Starting phenix.real_space_refine on Mon Mar 18 14:32:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/03_2024/7a5v_11657_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/03_2024/7a5v_11657.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/03_2024/7a5v_11657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/03_2024/7a5v_11657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/03_2024/7a5v_11657_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/03_2024/7a5v_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 3 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 dihedrals: 3 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: 17.93, per 1000 atoms: 0.85 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: 10.50 Conformation dependent library (CDL) restraints added in 5.8 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: 4.26 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: 7.35 Time building geometry restraints manager: 11.17 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 - 21.01: 11940 21.01 - 42.03: 645 42.03 - 63.04: 95 63.04 - 84.06: 55 84.06 - 105.07: 25 Dihedral angle restraints: 12760 sinusoidal: 5620 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 12757 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: 2.630 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: 11.600 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 70.630 Find NCS groups from input model: 1.340 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:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.260 ------------------------------------------------------------------------------- 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= 0.885 Angle : 1.593 8.558 28250 Z= 1.160 Chirality : 0.089 0.272 3185 Planarity : 0.018 0.105 3485 Dihedral : 14.871 105.069 8250 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 % Allowed : 3.57 % Favored : 95.95 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.015 TRP L 168 HIS 0.034 0.008 HIS D 107 PHE 0.093 0.018 PHE H 63 TYR 0.148 0.018 TYR A 157 ARG 0.030 0.004 ARG Q 180 *********************** 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 : 2.167 Fit side-chains REVERT: A 14 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6505 (tt0) REVERT: A 18 LYS cc_start: 0.6858 (tttt) cc_final: 0.6238 (tmmt) REVERT: A 49 MET cc_start: 0.7698 (mtp) cc_final: 0.6724 (pp-130) REVERT: A 137 MET cc_start: 0.8121 (mmp) cc_final: 0.7632 (mmm) REVERT: A 147 GLU cc_start: 0.7456 (tt0) cc_final: 0.7220 (tt0) REVERT: A 213 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7948 (ttp80) REVERT: A 215 LYS cc_start: 0.7759 (tttt) cc_final: 0.7525 (tttm) REVERT: A 227 MET cc_start: 0.7000 (mmt) cc_final: 0.6173 (mtp) REVERT: A 274 LYS cc_start: 0.7509 (mttt) cc_final: 0.7236 (mttp) REVERT: A 282 ASP cc_start: 0.7710 (m-30) cc_final: 0.7474 (m-30) REVERT: A 425 ARG cc_start: 0.6549 (ttt180) cc_final: 0.6061 (ttm110) REVERT: A 433 PHE cc_start: 0.7363 (t80) cc_final: 0.7141 (t80) REVERT: O 423 TRP cc_start: 0.7958 (m100) cc_final: 0.7717 (m100) REVERT: D 14 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6454 (tt0) REVERT: D 18 LYS cc_start: 0.7016 (tttt) cc_final: 0.6359 (tmmt) REVERT: D 48 ASP cc_start: 0.7896 (m-30) cc_final: 0.7396 (m-30) REVERT: D 49 MET cc_start: 0.7754 (mtp) cc_final: 0.6878 (tmm) REVERT: D 138 MET cc_start: 0.8169 (mtt) cc_final: 0.7946 (mtt) REVERT: D 147 GLU cc_start: 0.7399 (tt0) cc_final: 0.7165 (tt0) REVERT: D 173 LYS cc_start: 0.7642 (mttm) cc_final: 0.7439 (mtpt) REVERT: D 227 MET cc_start: 0.6925 (mmt) cc_final: 0.6050 (mtp) REVERT: D 274 LYS cc_start: 0.7408 (mttt) cc_final: 