Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 19:23:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/08_2023/7a5v_11657_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/08_2023/7a5v_11657.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/08_2023/7a5v_11657_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/08_2023/7a5v_11657_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/08_2023/7a5v_11657_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/08_2023/7a5v_11657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/08_2023/7a5v_11657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/08_2023/7a5v_11657_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/08_2023/7a5v_11657_updated.pdb" } resolution = 1.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians S 115 5.16 5 Cl 10 4.86 5 C 13175 2.51 5 N 3190 2.21 5 O 4665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 488": "NH1" <-> "NH2" Residue "D TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 488": "NH1" <-> "NH2" Residue "H TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H GLU 182": "OE1" <-> "OE2" Residue "H PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 270": "OE1" <-> "OE2" Residue "H PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 312": "NH1" <-> "NH2" Residue "H TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 488": "NH1" <-> "NH2" Residue "L TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L GLU 182": "OE1" <-> "OE2" Residue "L PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 270": "OE1" <-> "OE2" Residue "L PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 312": "NH1" <-> "NH2" Residue "L TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 488": "NH1" <-> "NH2" Residue "Q TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 155": "OE1" <-> "OE2" Residue "Q GLU 182": "OE1" <-> "OE2" Residue "Q PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 270": "OE1" <-> "OE2" Residue "Q PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 312": "NH1" <-> "NH2" Residue "Q TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 488": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 21155 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "O" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "O" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "E" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "I" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "L" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "M" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "Q" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "R" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 105 residue: pdb=" N AMET A 40 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 40 " occ=0.50 residue: pdb=" N AASN A 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 41 " occ=0.50 residue: pdb=" N ATYR A 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 66 " occ=0.50 residue: pdb=" N AASN A 85 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 85 " occ=0.50 residue: pdb=" N ASER A 104 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 104 " occ=0.50 residue: pdb=" N ALEU A 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 125 " occ=0.50 residue: pdb=" N AILE A 164 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 164 " occ=0.50 residue: pdb=" N AVAL A 198 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 198 " occ=0.50 residue: pdb=" N ASER A 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 209 " occ=0.50 residue: pdb=" N APHE A 212 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 212 " occ=0.50 residue: pdb=" N ALEU A 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 214 " occ=0.50 residue: pdb=" N ATHR A 225 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A 225 " occ=0.50 ... (remaining 93 not shown) Time building chain proxies: 16.80, per 1000 atoms: 0.79 Number of scatterers: 21155 At special positions: 0 Unit cell: (142.859, 139.612, 127.437, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 10 17.00 S 115 16.00 O 4665 8.00 N 3190 7.00 C 13175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG ACYS A 136 " - pdb=" SG ACYS A 150 " distance=2.05 Simple disulfide: pdb=" SG CYS O 409 " - pdb=" SG CYS O 483 " distance=2.06 Simple disulfide: pdb=" SG ACYS D 136 " - pdb=" SG ACYS D 150 " distance=2.05 Simple disulfide: pdb=" SG CYS E 409 " - pdb=" SG CYS E 483 " distance=2.06 Simple disulfide: pdb=" SG ACYS H 136 " - pdb=" SG ACYS H 150 " distance=2.05 Simple disulfide: pdb=" SG CYS I 409 " - pdb=" SG CYS I 483 " distance=2.06 Simple disulfide: pdb=" SG ACYS L 136 " - pdb=" SG ACYS L 150 " distance=2.05 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 483 " distance=2.06 Simple disulfide: pdb=" SG ACYS Q 136 " - pdb=" SG ACYS Q 150 " distance=2.05 Simple disulfide: pdb=" SG CYS R 409 " - pdb=" SG CYS R 483 " distance=2.06 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 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA G 3 " - " MAN G 4 " " BMA K 3 " - " MAN K 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA G 3 " - " MAN G 5 " " BMA K 3 " - " MAN K 5 " " BMA P 3 " - " MAN P 5 " " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " NAG-ASN " NAG A5405 " - " ASN A 8 " " NAG B 1 " - " ASN A 80 " " NAG C 1 " - " ASN A 149 " " NAG D5405 " - " ASN D 8 " " NAG F 1 " - " ASN D 80 " " NAG G 1 " - " ASN D 149 " " NAG H5405 " - " ASN H 8 " " NAG J 1 " - " ASN H 80 " " NAG K 1 " - " ASN H 149 " " NAG L5405 " - " ASN L 8 " " NAG N 1 " - " ASN L 80 " " NAG P 1 " - " ASN L 149 " " NAG Q5405 " - " ASN Q 8 " " NAG S 1 " - " ASN Q 80 " " NAG T 1 " - " ASN Q 149 " Time building additional restraints: 8.93 Conformation dependent library (CDL) restraints added in 4.2 seconds 5010 Ramachandran restraints generated. 