Starting phenix.real_space_refine on Sat Jun 29 01:10:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jf1_36206/06_2024/8jf1_36206_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jf1_36206/06_2024/8jf1_36206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jf1_36206/06_2024/8jf1_36206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jf1_36206/06_2024/8jf1_36206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jf1_36206/06_2024/8jf1_36206_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jf1_36206/06_2024/8jf1_36206_neut.pdb" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 11268 2.51 5 N 2500 2.21 5 O 3000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 36": "OE1" <-> "OE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "B PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 358": "NH1" <-> "NH2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "C ARG 456": "NH1" <-> "NH2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C ARG 555": "NH1" <-> "NH2" Residue "C PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 358": "NH1" <-> "NH2" Residue "D PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "D ARG 555": "NH1" <-> "NH2" Residue "D PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 16884 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3894 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 479} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 327 Unusual residues: {'AV0': 3, 'CLR': 1, 'NAG': 1, 'PLM': 1, 'Y01': 2} Classifications: {'undetermined': 8, 'water': 2} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3894 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 479} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 327 Unusual residues: {'AV0': 3, 'CLR': 1, 'NAG': 1, 'PLM': 1, 'Y01': 2} Classifications: {'undetermined': 8, 'water': 2} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3894 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 479} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 327 Unusual residues: {'AV0': 3, 'CLR': 1, 'NAG': 1, 'PLM': 1, 'Y01': 2} Classifications: {'undetermined': 8, 'water': 2} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3894 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 479} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 327 Unusual residues: {'AV0': 3, 'CLR': 1, 'NAG': 1, 'PLM': 1, 'Y01': 2} Classifications: {'undetermined': 8, 'water': 2} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1 AV0 A 603 " occ=0.50 ... (67 atoms not shown) pdb=" OCB AV0 A 603 " occ=0.50 residue: pdb=" C1 AV0 B 603 " occ=0.50 ... (67 atoms not shown) pdb=" OCB AV0 B 603 " occ=0.50 residue: pdb=" C1 AV0 C 603 " occ=0.50 ... (67 atoms not shown) pdb=" OCB AV0 C 603 " occ=0.50 residue: pdb=" C1 AV0 D 603 " occ=0.50 ... (67 atoms not shown) pdb=" OCB AV0 D 603 " occ=0.50 Time building chain proxies: 9.22, per 1000 atoms: 0.55 Number of scatterers: 16884 At special positions: 0 Unit cell: (90.636, 100.596, 74.7, 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 116 16.00 O 3000 8.00 N 2500 7.00 C 11268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS D 44 " distance=0.00 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS D 55 " distance=0.00 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS D 71 " distance=0.00 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS D 89 " distance=0.00 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS D 129 " distance=0.00 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS D 216 " distance=0.00 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS D 268 " distance=0.00 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS D 309 " distance=0.00 Simple disulfide: pdb=" SG CYS A 342 " - pdb=" SG CYS D 342 " distance=0.00 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS D 366 " distance=0.00 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS D 367 " distance=0.00 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS D 433 " distance=0.00 Simple disulfide: pdb=" SG CYS A 506 " - pdb=" SG CYS D 506 " distance=0.00 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS D 565 " distance=0.00 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS C 44 " distance=0.00 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS C 55 " distance=0.00 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS C 71 " distance=0.00 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS C 89 " distance=0.00 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS C 129 " distance=0.00 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS C 216 " distance=0.00 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS C 268 " distance=0.00 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS C 309 " distance=0.00 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS C 342 " distance=0.00 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS C 366 " distance=0.00 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS C 367 " distance=0.00 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS C 433 " distance=0.00 Simple disulfide: pdb=" SG CYS B 506 " - pdb=" SG CYS C 506 " distance=0.00 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS C 565 " distance=0.00 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 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! Possible link ignored !!! !!! HETATM12637 C7 NAG C 607 50.279 22.395 9.028 1.00176.24 C !!! !!! HETATM 8416 C7 NAG B 607 50.278 22.394 9.028 1.00176.24 C !!! !!! N-linked glycan : False !!! !!! O-linked glycan : False !!! !!! Glycan-glycan : True !!! !!! No oxygen atom found !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! Possible link ignored !!! !!! HETATM12631 C1 NAG C 607 47.608 20.634 10.390 1.00152.48 C !!! !!! HETATM 8410 C1 NAG B 607 47.607 20.633 10.390 1.00152.48 C !!! !!! N-linked glycan : False !!! !!! O-linked glycan : False !!! !!! Glycan-glycan : True !!! !!! No oxygen atom found !