0.7172 (mttp) REVERT: D 301 PHE cc_start: 0.7986 (t80) cc_final: 0.7682 (t80) REVERT: D 425 ARG cc_start: 0.6644 (ttt180) cc_final: 0.6116 (ttm110) REVERT: E 423 TRP cc_start: 0.7943 (m100) cc_final: 0.7719 (m100) REVERT: H 14 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6405 (tt0) REVERT: H 18 LYS cc_start: 0.6836 (tttt) cc_final: 0.6132 (tmmt) REVERT: H 21 LYS cc_start: 0.6448 (tttt) cc_final: 0.6140 (ttmm) REVERT: H 30 ASP cc_start: 0.8392 (m-30) cc_final: 0.8155 (m-30) REVERT: H 49 MET cc_start: 0.7734 (mtp) cc_final: 0.6807 (tmm) REVERT: H 138 MET cc_start: 0.8161 (mtt) cc_final: 0.7925 (mtt) REVERT: H 173 LYS cc_start: 0.7643 (mttm) cc_final: 0.7359 (mtpm) REVERT: H 179 GLU cc_start: 0.7772 (pm20) cc_final: 0.7554 (pm20) REVERT: H 227 MET cc_start: 0.7101 (mmt) cc_final: 0.5989 (ttp) REVERT: H 274 LYS cc_start: 0.7426 (mttt) cc_final: 0.7173 (mttp) REVERT: H 301 PHE cc_start: 0.7967 (t80) cc_final: 0.7574 (t80) REVERT: H 425 ARG cc_start: 0.6641 (ttt180) cc_final: 0.6173 (ttm110) REVERT: H 429 ILE cc_start: 0.6797 (tp) cc_final: 0.6501 (mt) REVERT: H 437 LEU cc_start: 0.7069 (mp) cc_final: 0.6766 (mp) REVERT: L 14 GLU cc_start: 0.6782 (mt-10) cc_final: 0.6420 (tt0) REVERT: L 18 LYS cc_start: 0.6948 (tttt) cc_final: 0.6505 (mtpt) REVERT: L 30 ASP cc_start: 0.8437 (m-30) cc_final: 0.8149 (t0) REVERT: L 49 MET cc_start: 0.7811 (mtp) cc_final: 0.6828 (tmm) REVERT: L 147 GLU cc_start: 0.7528 (tt0) cc_final: 0.7254 (tt0) REVERT: L 227 MET cc_start: 0.6996 (mmt) cc_final: 0.5877 (ttp) REVERT: L 274 LYS cc_start: 0.7497 (mttt) cc_final: 0.7257 (mttp) REVERT: L 301 PHE cc_start: 0.8009 (t80) cc_final: 0.7587 (t80) REVERT: L 425 ARG cc_start: 0.6677 (ttt180) cc_final: 0.6193 (ttm110) REVERT: Q 14 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6385 (tt0) REVERT: Q 18 LYS cc_start: 0.6858 (tttt) cc_final: 0.6198 (tmmt) REVERT: Q 48 ASP cc_start: 0.7828 (m-30) cc_final: 0.7330 (m-30) REVERT: Q 49 MET cc_start: 0.7651 (mtp) cc_final: 0.6712 (tmm) REVERT: Q 147 GLU cc_start: 0.7459 (tt0) cc_final: 0.7162 (tt0) REVERT: Q 213 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7922 (ttp80) REVERT: Q 227 MET cc_start: 0.7066 (mmt) cc_final: 0.6717 (mmp) REVERT: Q 274 LYS cc_start: 0.7437 (mttt) cc_final: 0.7209 (mttp) REVERT: Q 425 ARG cc_start: 0.6737 (ttt180) cc_final: 0.6255 (ttm110) REVERT: R 423 TRP cc_start: 0.7894 (m100) cc_final: 0.7675 (m100) outliers start: 10 outliers final: 5 residues processed: 317 average time/residue: 1.5922 time to fit residues: 562.5460 Evaluate side-chains 270 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 265 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 445 THR Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain I residue 445 THR Chi-restraints excluded: chain M residue 445 THR Chi-restraints excluded: chain R residue 445 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 0.1980 chunk 170 optimal weight: 0.0770 chunk 94 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 204 optimal weight: 0.6980 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN O 461 ASN D 224 GLN H 224 GLN I 461 ASN L 224 GLN Q 224 GLN R 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.163 20730 Z= 0.518 Angle : 1.314 24.042 28250 Z= 0.709 Chirality : 0.074 0.853 3185 Planarity : 0.016 0.370 3485 Dihedral : 12.992 115.614 3860 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.95 % Rotamer: Outliers : 0.76 % Allowed : 6.67 % Favored : 92.57 % Cbeta Deviations : 0.09 % 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: -0.41 (0.16), residues: 2505 helix: -0.92 (0.17), residues: 730 sheet: 0.58 (0.18), residues: 775 loop : -0.26 