2505 Oldfield, 0 Emsley, 2505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4480 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 35 sheets defined 29.8% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.634A pdb=" N TRP A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 removed outlier: 3.765A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 305 Processing helix chain 'A' and resid 310 through 446 removed outlier: 3.930A pdb=" N ILE A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Proline residue: A 432 - end of helix Processing helix chain 'O' and resid 449 through 451 No H-bonds generated for 'chain 'O' and resid 449 through 451' Processing helix chain 'O' and resid 496 through 498 No H-bonds generated for 'chain 'O' and resid 496 through 498' Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 226 through 241 removed outlier: 3.634A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 271 removed outlier: 3.765A pdb=" N THR D 271 " --> pdb=" O HIS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 305 Processing helix chain 'D' and resid 310 through 446 removed outlier: 3.930A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 449 through 451 No H-bonds generated for 'chain 'E' and resid 449 through 451' Processing helix chain 'E' and resid 496 through 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing helix chain 'H' and resid 85 through 90 Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 178 through 180 No H-bonds generated for 'chain 'H' and resid 178 through 180' Processing helix chain 'H' and resid 219 through 224 Processing helix chain 'H' and resid 226 through 241 removed outlier: 3.634A pdb=" N TRP H 237 " --> pdb=" O THR H 233 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL H 238 " --> pdb=" O ILE H 234 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER H 239 " --> pdb=" O LEU H 235 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE H 240 " --> pdb=" O SER H 236 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TRP H 241 " --> pdb=" O TRP H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 271 removed outlier: 3.766A pdb=" N THR H 271 " --> pdb=" O HIS H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 305 Processing helix chain 'H' and resid 310 through 446 removed outlier: 3.930A pdb=" N ILE H 429 " --> pdb=" O ARG H 425 " (cutoff:3.500A) Proline residue: H 432 - end of helix Processing helix chain 'I' and resid 449 through 451 No H-bonds generated for 'chain 'I' and resid 449 through 451' Processing helix chain 'I' and resid 496 through 498 No H-bonds generated for 'chain 'I' and resid 496 through 498' Processing helix chain 'L' and resid 9 through 20 Processing helix chain 'L' and resid 70 through 72 No H-bonds generated for 'chain 'L' and resid 70 through 72' Processing helix chain 'L' and resid 85 through 90 Processing helix chain 'L' and resid 171 through 173 No H-bonds generated for 'chain 'L' and resid 171 through 173' Processing helix chain 'L' and resid 178 through 180 No H-bonds generated for 'chain 'L' and resid 178 through 180' Processing helix chain 'L' and resid 219 through 224 Processing helix chain 'L' and resid 226 through 241 removed outlier: 3.634A pdb=" N TRP L 237 " --> pdb=" O THR L 233 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL L 238 " --> pdb=" O ILE L 234 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER L 239 " --> pdb=" O LEU L 235 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE L 240 " --> pdb=" O SER L 236 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TRP L 241 " --> pdb=" O TRP L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 271 removed outlier: 3.765A pdb=" N THR L 271 " --> pdb=" O HIS L 267 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 305 Processing helix chain 'L' and resid 310 through 446 removed outlier: 3.930A pdb=" N ILE L 429 " --> pdb=" O ARG L 425 " (cutoff:3.500A) Proline residue: L 432 - end of helix Processing helix chain 'M' and resid 449 through 451 No H-bonds generated for 'chain 'M' and resid 449 through 451' Processing helix chain 'M' and resid 496 through 498 No H-bonds generated for 'chain 'M' and resid 496 through 498' Processing helix chain 'Q' and resid 9 through 20 Processing helix chain 'Q' and resid 70 through 72 No H-bonds generated for 'chain 'Q' and resid 70 through 72' Processing helix chain 'Q' and resid 85 through 90 Processing helix chain 'Q' and resid 171 through 173 No H-bonds generated for 'chain 'Q' and resid 171 through 173' Processing