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! Possible link ignored !!! !!! HETATM16853 C2 NAG D 607 40.918 79.091 9.349 1.00161.66 C !!! !!! HETATM 4190 C2 NAG A 607 40.917 79.090 9.349 1.00161.66 C !!! !!! N-linked glycan : False !!! !!! O-linked glycan : False !!! !!! Glycan-glycan : True !!! !!! No oxygen atom found !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! Possible link ignored !!! !!! HETATM16857 C6 NAG D 607 43.227 82.437 10.599 1.00204.78 C !!! !!! HETATM 4194 C6 NAG A 607 43.226 82.436 10.599 1.00204.78 C !!! !!! N-linked glycan : False !!! !!! O-linked glycan : False !!! !!! Glycan-glycan : True !!! !!! No oxygen atom found !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Atom "HETATM12531 OBZ AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4089 OBZ AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16752 OBZ AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12531 OBZ AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8310 OBZ AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4089 OBZ AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16752 OBZ AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8310 OBZ AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12531 OBZ AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4089 OBZ AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4089 OBZ AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12531 OBZ AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16752 OBZ AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8310 OBZ AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16752 OBZ AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8310 OBZ AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12515 O5 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4073 O5 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12515 O5 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16736 O5 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8294 O5 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4073 O5 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16736 O5 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8294 O5 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8309 OBY AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16751 OBY AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8309 OBY AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4088 OBY AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12530 OBY AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16751 OBY AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4088 OBY AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12530 OBY AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12514 O4 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4072 O4 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8293 O4 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4072 O4 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12514 O4 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16735 O4 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8293 O4 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16735 O4 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4087 OBX AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12529 OBX AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16750 OBX AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12529 OBX AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4087 OBX AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8308 OBX AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16750 OBX AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8308 OBX AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12567 OAW Y01 C 604 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4125 OAW Y01 A 604 .*. O " rejected from bonding due to valence issues. Atom "HETATM16788 OAW Y01 D 604 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8346 OAW Y01 B 604 .*. O " rejected from bonding due to valence issues. Atom "HETATM16823 OAW Y01 D 605 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8381 OAW Y01 B 605 .*. O " rejected from bonding due to valence issues. Atom "HETATM12602 OAW Y01 C 605 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4160 OAW Y01 A 605 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8307 OBV AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16749 OBV AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8307 OBV AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4086 OBV AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16749 OBV AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12528 OBV AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4086 OBV AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12528 OBV AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8226 O1 AV0 B 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM16668 O1 AV0 D 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM12447 O1 AV0 C 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4005 O1 AV0 A 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM12460 OBV AV0 C 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4018 OBV AV0 A 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8290 O1 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16732 O1 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4069 O1 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12511 O1 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16681 OBV AV0 D 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8239 OBV AV0 B 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8163 O1 AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM16605 O1 AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3942 O1 AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12384 O1 AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12451 O5 AV0 C 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4009 O5 AV0 A 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM16672 O5 AV0 D 