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.117 0.010 TRP D 92 HIS 0.020 0.004 HIS M 414 PHE 0.178 0.010 PHE L 433 TYR 0.141 0.009 TYR L 126 ARG 0.111 0.004 ARG E 459 *********************** REFINEMENT MACRO_CYCLE 2 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 290 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 277 time to evaluate : 2.045 Fit side-chains REVERT: A 14 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6346 (tt0) REVERT: A 18 LYS cc_start: 0.6778 (tttt) cc_final: 0.6346 (mtpt) REVERT: A 49 MET cc_start: 0.7596 (mtp) cc_final: 0.6694 (tmm) REVERT: A 137 MET cc_start: 0.8109 (mmp) cc_final: 0.7620 (mmm) REVERT: A 147 GLU cc_start: 0.7383 (tt0) cc_final: 0.7124 (tt0) REVERT: A 215 LYS cc_start: 0.7678 (tttt) cc_final: 0.7444 (tttm) REVERT: A 227 MET cc_start: 0.6942 (mmt) cc_final: 0.5908 (ttm) REVERT: A 274 LYS cc_start: 0.7482 (mttt) cc_final: 0.7191 (mttp) REVERT: A 282 ASP cc_start: 0.7640 (m-30) cc_final: 0.7436 (m-30) REVERT: A 425 ARG cc_start: 0.6467 (ttt180) cc_final: 0.6022 (ttm110) REVERT: O 423 TRP cc_start: 0.7812 (m100) cc_final: 0.7589 (m100) REVERT: D 14 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6381 (tt0) REVERT: D 18 LYS cc_start: 0.6901 (tttt) cc_final: 0.6280 (pptt) REVERT: D 48 ASP cc_start: 0.7805 (m-30) cc_final: 0.7299 (m-30) REVERT: D 49 MET cc_start: 0.7647 (mtp) cc_final: 0.6816 (tmm) REVERT: D 147 GLU cc_start: 0.7352 (tt0) cc_final: 0.7108 (tt0) REVERT: D 173 LYS cc_start: 0.7555 (mttm) cc_final: 0.7247 (mmmt) REVERT: D 227 MET cc_start: 0.6813 (mmt) cc_final: 0.5960 (mtp) REVERT: D 274 LYS cc_start: 0.7295 (mttt) cc_final: 0.7023 (mttp) REVERT: D 301 PHE cc_start: 0.7818 (t80) cc_final: 0.7538 (t80) REVERT: D 425 ARG cc_start: 0.6598 (ttt180) cc_final: 0.6095 (ttm110) REVERT: E 423 TRP cc_start: 0.7832 (m100) cc_final: 0.7592 (m100) REVERT: E 470 MET cc_start: 0.5444 (mtp) cc_final: 0.4767 (mtt) REVERT: H 14 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6150 (tt0) REVERT: H 18 LYS cc_start: 0.6667 (tttt) cc_final: 0.6008 (tmmt) REVERT: H 21 LYS cc_start: 0.6288 (tttt) cc_final: 0.6009 (ttmm) REVERT: H 30 ASP cc_start: 0.8145 (m-30) cc_final: 0.7897 (m-30) REVERT: H 49 MET cc_start: 0.7693 (mtp) cc_final: 0.6690 (tmm) REVERT: H 173 LYS cc_start: 0.7608 (mttm) cc_final: 0.7349 (mtpm) REVERT: H 227 MET cc_start: 0.7100 (mmt) cc_final: 0.6009 (ttp) REVERT: H 274 LYS cc_start: 0.7395 (mttt) cc_final: 0.7117 (mttp) REVERT: H 301 PHE cc_start: 0.7822 (t80) cc_final: 0.7396 (t80) REVERT: H 425 ARG cc_start: 0.6560 (ttt180) cc_final: 0.6164 (ttm110) REVERT: H 429 ILE cc_start: 0.6707 (tp) cc_final: 0.6344 (mm) REVERT: H 437 LEU cc_start: 0.7018 (mp) cc_final: 0.6763 (mp) REVERT: L 14 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6426 (tt0) REVERT: L 18 LYS cc_start: 0.6920 (tttt) cc_final: 0.6475 (mtpt) REVERT: L 49 MET cc_start: 0.7554 (mtp) cc_final: 0.6751 (tmm) REVERT: L 147 GLU cc_start: 0.7438 (tt0) cc_final: 0.7178 (tt0) REVERT: L 227 MET cc_start: 0.6960 (mmt) cc_final: 0.6150 (ttp) REVERT: L 425 ARG cc_start: 0.6605 (ttt180) cc_final: 0.6147 (ttm110) REVERT: M 458 SER cc_start: 0.5083 (OUTLIER) cc_final: 0.4312 (p) REVERT: M 459 ARG cc_start: 0.4740 (OUTLIER) cc_final: 0.4156 (ptm160) REVERT: M 471 ASN cc_start: 0.3301 (OUTLIER) cc_final: 0.2938 (p0) REVERT: Q 14 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6295 (tt0) REVERT: Q 18 LYS cc_start: 0.6788 (tttt) cc_final: 0.6162 (tmmt) REVERT: Q 48 ASP cc_start: 0.7758 (m-30) cc_final: 0.7273 (m-30) REVERT: Q 49 MET cc_start: 0.7591 (mtp) cc_final: 0.6699 (pp-130) REVERT: Q 147 GLU cc_start: 0.7354 (tt0) cc_final: 0.7082 (tt0) REVERT: Q 227 MET