helix chain 'Q' and resid 178 through 180 No H-bonds generated for 'chain 'Q' and resid 178 through 180' Processing helix chain 'Q' and resid 219 through 224 Processing helix chain 'Q' and resid 226 through 241 removed outlier: 3.634A pdb=" N TRP Q 237 " --> pdb=" O THR Q 233 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL Q 238 " --> pdb=" O ILE Q 234 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER Q 239 " --> pdb=" O LEU Q 235 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE Q 240 " --> pdb=" O SER Q 236 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TRP Q 241 " --> pdb=" O TRP Q 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 247 through 271 removed outlier: 3.765A pdb=" N THR Q 271 " --> pdb=" O HIS Q 267 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 305 Processing helix chain 'Q' and resid 310 through 446 removed outlier: 3.930A pdb=" N ILE Q 429 " --> pdb=" O ARG Q 425 " (cutoff:3.500A) Proline residue: Q 432 - end of helix Processing helix chain 'R' and resid 449 through 451 No H-bonds generated for 'chain 'R' and resid 449 through 451' Processing helix chain 'R' and resid 496 through 498 No H-bonds generated for 'chain 'R' and resid 496 through 498' Processing sheet with id= A, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.201A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.964A pdb=" N MET A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.700A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.883A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR A 131 " --> pdb=" O ASER A 104 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'O' and resid 2 through 7 Processing sheet with id= F, first strand: chain 'O' and resid 506 through 508 removed outlier: 3.717A pdb=" N ILE O 420 " --> pdb=" O LYS O 486 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG O 425 " --> pdb=" O PHE O 434 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N PHE O 434 " --> pdb=" O ARG O 425 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'O' and resid 484 through 486 removed outlier: 3.716A pdb=" N TYR O 501 " --> pdb=" O ALA O 485 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 164 through 168 removed outlier: 6.201A pdb=" N VAL D 36 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR D 167 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL D 38 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.964A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.700A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.884A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR D 131 " --> pdb=" O ASER D 104 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 2 through 7 Processing sheet with id= M, first strand: chain 'E' and resid 506 through 508 removed outlier: 3.717A pdb=" N ILE E 420 " --> pdb=" O LYS E 486 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG E 425 " --> pdb=" O PHE E 434 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N PHE E 434 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 484 through 486 removed outlier: 3.716A pdb=" N TYR E 501 " --> pdb=" O ALA E 485 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 164 through 168 removed outlier: 6.201A pdb=" N VAL H 36 " --> pdb=" O GLU H 165 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR H 167 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL H 38 " --> pdb=" O TYR H 167 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS H 37 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG H 68 " --> pdb=" O CYS H 37 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR H 60 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE H 47 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR H 58 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE H 116 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.964A pdb=" N MET H 49 " --> pdb=" O THR H 58 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 96 through 98 removed outlier: 3.700A pdb=" N SER H 156 " --> pdb=" O PRO H 206 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU H 190 " --> pdb=" O ARG H 213 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS H 215 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE H 188 " --> pdb=" O LYS H 215 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 101 through 106 removed outlier: 6.883A pdb=" N THR H 133 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASER H 104 " --> pdb=" O THR H 131 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR H 131 " --> pdb=" O ASER H 104 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 2 through 7 Processing sheet with id= T, first strand: chain 'I' and resid 506 through 508 removed outlier: 3.717A pdb=" N ILE I 420 " --> pdb=" O LYS I 486 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG I 425 " --> pdb=" O PHE I 434 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N PHE I 434 " --> pdb=" O ARG I 425 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 484 through 486 removed outlier: 3.717A pdb=" N TYR I 501 " --> pdb=" O ALA I 485 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 164 through 168 removed outlier: 6.201A pdb=" N VAL