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8230 O5 AV0 B 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4086 OBV AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12528 OBV AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8307 OBV AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16749 OBV AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16735 O4 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8293 O4 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12405 OCB AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3963 OCB AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8308 OBX AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16750 OBX AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3959 OBV AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12401 OBV AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12532 OCB AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4090 OCB AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16626 OCB AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8184 OCB AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4087 OBX AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12529 OBX AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16753 OCB AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8311 OCB AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12514 O4 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4072 O4 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8180 OBV AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM16622 OBV AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3946 O5 AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12388 O5 AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3945 O4 AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12387 O4 AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8167 O5 AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM16609 O5 AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM16608 O4 AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8166 O4 AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12450 O4 AV0 C 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4008 O4 AV0 A 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8229 O4 AV0 B 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM16671 O4 AV0 D 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM12515 O5 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4073 O5 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12529 OBX AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4087 OBX AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16736 O5 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8294 O5 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16750 OBX AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8308 OBX AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8290 O1 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16732 O1 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8290 O1 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4069 O1 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16732 O1 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12511 O1 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12511 O1 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4069 O1 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8310 OBZ AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16752 OBZ AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16623 OBX AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8181 OBX AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12402 OBX AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3960 OBX AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4089 OBZ AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12531 OBZ AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4200 O5 NAG A 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM12642 O5 NAG C 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8240 OBX AV0 B 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM16682 OBX AV0 D 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8183 OBZ AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM16625 OBZ AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3962 OBZ AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12404 OBZ AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8421 O5 NAG B 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16863 O5 NAG D 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM12461 OBX AV0 C 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4019 OBX AV0 A 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM12530 OBY AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4088 OBY AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16751 OBY AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8309 OBY AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3961 OBY AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12403 OBY AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8182 OBY AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM16624 OBY AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM16626 OCB AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8184 OCB AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8241 OBY AV0 B 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM16683 OBY AV0 D 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8294 O5 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16736 O5 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12450 O4 AV0 C 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4008 O4 AV0 A 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4019 OBX AV0 A 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM12461 OBX AV0 C 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4090 OCB AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12532 OCB AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12387 