cc_start: 0.6981 (mmt) cc_final: 0.6085 (mtp) REVERT: Q 274 LYS cc_start: 0.7378 (mttt) cc_final: 0.7159 (mttp) REVERT: Q 425 ARG cc_start: 0.6572 (ttt180) cc_final: 0.6095 (ttm110) REVERT: R 423 TRP cc_start: 0.7780 (m100) cc_final: 0.7363 (m100) outliers start: 13 outliers final: 4 residues processed: 286 average time/residue: 1.5065 time to fit residues: 482.6150 Evaluate side-chains 266 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 259 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain I residue 509 THR Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain M residue 458 SER Chi-restraints excluded: chain M residue 459 ARG Chi-restraints excluded: chain M residue 471 ASN Chi-restraints excluded: chain Q residue 278 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 221 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 202 optimal weight: 30.0000 chunk 69 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN D 224 GLN E 461 ASN L 224 GLN Q 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20730 Z= 0.199 Angle : 0.662 6.982 28250 Z= 0.359 Chirality : 0.048 0.175 3185 Planarity : 0.005 0.050 3485 Dihedral : 10.483 79.621 3856 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.33 % Allowed : 6.33 % Favored : 93.33 % 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: 1.29 (0.16), residues: 2505 helix: 1.25 (0.19), residues: 685 sheet: 0.91 (0.18), residues: 785 loop : 0.73 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 168 HIS 0.006 0.001 HIS D 107 PHE 0.020 0.002 PHE A 221 TYR 0.031 0.002 TYR Q 157 ARG 0.009 0.001 ARG Q 28 *********************** REFINEMENT MACRO_CYCLE 3 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 283 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 277 time to evaluate : 1.726 Fit side-chains REVERT: A 14 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6256 (tt0) REVERT: A 18 LYS cc_start: 0.6838 (tttt) cc_final: 0.6384 (mtpt) REVERT: A 49 MET cc_start: 0.7472 (mtp) cc_final: 0.6633 (pp-130) REVERT: A 137 MET cc_start: 0.8072 (mmp) cc_final: 0.7557 (mmm) REVERT: A 227 MET cc_start: 0.6907 (mmt) cc_final: 0.5838 (ttm) REVERT: A 425 ARG cc_start: 0.6480 (ttt180) cc_final: 0.6055 (ttm110) REVERT: D 14 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6411 (tt0) REVERT: D 18 LYS cc_start: 0.6803 (tttt) cc_final: 0.6377 (ttpp) REVERT: D 21 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.6035 (tppt) REVERT: D 48 ASP cc_start: 0.7759 (m-30) cc_final: 0.7259 (m-30) REVERT: D 49 MET cc_start: 0.7470 (mtp) cc_final: 0.6598 (tmm) REVERT: D 147 GLU cc_start: 0.7306 (tt0) cc_final: 0.7070 (tt0) REVERT: D 173 LYS cc_start: 0.7592 (mttm) cc_final: 0.7263 (mmtt) REVERT: D 227 MET cc_start: 0.6993 (mmt) cc_final: 0.5952 (ttp) REVERT: D 301 PHE cc_start: 0.7766 (t80) cc_final: 0.7506 (t80) REVERT: D 425 ARG cc_start: 0.6542 (ttt180) cc_final: 0.6053 (ttm110) REVERT: E 423 TRP cc_start: 0.7863 (m100) cc_final: 0.7642 (m100) REVERT: E 470 MET cc_start: 0.5475 (mtp) cc_final: 0.4856 (mtt) REVERT: H 14 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6207 (tt0) REVERT: H 18 LYS cc_start: 0.6767 (tttt) cc_final: 0.6069 (tmmt) REVERT: H 30 ASP cc_start: 0.8342 (m-30) cc_final: 0.8097 (m-30) REVERT: H 49 MET cc_start: 0.7528 (mtp) cc_final: 0.6577 (tmm) REVERT: H 173 LYS cc_start: 0.7600 (mttm) cc_final: 0.7309 (mtpm) REVERT: H 227 MET cc_start: 0.7092 (mmt) cc_final: 0.6020 (ttm) REVERT: H 274 LYS cc_start: 0.7372 (mttt) cc_final: 0.7154 (mttp) REVERT: H 425 ARG cc_start: 0.6393 (ttt180) cc_final: 0.5987 (ttm110) REVERT: H 429 ILE cc_start: 0.6625 (tp) cc_final: 0.6299 (mm) REVERT: H 437 LEU cc_start: 0.7064 (mp) cc_final: 