L 36 " --> pdb=" O GLU L 165 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR L 167 " --> pdb=" O VAL L 36 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL L 38 " --> pdb=" O TYR L 167 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS L 37 " --> pdb=" O ARG L 68 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ARG L 68 " --> pdb=" O CYS L 37 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR L 60 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE L 47 " --> pdb=" O THR L 58 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR L 58 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE L 116 " --> pdb=" O LEU L 83 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 49 through 51 removed outlier: 3.964A pdb=" N MET L 49 " --> pdb=" O THR L 58 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 96 through 98 removed outlier: 3.700A pdb=" N SER L 156 " --> pdb=" O PRO L 206 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU L 190 " --> pdb=" O ARG L 213 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS L 215 " --> pdb=" O ILE L 188 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE L 188 " --> pdb=" O LYS L 215 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 101 through 106 removed outlier: 6.883A pdb=" N THR L 133 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASER L 104 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR L 131 " --> pdb=" O ASER L 104 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 2 through 7 Processing sheet with id= AA, first strand: chain 'M' and resid 506 through 508 removed outlier: 3.717A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'M' and resid 484 through 486 removed outlier: 3.716A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 164 through 168 removed outlier: 6.201A pdb=" N VAL Q 36 " --> pdb=" O GLU Q 165 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR Q 167 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL Q 38 " --> pdb=" O TYR Q 167 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS Q 37 " --> pdb=" O ARG Q 68 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG Q 68 " --> pdb=" O CYS Q 37 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR Q 60 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE Q 47 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR Q 58 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE Q 116 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Q' and resid 49 through 51 removed outlier: 3.964A pdb=" N MET Q 49 " --> pdb=" O THR Q 58 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Q' and resid 96 through 98 removed outlier: 3.700A pdb=" N SER Q 156 " --> pdb=" O PRO Q 206 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU Q 190 " --> pdb=" O ARG Q 213 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS Q 215 " --> pdb=" O ILE Q 188 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE Q 188 " --> pdb=" O LYS Q 215 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Q' and resid 101 through 106 removed outlier: 6.883A pdb=" N THR Q 133 " --> pdb=" O LYS Q 102 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASER Q 104 " --> pdb=" O THR Q 131 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR Q 131 " --> pdb=" O ASER Q 104 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'R' and resid 2 through 7 Processing sheet with id= AH, first strand: chain 'R' and resid 506 through 508 removed outlier: 3.717A pdb=" N ILE R 420 " --> pdb=" O LYS R 486 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG R 425 " --> pdb=" O PHE R 434 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N PHE R 434 " --> pdb=" O ARG R 425 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'R' and resid 484 through 486 removed outlier: 3.717A pdb=" N TYR R 501 " --> pdb=" O ALA R 485 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2660 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: 7.91 Time building geometry restraints manager: 9.58 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: 3303 1.32 - 1.45: 5962 1.45 - 1.57: 11270 1.57 - 1.70: 5 1.70 - 1.83: 190 Bond restraints: 20730 Sorted by residual: bond pdb=" N LEU A 272 " pdb=" CA LEU A 272 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.91e+01 bond pdb=" N LEU D 272 " pdb=" CA LEU D 272 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.89e+01 bond pdb=" N LEU Q 272 " pdb=" CA LEU Q 272 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.88e+01 bond pdb=" N BILE H 164 " pdb=" CA BILE H 164 " ideal model delta sigma weight residual 1.458 1.509 -0.051 1.18e-02 7.18e+03 1.88e+01 bond pdb=" N BILE L 164 " pdb=" CA BILE L 164 " ideal model delta sigma weight residual 1.458 1.508 -0.051 1.18e-02 7.18e+03 1.85e+01 ... (remaining 20725 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.34: 553 106.34 - 113.38: 10851 113.38 - 120.42: 9389 120.42 - 127.46: 7297 127.46 - 134.50: 160 Bond angle restraints: 28250 Sorted by residual: angle pdb=" CA PHE H 166 " pdb=" CB PHE H 166 " pdb=" CG PHE H 166 " ideal model delta sigma weight residual 113.80 118.54 -4.74 1.00e+00 1.00e+00 2.25e+01 angle pdb=" CA PHE A 166 " pdb=" CB PHE A 166 " pdb=" CG PHE A 166 " ideal model delta sigma weight residual 113.80 118.52 -4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA PHE D 166 " pdb=" CB PHE D 166 " pdb=" CG PHE D 166 " ideal model delta sigma weight residual 113.80 118.52 -4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA PHE Q 166 " pdb=" CB PHE Q 166 " pdb=" CG PHE Q 166 " ideal model delta sigma weight residual 113.80 118.52 -4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA PHE L 166 " pdb=" CB PHE L 166 " pdb=" CG PHE L 166 " ideal model delta sigma weight residual 113.80 118.50 -4.70 1.00e+00 1.00e+00 2.21e+01 ... (remaining 28245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 10830 17.66 - 35.32: 920 35.32 - 52.99: 135 52.99 - 70.65: 30 70.65 - 88.31: 30 Dihedral angle restraints: 11945 sinusoidal: 4805 harmonic: 7140 Sorted by residual: dihedral pdb=" CA SER D 46 " pdb=" C SER D 46 " pdb=" N ILE D 47 " pdb=" CA ILE D 47 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA SER Q 46 " pdb=" C SER Q 46 " pdb=" N ILE Q 47 " pdb=" CA ILE Q 47 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N ILE A 47 " pdb=" CA ILE A 47 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 11942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1325 0.054 - 0.109: 1148 0.109 - 0.163: 538 0.163 - 0.217: 139 0.217 - 0.272: 35 Chirality restraints: 3185 Sorted by residual: chirality pdb=" C1 MAN K 4 " pdb=" O3 BMA K 3 " pdb=" C2 MAN K 4 " pdb=" O5 MAN K 4 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.33e+01 chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.32e+01 chirality pdb=" C1 MAN P 4 " pdb=" O3 BMA P 3 " pdb=" C2 MAN P 4 " pdb=" O5 MAN P 4 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.29e+01 ... (remaining 3182 not shown) Planarity restraints: 3500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 157 " 0.148 2.00e-02 2.50e+03 7.93e-02 1.26e+02 pdb=" CG TYR A 157 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR A 157 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR A 157 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR A 157 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 157 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 157 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR A 157 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 157 " -0.148 2.00e-02 2.50e+03 7.92e-02 1.26e+02 pdb=" CG TYR L 157 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR L 157 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR L 157 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR L 157 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR L 157 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR L 157 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR L 157 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 157 " 0.148 2.00e-02 2.50e+03 7.92e-02 1.25e+02 pdb=" CG TYR Q 157 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 157 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 157 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 157 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 157 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR Q 157 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR Q 157 " 0.119 2.00e-02 2.50e+03 ... (remaining 3497 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 10 0.98 - 1.96: 10 1.96 - 2.94: 9714 2.94 - 3.92: 62783 3.92 - 4.90: 123008 Warning: very small nonbonded interaction distances. Nonbonded interactions: 195525 Sorted by model distance: nonbonded pdb="CL CL A5409 " pdb="CL CL D5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5409 " pdb="CL CL H5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5409 " pdb="CL CL L5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5409 " pdb="CL CL Q5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL D5409 " pdb="CL CL H5409 " model vdw 0.000 3.340 ... (remaining 195520 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' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 84 or resid 86 through 1 \ 03 or resid 105 through 111 or resid 113 through 124 or resid 126 through 135 or \ resid 137 through 149 or resid 151 through 163 or resid 165 through 197 or resi \ d 199 through 208 or resid 210 through 211 or resid 213 or resid 215 through 224 \ or resid 226 through 228 or resid 230 through 240 or resid 244 through 278 or r \ esid 280 through 425 or resid 427 through 433 or resid 435 through 447 or resid \ 5401 through 5410)) selection = (chain 'D' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 84 or resid 86 through 1 \ 03 or resid 105 through 111 or resid 113 through 124 or resid 126 through 135 or \ resid 137 through 149 or resid 151 through 163 or resid 165 through 197 or resi \ d 199 through 208 or resid 210 through 211 or resid 213 or resid 215 through 224 \ or resid 226 through 228 or resid 230 through 240 or resid 244 through 278 or r \ esid 280 through 425 or resid 427 through 433 or resid 435 through 447 or resid \ 5401 through 5410)) selection = (chain 'H' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 84 or resid 86 through 1 \ 03 or resid 105 through 111 or resid 113 through 124 