O4 AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3945 O4 AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4020 OBY AV0 A 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM12462 OBY AV0 C 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM16753 OCB AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8311 OCB AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4073 O5 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12515 O5 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12514 O4 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4072 O4 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16609 O5 AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8167 O5 AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3963 OCB AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12405 OCB AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM16608 O4 AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8166 O4 AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM16668 O1 AV0 D 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8226 O1 AV0 B 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8293 O4 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16735 O4 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12388 O5 AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3946 O5 AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM16671 O4 AV0 D 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8229 O4 AV0 B 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8163 O1 AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM16605 O1 AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8240 OBX AV0 B 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM16682 OBX AV0 D 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM12447 O1 AV0 C 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4005 O1 AV0 A 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM12511 O1 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4069 O1 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12460 OBV AV0 C 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4018 OBV AV0 A 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4088 OBY AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12530 OBY AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8290 O1 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16732 O1 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3942 O1 AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12384 O1 AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM16681 OBV AV0 D 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8239 OBV AV0 B 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8309 OBY AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12530 OBY AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16751 OBY AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4088 OBY AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8309 OBY AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16751 OBY AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8307 OBV AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16749 OBV AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16863 O5 NAG D 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8421 O5 NAG B 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4086 OBV AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12528 OBV AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8180 OBV AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM16622 OBV AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12401 OBV AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3959 OBV AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12642 O5 NAG C 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4200 O5 NAG A 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4086 OBV AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12528 OBV AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8307 OBV AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16749 OBV AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12528 OBV AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4086 OBV AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8307 OBV AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16749 OBV AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12404 OBZ AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3962 OBZ AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4089 OBZ AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12531 OBZ AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8310 OBZ AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16752 OBZ AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16625 OBZ AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8183 OBZ AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4088 OBY AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16751 OBY AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8230 O5 AV0 B 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM16672 O5 AV0 D 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM16624 OBY AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8182 OBY AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12402 OBX AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3960 OBX AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM12451 O5 AV0 C 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4009 O5 AV0 A 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM12403 OBY AV0 C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3961 OBY AV0 A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8181 OBX AV0 B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM16623 OBX AV0 D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4160 OAW Y01 A 605 .*. O " rejected from bonding due to valence issues. Atom "HETATM12602 OAW Y01 C 605 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8381 OAW Y01 B 605 .