0.6828 (mp) REVERT: L 14 GLU cc_start: 0.6619 (mt-10) cc_final: 0.6316 (tt0) REVERT: L 49 MET cc_start: 0.7561 (mtp) cc_final: 0.6738 (tmm) REVERT: L 147 GLU cc_start: 0.7412 (tt0) cc_final: 0.7178 (tt0) REVERT: L 227 MET cc_start: 0.7060 (mmt) cc_final: 0.5977 (ttp) REVERT: L 268 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5994 (tt) REVERT: L 425 ARG cc_start: 0.6532 (ttt180) cc_final: 0.6099 (ttm110) REVERT: Q 14 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6247 (tt0) REVERT: Q 18 LYS cc_start: 0.6828 (tttt) cc_final: 0.6355 (mtmp) REVERT: Q 48 ASP cc_start: 0.7699 (m-30) cc_final: 0.7238 (m-30) REVERT: Q 49 MET cc_start: 0.7448 (mtp) cc_final: 0.6582 (pp-130) REVERT: Q 147 GLU cc_start: 0.7378 (tt0) cc_final: 0.7135 (tt0) REVERT: Q 227 MET cc_start: 0.6948 (mmt) cc_final: 0.6595 (mmp) REVERT: Q 274 LYS cc_start: 0.7383 (mttt) cc_final: 0.7177 (mttp) REVERT: Q 425 ARG cc_start: 0.6532 (ttt180) cc_final: 0.6080 (ttm110) REVERT: R 423 TRP cc_start: 0.7752 (m100) cc_final: 0.7521 (m100) outliers start: 6 outliers final: 1 residues processed: 278 average time/residue: 1.5306 time to fit residues: 474.7969 Evaluate side-chains 265 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 262 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain L residue 268 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 194 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN D 224 GLN H 224 GLN L 224 GLN Q 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20730 Z= 0.155 Angle : 0.585 6.278 28250 Z= 0.316 Chirality : 0.046 0.166 3185 Planarity : 0.004 0.035 3485 Dihedral : 9.356 72.253 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.71 % Allowed : 6.19 % Favored : 93.10 % 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: 1.82 (0.17), residues: 2505 helix: 1.83 (0.19), residues: 685 sheet: 1.17 (0.18), residues: 780 loop : 1.00 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 423 HIS 0.003 0.001 HIS D 107 PHE 0.016 0.002 PHE Q 221 TYR 0.030 0.002 TYR D 299 ARG 0.008 0.001 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 4 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 282 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 269 time to evaluate : 2.167 Fit side-chains REVERT: A 14 GLU cc_start: 0.6499 (mt-10) cc_final: 0.6220 (tt0) REVERT: A 18 LYS cc_start: 0.6804 (tttt) cc_final: 0.6365 (mtpt) REVERT: A 49 MET cc_start: 0.7438 (mtp) cc_final: 0.6609 (pp-130) REVERT: A 137 MET cc_start: 0.8058 (mmp) cc_final: 0.7586 (mmm) REVERT: A 227 MET cc_start: 0.6875 (mmt) cc_final: 0.5806 (ttm) REVERT: A 425 ARG cc_start: 0.6408 (ttt180) cc_final: 0.5990 (ttm110) REVERT: D 14 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6427 (tt0) REVERT: D 18 LYS cc_start: 0.6758 (tttt) cc_final: 0.6275 (ttpp) REVERT: D 21 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.6053 (tppt) REVERT: D 48 ASP cc_start: 0.7714 (m-30) cc_final: 0.7212 (m-30) REVERT: D 49 MET cc_start: 0.7412 (mtp) cc_final: 0.6433 (pp-130) REVERT: D 147 GLU cc_start: 0.7313 (tt0) cc_final: 0.6979 (tt0) REVERT: D 173 LYS cc_start: 0.7630 (mttm) cc_final: 0.7320 (mmmt) REVERT: D 227 MET cc_start: 0.6993 (mmt) cc_final: 0.5945 (ttp) REVERT: D 425 ARG cc_start: 0.6545 (ttt180) cc_final: 0.5901 (mtm-85) REVERT: H 14 GLU cc_start: 0.6518 (mt-10) cc_final: 0.6278 (tt0) REVERT: H 18 LYS cc_start: 0.6776 (tttt) cc_final: 0.6089 (tmmt) REVERT: H 30 ASP cc_start: 0.8332 (m-30) cc_final: 0.8028 (m-30) REVERT: H 49 MET cc_start: 0.7499 (mtp) cc_final: 0.6594 (tmm) REVERT: H 70 LYS cc_start: 0.8089 (mttp) cc_final: 0.7310 (mppt) REVERT: H 173 LYS cc_start: 0.7576 (mttm) cc_final: 0.7341 (mtmm) REVERT: H 