or resid 126 through 135 or \ resid 137 through 149 or resid 151 through 163 or resid 165 through 197 or resi \ d 199 through 208 or resid 210 through 211 or resid 213 or resid 215 through 224 \ or resid 226 through 228 or resid 230 through 240 or resid 244 through 278 or r \ esid 280 through 425 or resid 427 through 433 or resid 435 through 447 or resid \ 5401 through 5410)) selection = (chain 'L' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 84 or resid 86 through 1 \ 03 or resid 105 through 111 or resid 113 through 124 or resid 126 through 135 or \ resid 137 through 149 or resid 151 through 163 or resid 165 through 197 or resi \ d 199 through 208 or resid 210 through 211 or resid 213 or resid 215 through 224 \ or resid 226 through 228 or resid 230 through 240 or resid 244 through 278 or r \ esid 280 through 425 or resid 427 through 433 or resid 435 through 447 or resid \ 5401 through 5410)) selection = (chain 'Q' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 84 or resid 86 through 1 \ 03 or resid 105 through 111 or resid 113 through 124 or resid 126 through 135 or \ resid 137 through 149 or resid 151 through 163 or resid 165 through 197 or resi \ d 199 through 208 or resid 210 through 211 or resid 213 or resid 215 through 224 \ or resid 226 through 228 or resid 230 through 240 or resid 244 through 278 or r \ esid 280 through 425 or resid 427 through 433 or resid 435 through 447 or resid \ 5401 through 5410)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'S' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'O' selection = chain 'R' } 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=0.20 max=1.00 mean=0.96 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: 2.680 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: 12.320 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 65.320 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.014 0.083 20730 Z= 0.891 Angle : 1.597 8.558 28250 Z= 1.160 Chirality : 0.089 0.272 3185 Planarity : 0.018 0.105 3485 Dihedral : 13.746 88.312 7435 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 2505 helix: -0.26 (0.17), residues: 675 sheet: 0.75 (0.19), residues: 695 loop : -0.25 (0.17), residues: 1135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5010 Ramachandran restraints generated. 2505 Oldfield, 0 Emsley, 2505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5010 Ramachandran restraints generated. 2505 Oldfield, 0 Emsley, 2505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 307 time to evaluate : 2.205 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 317 average time/residue: 1.5881 time to fit residues: 561.8084 Evaluate side-chains 250 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 245 time to evaluate : 2.023 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 2.8477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.6357 > 50: distance: 9 - 93: 15.064 distance: 12 - 90: 6.482 distance: 59 - 84: 18.525 distance: 62 - 81: 5.219 distance: 75 - 81: 7.954 distance: 81 - 82: 12.934 distance: 82 - 83: 14.186 distance: 82 - 85: 15.967 distance: 83 - 84: 10.017 distance: 83 - 90: 19.569 distance: 85 - 86: 23.136 distance: 86 - 87: 15.114 distance: 87 - 88: 13.293 distance: 87 - 89: 6.717 distance: 90 - 91: 17.588 distance: 91 - 92: 5.396 distance: 91 - 94: 12.888 distance: 92 - 93: 14.005 distance: 92 - 98: 27.256 distance: 94 - 95: 12.475 distance: 95 - 96: 10.069 distance: 96 - 97: 17.836 distance: 98 - 99: 23.077 distance: 99 - 100: 15.888 distance: 99 - 102: 7.728 distance: 100 - 101: 15.408 distance: 100 - 106: 28.950 distance: 102 - 103: 31.399 distance: 103 - 104: 18.943 distance: 103 - 105: 19.008 distance: 106 - 107: 19.136 distance: 107 - 108: 5.401 distance: 107 - 110: 15.815 distance: 108 - 109: 8.418 distance: 108 - 114: 16.885 distance: 110 - 111: 7.075 distance: 114 - 115: 11.721 distance: 115 - 116: 12.426 distance: 115 - 118: 21.943 distance: 116 - 117: 12.394 distance: 116 - 122: 9.387 distance: 118 - 119: 9.279 distance: 119 - 120: 20.215 distance: 119 - 121: 18.279 distance: 122 - 123: 19.319 distance: 123 - 124: 26.052 distance: 123 - 126: 15.801 distance: 124 - 125: 12.465 distance: 124 - 131: 33.144 distance: 126 - 127: 10.165 distance: 127 - 128: 28.564 distance: 128 - 129: 13.277 distance: 129 - 130: 18.177 distance: 131 - 132: 3.752 distance: 131 - 137: 7.932 distance: 132 - 133: 13.124 distance: 132 - 135: 9.186 distance: 133 - 134: 19.992 distance: 133 - 138: 11.645 distance: 135 - 136: 6.487 distance: 136 - 137: 12.031 distance: 138 - 139: 4.033 distance: 139 - 140: 7.427 distance: 139 - 142: 12.007 distance: 140 - 141: 9.953 distance: 140 - 147: 9.238 distance: 142 - 143: 36.649 distance: 143 - 144: 27.109 distance: 144 - 145: 24.527 distance: 144 - 146: 24.119 distance: 147 - 148: 5.408 distance: 148 - 149: 5.325 distance: 148 - 151: 4.280 distance: 149 - 150: 4.978 distance: 149 - 155: 7.385 distance: 151 - 152: 8.601 distance: 152 - 153: 9.395 distance: 152 - 154: 16.599 distance: 155 - 156: 3.298 distance: 156 - 157: 3.350 distance: 156 - 159: 4.230 distance: 157 - 158: 3.657 distance: 157 - 162: 3.278 distance: 162 - 177: 3.271