*. O " rejected from bonding due to valence issues. Atom "HETATM16823 OAW Y01 D 605 .*. O " rejected from bonding due to valence issues. Atom "HETATM12567 OAW Y01 C 604 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4125 OAW Y01 A 604 .*. O " rejected from bonding due to valence issues. Atom "HETATM16788 OAW Y01 D 604 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8346 OAW Y01 B 604 .*. O " rejected from bonding due to valence issues. Atom "HETATM16683 OBY AV0 D 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8241 OBY AV0 B 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4020 OBY AV0 A 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM12462 OBY AV0 C 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8294 O5 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16736 O5 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4073 O5 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16736 O5 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12515 O5 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8294 O5 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4073 O5 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12515 O5 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12511 O1 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4069 O1 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12511 O1 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8290 O1 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16732 O1 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4069 O1 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8290 O1 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16732 O1 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4072 O4 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12514 O4 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4072 O4 AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8293 O4 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12514 O4 AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16735 O4 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8293 O4 AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16735 O4 AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8308 OBX AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16750 OBX AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8308 OBX AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4087 OBX AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12529 OBX AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16750 OBX AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12529 OBX AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4087 OBX AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4089 OBZ AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12531 OBZ AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM12531 OBZ AV0 C 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 4089 OBZ AV0 A 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16752 OBZ AV0 D 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8310 OBZ AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8310 OBZ AV0 B 603 .*. O " rejected from bonding due to valence issues. Atom "HETATM16752 OBZ AV0 D 603 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.92 Conformation dependent library (CDL) restraints added in 3.0 seconds 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3704 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 0 sheets defined 75.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 40 through 60 removed outlier: 4.345A pdb=" N GLY A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.676A pdb=" N PHE A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 101 removed outlier: 3.677A pdb=" N THR A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.752A pdb=" N LEU A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Proline residue: A 117 - end of helix removed outlier: 3.516A pdb=" N LEU A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 128 Processing helix chain 'A' and resid 131 through 136 Processing helix chain 'A' and resid 145 through 174 Proline residue: A 151 - end of helix removed outlier: 3.591A pdb=" N VAL A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 184 through 206 Proline residue: A 190 - end of helix removed outlier: 3.524A pdb=" N ARG A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 231 removed outlier: 3.508A pdb=" N ASN A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.717A pdb=" N LYS A 253 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET A 254 " --> pdb=" O ILE A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 254' Processing helix chain 'A' and resid 255 through 274 removed outlier: 3.991A pdb=" N LEU A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N CYS A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR A 269 " --> pdb=" O TRP A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 4.346A pdb=" N ILE A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 347 removed outlier: 3.675A pdb=" N ALA A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 374 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 396 through 411 removed outlier: 3.622A pdb=" N VAL A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 removed outlier: 3.506A pdb=" N THR A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 427 through 445 removed outlier: 3.959A pdb=" N MET A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 442 " --> pdb=" O MET A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 454 through 478 Proline residue: A 472 - end of helix Processing helix chain 'A' and resid 491 through 497 removed outlier: 3.714A pdb=" N VAL A 495 " --> pdb=" O GLN A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 523 through 528 removed outlier: 3.748A pdb=" N LYS A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 545 Processing helix chain 'A' and resid 549 through 556 Processing helix chain 'B' and resid 40 through 60 removed outlier: 4.345A pdb=" N