227 MET cc_start: 0.7022 (mmt) cc_final: 0.5928 (ttp) REVERT: H 268 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6054 (tt) REVERT: H 274 LYS cc_start: 0.7358 (mttt) cc_final: 0.7115 (mttp) REVERT: H 425 ARG cc_start: 0.6462 (ttt180) cc_final: 0.6062 (ttm110) REVERT: H 429 ILE cc_start: 0.6647 (tp) cc_final: 0.6301 (mm) REVERT: H 437 LEU cc_start: 0.7035 (mp) cc_final: 0.6791 (mp) REVERT: L 14 GLU cc_start: 0.6566 (mt-10) cc_final: 0.6299 (pt0) REVERT: L 49 MET cc_start: 0.7538 (mtp) cc_final: 0.6723 (tmm) REVERT: L 147 GLU cc_start: 0.7383 (tt0) cc_final: 0.7171 (tt0) REVERT: L 227 MET cc_start: 0.7055 (mmt) cc_final: 0.5970 (ttp) REVERT: L 268 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6071 (tt) REVERT: L 425 ARG cc_start: 0.6491 (ttt180) cc_final: 0.6057 (ttm110) REVERT: Q 14 GLU cc_start: 0.6460 (mt-10) cc_final: 0.6254 (pt0) REVERT: Q 18 LYS cc_start: 0.6830 (tttt) cc_final: 0.6212 (tmmt) REVERT: Q 48 ASP cc_start: 0.7642 (m-30) cc_final: 0.7192 (m-30) REVERT: Q 49 MET cc_start: 0.7420 (mtp) cc_final: 0.6586 (pp-130) REVERT: Q 147 GLU cc_start: 0.7341 (tt0) cc_final: 0.7082 (tt0) REVERT: Q 227 MET cc_start: 0.6940 (mmt) cc_final: 0.6034 (ttp) REVERT: Q 274 LYS cc_start: 0.7345 (mttt) cc_final: 0.7127 (mttp) REVERT: Q 425 ARG cc_start: 0.6601 (ttt180) cc_final: 0.6161 (ttm110) REVERT: R 423 TRP cc_start: 0.7766 (m100) cc_final: 0.7528 (m100) outliers start: 13 outliers final: 1 residues processed: 274 average time/residue: 1.5361 time to fit residues: 471.1917 Evaluate side-chains 270 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 266 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain L residue 268 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 0.3980 chunk 123 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 150 optimal weight: 0.0370 chunk 0 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.0864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN D 224 GLN H 224 GLN L 224 GLN Q 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20730 Z= 0.169 Angle : 0.604 6.355 28250 Z= 0.324 Chirality : 0.047 0.192 3185 Planarity : 0.004 0.039 3485 Dihedral : 8.908 67.583 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 0.71 % Allowed : 6.67 % Favored : 92.62 % 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: 1.88 (0.17), residues: 2505 helix: 1.84 (0.19), residues: 685 sheet: 1.20 (0.18), residues: 790 loop : 1.06 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 423 HIS 0.004 0.001 HIS D 107 PHE 0.016 0.002 PHE A 98 TYR 0.031 0.002 TYR A 299 ARG 0.006 0.001 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 5 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 284 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 272 time to evaluate : 2.108 Fit side-chains REVERT: A 14 GLU cc_start: 0.6555 (mt-10) cc_final: 0.6293 (tt0) REVERT: A 18 LYS cc_start: 0.6827 (tttt) cc_final: 0.6387 (mtpt) REVERT: A 49 MET cc_start: 0.7451 (mtp) cc_final: 0.6676 (pp-130) REVERT: A 137 MET cc_start: 0.8090 (mmp) cc_final: 0.7624 (mmm) REVERT: A 227 MET cc_start: 0.6881 (mmt) cc_final: 0.5811 (ttm) REVERT: A 425 ARG cc_start: 0.6424 (ttt180) cc_final: 0.6006 (ttm110) REVERT: D 14 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6258 (tt0) REVERT: D 18 LYS cc_start: 0.6784 (tttt) cc_final: 0.6226 (mtmm) REVERT: D 21 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.6060 (tppt) REVERT: D 48 ASP cc_start: 0.7703 (m-30) cc_final: 0.7204 (m-30) REVERT: D 49 MET cc_start: 0.7389 (mtp) cc_final: 0.6428 (pp-130) REVERT: D 147 GLU cc_start: 0.7314 (tt0) cc_final: 0.6991 (tt0) REVERT: D 173 LYS cc_start: 0.7601 (mttm) cc_final: 0.7294 (mmmt) REVERT: D 227 MET cc_start: 0.7000 (mmt) cc_final: 0.5957 (ttp) REVERT: D 425 ARG cc_start: 0.6529 (ttt180) cc_final: 0.5892 (mtm-85) REVERT: H 14 GLU cc_start: 0.6545 (mt-10) cc_final: 0.6301 (tt0) REVERT: H 18 LYS cc_start: 0.6784 (tttt) cc_final: 0.6112 (tmmt) REVERT: H 30 ASP cc_start: 0.8310 (m-30) cc_final: 0.7986 (m-30) REVERT: H 49 MET cc_start: 0.7479 (mtp) cc_final: 0.6614 (tmm) REVERT: H 70 LYS cc_start: 0.8077 (mttp) cc_final: 0.7300 (mppt) REVERT: H 173 LYS cc_start: 0.7582 (mttm) cc_final: 0.7344 (mtmm) REVERT: H 227 MET cc_start: 0.7042 (mmt) cc_final: 0.5955 (ttp) REVERT: H 268 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6105 (tt) REVERT: H 425 ARG cc_start: 0.6361 (ttt180) cc_final: 0.5972 (ttm110) REVERT: H 429 ILE cc_start: 0.6660 (tp) cc_final: 0.6296 (mm) REVERT: H 437 LEU cc_start: 0.7048 (mp) cc_final: 0.6804 (mp) REVERT: L 14 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6329 (pt0) REVERT: L 49 MET cc_start: 0.7563 (mtp) cc_final: 0.6706 (tmm) REVERT: L 227 MET cc_start: 0.7062 (mmt) cc_final: 0.6219 (ttp) REVERT: L 425 ARG cc_start: 0.6487 (ttt180) cc_final: 0.6057 (ttm110) REVERT: Q 14 GLU cc_start: 0.6498 (mt-10) cc_final: 0.6230 (tt0) REVERT: Q 18 LYS cc_start: 0.6863 (tttt) cc_final: 0.6228 (tmmt) REVERT: Q 48 ASP cc_start: 0.7623 (m-30) cc_final: 0.7165 (m-30) REVERT: Q 49 MET cc_start: 0.7432 (mtp) cc_final: 0.6609 (pp-130) REVERT: Q 147 GLU cc_start: 0.7353 (tt0) cc_final: 0.7117 (tt0) REVERT: Q 227 MET cc_start: 0.6936 (mmt) cc_final: 0.6032 (ttp) REVERT: Q 274 LYS cc_start: 0.7351 (mttt) cc_final: 0.7139 (mttp) REVERT: Q 425 ARG cc_start: 0.6491 (ttt180) cc_final: 0.5914 (mtm-85) REVERT: R 423 TRP cc_start: 0.7791 (m100) cc_final: 0.7516 (m100) outliers start: 12 outliers final: 3 residues processed: 276 average time/residue: 1.5421 time to fit residues: 475.7325 Evaluate side-chains 271 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 266 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain M residue 420 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 217 optimal weight: 0.0000 chunk 180 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 overall best weight: 1.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN L 224 GLN Q 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20730 Z= 0.213 Angle : 0.661 6.589 28250 Z= 0.355 Chirality : 0.049 0.211 3185 Planarity : 0.005 0.048 3485 Dihedral : 9.008 66.677 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.71 % Allowed : 6.67 % Favored : 92.62 % 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: 1.75 (0.17), residues: 2505 helix: 1.66 (0.19), residues: 685 sheet: 1.08 (0.18), residues: 795 loop : 1.08 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 423 HIS 0.006 0.001 HIS D 107 PHE 0.021 0.002 PHE A 98 TYR 0.033 0.003 TYR Q 157 ARG 0.009 0.001 ARG H 213 *********************** REFINEMENT MACRO_CYCLE 6 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 273 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 261 time to evaluate : 2.174 Fit side-chains REVERT: A 14 GLU cc_start: 0.6513 (mt-10) cc_final: 0.6280 (tt0) REVERT: A 18 LYS cc_start: 0.6830 (tttt) cc_final: 0.6409 (mtpt) REVERT: A 49 MET cc_start: 0.7448 (mtp) cc_final: 0.6661 (pp-130) REVERT: A 227 MET cc_start: 0.6917 (mmt) cc_final: 0.5839 (ttm) REVERT: A 425 ARG cc_start: 0.6442 (ttt180) cc_final: 0.6011 (ttm110) REVERT: D 14 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6401 (tt0) REVERT: D 18 LYS cc_start: 0.6785 (tttt) cc_final: 0.6312 (mtmp) REVERT: D 21 LYS cc_start: 0.6548 (OUTLIER) cc_final: 0.6141 (tppt) REVERT: D 48 ASP cc_start: 0.7716 (m-30) cc_final: 0.7215 (m-30) REVERT: D 49 