.039 0.179 4134 Planarity : 0.005 0.048 4716 Dihedral : 3.788 16.325 3732 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 1.91 % 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: 2.27 (0.15), residues: 3318 helix: 2.28 (0.11), residues: 2136 sheet: 2.54 (0.47), residues: 162 loop : -0.37 (0.21), residues: 1020 *********************** 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 652 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 602 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 31 residues processed: 618 average time/residue: 1.5735 time to fit residues: 1105.1070 Evaluate side-chains 636 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 605 time to evaluate : 2.785 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 9 residues processed: 22 average time/residue: 0.6092 time to fit residues: 21.5966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 193 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 205 optimal weight: 0.0670 chunk 220 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 254 optimal weight: 0.6980 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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 50 GLN B 53 GLN B 350 GLN C 11 ASN C 41 ASN C 49 GLN C 121 ASN D 53 GLN D 126 HIS E 50 GLN 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 27264 Z= 0.170 Angle : 0.474 12.273 37062 Z= 0.249 Chirality : 0.037 0.151 4134 Planarity : 0.004 0.046 4716 Dihedral : 3.631 16.208 3732 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 1.45 % 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: 2.50 (0.16), residues: 3318 helix: 2.46 (0.11), residues: 2136 sheet: 2.60 (0.48), residues: 162 loop : -0.29 (0.21), residues: 1020 *********************** 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 640 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 602 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 19 residues processed: 619 average time/residue: 1.5776 time to fit residues: 1114.6731 Evaluate side-chains 618 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 599 time to evaluate : 3.099 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 9 residues processed: 10 average time/residue: 0.9441 time to fit residues: 15.7063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 301 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 chunk 285 optimal weight: 5.9990 chunk 300 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 50 GLN B 53 GLN B 350 GLN C 11 ASN C 41 ASN C 49 GLN C 53 GLN C 121 ASN D 41 ASN D 49 GLN E 50 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: 0.7801 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.059 27264 Z= 0.566 Angle : 0.679 13.544 37062 Z= 0.357 Chirality : 0.048 0.227 4134 Planarity : 0.006 0.052 4716 Dihedral : 4.208 21.146 3732 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.15), residues: 3318 helix: 1.80 (0.11), residues: 2142 sheet: 2.47 (0.47), residues: 162 loop : -0.43 (0.21), residues: 1014 *********************** 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 674 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 630 time to evaluate : 3.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 26 residues processed: 642 average time/residue: 1.5921 time to fit residues: 1158.8300 Evaluate side-chains 650 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 624 time to evaluate : 3.125 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 9 residues processed: 17 average time/residue: 0.6240 time to fit residues: 18.6124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 194 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 334 optimal weight: 1.9990 chunk 308 optimal weight: 8.9990 chunk 266 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 205 optimal weight: 0.3980 chunk 163 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 53 GLN A 74 GLN A 121 ASN ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 50 GLN B 53 GLN B 350 GLN C 11 ASN C 41 ASN C 49 GLN C 121 ASN C 126 HIS D 49 GLN D 126 HIS E 50 GLN E 53 GLN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 27264 Z= 0.156 Angle : 0.485 12.466 37062 Z= 0.258 Chirality : 0.037 0.153 4134 Planarity : 0.004 0.047 4716 Dihedral : 3.776 15.979 3732 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.92 % 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: 2.25 (0.11), residues: 2142 sheet: 2.60 (0.47), residues: 162 loop : -0.26 (0.21), residues: 1014 ********************** 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 622 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 598 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 609 average time/residue: 1.6126 time to fit residues: 1118.2993 Evaluate side-chains 612 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 600 time to evaluate : 3.012 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 1.5650 time to fit residues: 13.1344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 81 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 266 optimal weight: 0.2980 chunk 111 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 53 GLN A 121 ASN ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 49 GLN B 50 GLN B 53 GLN B 350 GLN C 11 ASN C 41 ASN C 49 GLN C 53 GLN C 121 ASN D 41 ASN D 49 GLN D 126 HIS E 49 GLN E 50 GLN E 53 GLN E 342 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.141975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119891 restraints weight = 33488.619| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.69 r_work: 0.3352 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 27264 Z= 0.189 Angle : 0.490 12.330 37062 Z= 0.258 Chirality : 0.037 0.158 4134 Planarity : 0.004 0.047 4716 Dihedral : 3.700 16.417 3732 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.96 % 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: 2.45 (0.15), residues: 3318 helix: 2.38 (0.11), residues: 2142 sheet: 2.60 (0.47), residues: 162 loop : -0.21 (0.21), residues: 1014 =============================================================================== Job complete usr+sys time: 14216.07 seconds wall clock time: 248 minutes 2.96 seconds (14882.96 seconds total)