GLY B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.676A pdb=" N PHE B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 101 removed outlier: 3.677A pdb=" N THR B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 124 removed outlier: 3.752A pdb=" N LEU B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Proline residue: B 117 - end of helix removed outlier: 3.516A pdb=" N LEU B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 128 Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 145 through 174 Proline residue: B 151 - end of helix removed outlier: 3.591A pdb=" N VAL B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 179 Processing helix chain 'B' and resid 184 through 206 Proline residue: B 190 - end of helix removed outlier: 3.524A pdb=" N ARG B 206 " --> pdb=" O ALA B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 231 removed outlier: 3.508A pdb=" N ASN B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.717A pdb=" N LYS B 253 " --> pdb=" O GLN B 250 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET B 254 " --> pdb=" O ILE B 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 254' Processing helix chain 'B' and resid 255 through 274 removed outlier: 3.991A pdb=" N LEU B 259 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 266 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N CYS B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR B 269 " --> pdb=" O TRP B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 removed outlier: 4.346A pdb=" N ILE B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 347 removed outlier: 3.675A pdb=" N ALA B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 374 Processing helix chain 'B' and resid 383 through 393 Processing helix chain 'B' and resid 396 through 411 removed outlier: 3.622A pdb=" N VAL B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 422 removed outlier: 3.506A pdb=" N THR B 417 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 427 through 445 removed outlier: 3.959A pdb=" N MET B 431 " --> pdb=" O ILE B 427 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 442 " --> pdb=" O MET B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 449 Processing helix chain 'B' and resid 454 through 478 Proline residue: B 472 - end of helix Processing helix chain 'B' and resid 491 through 497 removed outlier: 3.714A pdb=" N VAL B 495 " --> pdb=" O GLN B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 518 through 523 Processing helix chain 'B' and resid 523 through 528 removed outlier: 3.748A pdb=" N LYS B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 549 through 556 Processing helix chain 'C' and resid 40 through 60 removed outlier: 4.345A pdb=" N GLY C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.676A pdb=" N PHE C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 101 removed outlier: 3.677A pdb=" N THR C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 124 removed outlier: 3.752A pdb=" N LEU C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Proline residue: C 117 - end of helix removed outlier: 3.516A pdb=" N LEU C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 128 Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 145 through 174 Proline residue: C 151 - end of helix removed outlier: 3.591A pdb=" N VAL C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 184 through 206 Proline residue: C 190 - end of helix removed outlier: 3.524A pdb=" N ARG C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 231 removed outlier: 3.508A pdb=" N ASN C 230 " --> pdb=" O GLN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.717A pdb=" N LYS C 253 " --> pdb=" O GLN C 250 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET C 254 " --> pdb=" O ILE C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 254' Processing helix chain 'C' and resid 255 through 274 removed outlier: 3.991A pdb=" N LEU C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 266 " --> pdb=" O MET C 262 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N CYS C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR C 269 " --> pdb=" O TRP C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 removed outlier: 4.346A pdb=" N ILE C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 347 removed outlier: 3.675A pdb=" N ALA C 327 " --> pdb=" O GLY C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 374 Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 396 through 411 removed outlier: 3.622A pdb=" N VAL C 400 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 422 removed outlier: 3.506A pdb=" N THR C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 426 No H-bonds generated for 'chain 'C' and resid 424 through 426' Processing helix chain 'C' and resid 427 through 445 removed outlier: 3.959A pdb=" N MET C 431 " --> pdb=" O ILE C 427 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 442 " --> pdb=" O MET C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 449 Processing helix chain 'C' and resid 454 through 478 Proline residue: C 472 - end of helix Processing helix chain 'C' and resid 491 through 497 removed outlier: 3.714A pdb=" N VAL C 495 " --> pdb=" O GLN C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 515 Processing helix chain 'C' and resid 518 through 523 Processing helix chain 'C' and resid 523 through 528 removed outlier: 3.748A pdb=" N LYS C 528 " --> pdb=" O LEU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 545 Processing helix chain 'C' and resid 549 through 556 Processing helix chain 'D' and resid 40 through 60 removed outlier: 4.345A pdb=" N GLY D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.676A pdb=" N PHE D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 101 removed outlier: 3.677A pdb=" N THR D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 124 removed outlier: 3.752A pdb=" N LEU D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Proline residue: D 117 - end of helix removed outlier: 3.516A pdb=" N LEU D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 128 Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 145 through 174 Proline residue: D 151 - end of helix removed outlier: 3.591A pdb=" N VAL D 156 " --> pdb=" O ARG D 152 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 184 through 206 Proline residue: D 190 - end of helix removed outlier: 3.524A pdb=" N ARG D 206 " --> pdb=" O ALA D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.508A pdb=" N ASN D 230 " --> pdb=" O GLN D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.717A pdb=" N LYS D 253 " --> pdb=" O GLN D 250 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET D 254 " --> pdb=" O ILE D 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 250 through 254' Processing helix chain 'D' and resid 255 through 274 removed outlier: 3.991A pdb=" N LEU D 259 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 266 " --> pdb=" O MET D 262 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N CYS D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR D 269 " --> pdb=" O TRP D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 removed outlier: 4.346A pdb=" N ILE D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 347 removed outlier: 3.675A pdb=" N ALA D 327 " --> pdb=" O GLY D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 374 Processing helix chain 'D' and resid 383 through 393 Processing helix chain 'D' and resid 396 through 411 removed outlier: 3.622A pdb=" N VAL D 400 " --> pdb=" O SER D 396 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 422 removed outlier: 3.506A pdb=" N THR D 417 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE D 420 " --> pdb=" O PHE D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 426 No H-bonds generated for 'chain 'D' and resid 424 through 426' Processing helix chain 'D' and resid 427 through 445 removed outlier: 3.959A pdb=" N MET D 431 " --> pdb=" O ILE D 427 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 442 " --> pdb=" O MET D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 449 Processing helix chain 'D' and resid 454 through 478 Proline residue: D 472 - end of helix Processing helix chain 'D' and resid 491 through 497 removed outlier: 3.714A pdb=" N VAL D 495 " --> pdb=" O GLN D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 515 Processing helix chain 'D' and resid 518 through 523 Processing helix chain 'D' and resid 523 through 528 removed outlier: 3.748A pdb=" N LYS D 528 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 545 Processing helix chain 'D' and resid 549 through 556 968 hydrogen bonds defined for protein. 2844 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: 7.04 Time building geometry restraints manager: 22.36 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: 2804 1.32 - 1.45: 4220 1.45 - 1.58: 10136 1.58 - 1.71: 0 1.71 - 1.84: 176 Bond restraints: 17336 Sorted by residual: bond pdb=" CE1 HIS A 77 " pdb=" NE2 HIS A 77 " ideal model delta sigma weight residual 1.321 1.368 -0.047 1.00e-02 1.00e+04 2.22e+01 bond pdb=" CE1 HIS C 77 " pdb=" NE2 HIS C 77 " ideal model delta sigma weight residual 1.321 1.368 -0.047 1.00e-02 1.00e+04 2.22e+01 bond pdb=" CE1 HIS D 77 " pdb=" NE2 HIS D 77 " ideal model delta sigma weight residual 1.321 1.368 -0.047 1.00e-02 1.00e+04 2.22e+01 bond pdb=" CE1 HIS B 77 " pdb=" NE2 HIS B 77 " ideal model delta sigma weight residual 1.321 1.368 -0.047 1.00e-02 1.00e+04 2.22e+01 bond pdb=" N LEU B 104 " pdb=" CA LEU B 104 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.92e+01 ... (remaining 17331 not shown) Histogram of bond angle deviations from ideal: 95.32 - 103.30: 336 103.30 - 111.28: 6212 111.28 - 119.25: 10316 119.25 - 127.23: 6636 127.23 - 135.21: 176 Bond angle restraints: 23676 Sorted by residual: angle pdb=" CA GLY B 312 " pdb=" C GLY B 312 " pdb=" O GLY B 312 " ideal model delta sigma weight residual 122.45 117.97 4.48 7.20e-01 1.93e+00 3.87e+01 angle pdb=" CA GLY C 312 " pdb=" C GLY C 312 " pdb=" O GLY C 312 " ideal model delta sigma weight residual 122.45 117.97 4.48 7.20e-01 1.93e+00 3.87e+01 angle pdb=" CA GLY A 312 " pdb=" C GLY A 312 " pdb=" O GLY A 312 " ideal model delta sigma weight residual 122.45 117.97 4.48 7.20e-01 1.93e+00 3.87e+01 angle pdb=" CA GLY D 312 " pdb=" C GLY D 312 " pdb=" O GLY D 312 " ideal model delta sigma weight residual 122.45 117.97 4.48 7.20e-01 1.93e+00 3.87e+01 angle pdb=" N MET A 452 " pdb=" CA MET A 452 " pdb=" C MET A 452 " ideal model delta sigma weight residual 112.72 106.69 6.03 1.14e+00 7.69e-01 2.80e+01 ... (remaining 23671 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 28.78: 11279 28.78 - 57.56: 371 57.56 - 86.34: 98 86.34 - 115.12: 0 115.12 - 143.90: 16 Dihedral angle restraints: 11764 sinusoidal: 5964 harmonic: 5800 Sorted by residual: dihedral pdb=" CB CYS B 216 " pdb=" SG CYS B 216 " pdb=" SG CYS C 216 " pdb=" CB CYS C 216 " ideal model delta sinusoidal sigma weight residual -86.00 0.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS A 342 " pdb=" SG CYS A 342 " pdb=" SG CYS D 342 " pdb=" CB CYS D 342 " ideal model delta sinusoidal sigma weight residual -86.00 0.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS B 366 " pdb=" SG CYS B 366 " pdb=" SG CYS C 366 " pdb=" CB CYS C 366 " ideal model delta sinusoidal sigma weight residual -86.00 0.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 ... (remaining 11761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1340 0.046 - 0.092: 908 0.092 - 0.138: 416 0.138 - 0.184: 208 0.184 - 0.230: 56 Chirality restraints: 2928 Sorted by residual: chirality pdb=" CA TRP D 149 " pdb=" N TRP D 149 " pdb=" C TRP D 149 " pdb=" CB TRP D 149 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA TRP A 149 " pdb=" N TRP A 149 " pdb=" C TRP A 149 " pdb=" CB TRP A 149 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA TRP B 149 " pdb=" N TRP B 149 " pdb=" C TRP B 149 " pdb=" CB TRP B 149 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2925 not shown) Planarity restraints: 2712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 52 " -0.030 2.00e-02 2.50e+03 3.50e-02 2.45e+01 pdb=" CG TYR D 52 " 0.084 2.00e-02 2.50e+03 pdb=" CD1 TYR D 52 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR D 52 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR D 52 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR D 52 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR D 52 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 52 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 52 " 0.030 2.00e-02 2.50e+03 3.50e-02 2.45e+01 pdb=" CG TYR C 52 " -0.084 2.00e-02 2.50e+03 pdb=" CD1 TYR C 52 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR C 52 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR C 52 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR C 52 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR C 52 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 52 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 52 " 0.030 2.00e-02 2.50e+03 3.50e-02 2.45e+01 pdb=" CG TYR B 52 " -0.084 2.00e-02 2.50e+03 pdb=" CD1 TYR B 52 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 52 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR B 52 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR B 52 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 52 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 52 " -0.019 2.00e-02 2.50e+03 ... (remaining 2709 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 8568 0.98 - 1.96: 17846 1.96 - 2.94: 38328 2.94 - 3.92: 102572 3.92 - 4.90: 190260 Warning: very small nonbonded interaction distances. Nonbonded interactions: 357574 Sorted by model distance: nonbonded pdb=" CG2 ILE A 160 " pdb=" CG2 ILE D 160 " model vdw 0.001 3.880 nonbonded pdb=" CD1 TYR B 340 " pdb=" CD1 TYR C 340 " model vdw 0.001 3.640 nonbonded pdb=" CD PRO A 151 " pdb=" CD PRO D 151 " model vdw 0.001 3.840 nonbonded pdb=" CZ ARG A 304 " pdb=" CZ ARG D 304 " model vdw 0.001 3.500 nonbonded pdb=" CG2 ILE A 305 " pdb=" CG2 ILE D 305 " model vdw 0.001 3.880 ... (remaining 357569 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' } 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=0.99 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: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 70.720 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 0.015 0.059 17336 Z= 0.946 Angle : 1.884 8.572 23676 Z= 1.362 Chirality : 0.078 0.230 2928 Planarity : 0.012 0.126 2712 Dihedral : 14.779 143.897 7976 Min Nonbonded Distance : 0.001 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.71 % Allowed : 5.23 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.90 (0.17), residues: 2020 helix: -1.30 (0.12), residues: 1392 sheet: None (None), residues: 0 loop : -0.70 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.011 TRP C 265 HIS 0.009 0.003 HIS B 74 PHE 0.035 0.009 PHE C 107 TYR 0.084 0.009 TYR C 52 ARG 0.017 0.002 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 377 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 12 residues processed: 385 average time/residue: 1.0308 time to fit residues: 459.9729 Evaluate side-chains 389 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 377 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 452 MET Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain D residue 452 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.226 > 50: distance: 35 - 72: 3.167 distance: 49 - 80: 3.293 distance: 69 - 96: 3.136 distance: 71 - 250: 8.280 distance: 75 - 100: 3.325 distance: 83 - 106: 3.253 distance: 91 - 113: 3.263 distance: 99 - 118: 3.449 distance: 197 - 198: 9.339 distance: 197 - 203: 7.166 distance: 198 - 199: 3.357 distance: 198 - 201: 7.726 distance: 199 - 200: 6.132 distance: 199 - 204: 5.990 distance: 201 - 202: 25.347 distance: 202 - 203: 24.443 distance: 204 - 205: 5.174 distance: 204 - 210: 13.582 distance: 205 - 206: 5.687 distance: 205 - 208: 7.075 distance: 206 - 211: 8.007 distance: 207 - 245: 23.276 distance: 208 - 209: 8.437 distance: 209 - 210: 6.194 distance: 211 - 212: 8.868 distance: 212 - 213: 8.601 distance: 212 - 215: 5.822 distance: 213 - 214: 6.395 distance: 214 - 251: 10.328 distance: 215 - 216: 13.232 distance: 216 - 217: 10.108 distance: 216 - 218: 6.150 distance: 218 - 220: 4.513 distance: 218 - 221: 4.760 distance: 219 - 220: 4.356 distance: 220 - 222: 5.438 distance: 221 - 223: 9.957 distance: 222 - 224: 7.320 distance: 223 - 224: 3.407 distance: 225 - 226: 4.415 distance: 226 - 227: 4.837 distance: 227 - 228: 9.194 distance: 227 - 237: 13.655 distance: 228 - 259: 20.482 distance: 229 - 230: 5.622 distance: 230 - 231: 6.325 distance: 230 - 232: 4.209 distance: 231 - 233: 4.448 distance: 232 - 234: 10.164 distance: 233 - 235: 3.827 distance: 235 - 236: 5.281 distance: 237 - 238: 13.020 distance: 238 - 239: 4.384 distance: 238 - 241: 7.388 distance: 239 - 245: 11.263 distance: 240 - 267: 16.848 distance: 241 - 242: 21.315 distance: 242 - 243: 4.035 distance: 242 - 244: 11.838 distance: 245 - 246: 27.838 distance: 246 - 247: 15.668 distance: 246 - 249: 13.465 distance: 247 - 248: 12.025 distance: 248 - 275: 14.280 distance: 249 - 250: 16.898 distance: 251 - 252: 3.465 distance: 252 - 253: 7.987 distance: 252 - 255: 4.951 distance: 253 - 254: 9.232 distance: 253 - 259: 12.697 distance: 254 - 279: 9.954 distance: 256 - 258: 15.278 distance: 259 - 260: 7.495 distance: 260 - 261: 14.174 distance: 260 - 263: 6.772 distance: 261 - 262: 16.222 distance: 261 - 267: 10.414 distance: 262 - 285: 30.579 distance: 263 - 264: 20.036 distance: 264 - 265: 13.152 distance: 264 - 266: 18.990 distance: 267 - 268: 19.903 distance: 268 - 269: 16.704 distance: 268 - 271: 18.586 distance: 269 - 270: 14.891 distance: 269 - 275: 8.327 distance: 270 - 292: 24.282 distance: 271 - 272: 28.365 distance: 272 - 273: 39.085 distance: 272 - 274: 52.226 distance: 275 - 276: 13.457 distance: 276 - 277: 15.245 distance: 277 - 278: 5.055 distance: 277 - 279: 7.283 distance: 278 - 297: 4.684