MET cc_start: 0.7405 (mtp) cc_final: 0.6445 (pp-130) REVERT: D 227 MET cc_start: 0.7006 (mmt) cc_final: 0.5988 (ttp) REVERT: D 425 ARG cc_start: 0.6506 (ttt180) cc_final: 0.6034 (ttm110) REVERT: H 18 LYS cc_start: 0.6770 (tttt) cc_final: 0.6090 (tmmt) REVERT: H 49 MET cc_start: 0.7482 (mtp) cc_final: 0.6566 (tmm) REVERT: H 173 LYS cc_start: 0.7582 (mttm) cc_final: 0.7344 (mtmm) REVERT: H 227 MET cc_start: 0.7032 (mmt) cc_final: 0.5945 (ttp) REVERT: H 268 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.6091 (tt) REVERT: H 425 ARG cc_start: 0.6362 (ttt180) cc_final: 0.5962 (ttm110) REVERT: H 429 ILE cc_start: 0.6637 (tp) cc_final: 0.6264 (mm) REVERT: H 437 LEU cc_start: 0.7015 (mp) cc_final: 0.6797 (mp) REVERT: L 14 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6356 (pt0) REVERT: L 49 MET cc_start: 0.7544 (mtp) cc_final: 0.6695 (tmm) REVERT: L 227 MET cc_start: 0.7075 (mmt) cc_final: 0.5958 (ttp) REVERT: L 425 ARG cc_start: 0.6492 (ttt180) cc_final: 0.6056 (ttm110) REVERT: Q 14 GLU cc_start: 0.6496 (mt-10) cc_final: 0.6285 (pt0) REVERT: Q 18 LYS cc_start: 0.6909 (tttt) cc_final: 0.6258 (tmmt) REVERT: Q 48 ASP cc_start: 0.7644 (m-30) cc_final: 0.7177 (m-30) REVERT: Q 49 MET cc_start: 0.7433 (mtp) cc_final: 0.6574 (pp-130) REVERT: Q 147 GLU cc_start: 0.7359 (tt0) cc_final: 0.7151 (tt0) REVERT: Q 227 MET cc_start: 0.6970 (mmt) cc_final: 0.6044 (mtp) REVERT: Q 274 LYS cc_start: 0.7358 (mttt) cc_final: 0.7145 (mttp) REVERT: Q 425 ARG cc_start: 0.6517 (ttt180) cc_final: 0.6057 (ttm110) REVERT: R 459 ARG cc_start: 0.4932 (OUTLIER) cc_final: 0.4645 (pmt-80) outliers start: 12 outliers final: 6 residues processed: 267 average time/residue: 1.4999 time to fit residues: 449.7727 Evaluate side-chains 270 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 261 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain R residue 459 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 135 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN L 224 GLN ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20730 Z= 0.321 Angle : 0.784 7.628 28250 Z= 0.420 Chirality : 0.054 0.243 3185 Planarity : 0.006 0.064 3485 Dihedral : 9.772 70.635 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.81 % Allowed : 7.00 % Favored : 92.19 % 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: 1.53 (0.17), residues: 2505 helix: 1.32 (0.19), residues: 685 sheet: 1.04 (0.18), residues: 795 loop : 0.99 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP I 423 HIS 0.010 0.002 HIS D 107 PHE 0.031 0.003 PHE L 98 TYR 0.036 0.004 TYR D 157 ARG 0.014 0.001 ARG Q 28 *********************** REFINEMENT MACRO_CYCLE 7 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 273 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 259 time to evaluate : 2.276 Fit side-chains REVERT: A 14 GLU cc_start: 0.6541 (mt-10) cc_final: 0.6335 (tt0) REVERT: A 49 MET cc_start: 0.7456 (mtp) cc_final: 0.6657 (pp-130) REVERT: A 227 MET cc_start: 0.6884 (mmt) cc_final: 0.5802 (ttm) REVERT: A 425 ARG cc_start: 0.6503 (ttt180) cc_final: 0.6071 (ttm110) REVERT: O 439 SER cc_start: 0.7441 (OUTLIER) cc_final: 0.7176 (t) REVERT: O 459 ARG cc_start: 0.5239 (OUTLIER) cc_final: 0.3877 (ppt170) REVERT: D 14 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6463 (tt0) REVERT: D 18 LYS cc_start: 0.6837 (tttt) cc_final: 0.6216 (tmmt) REVERT: D 21 LYS cc_start: 0.6582 (OUTLIER) cc_final: 0.6163 (tppt) REVERT: D 48 ASP cc_start: 0.7718 (m-30) cc_final: 0.7212 (m-30) REVERT: D 49 MET cc_start: 0.7424 (mtp) cc_final: 0.6448 (pp-130) REVERT: D 147 GLU cc_start: 0.7355 (tt0) cc_final: 0.7038 (tt0) REVERT: D 227 MET cc_start: 0.6942 (mmt) cc_final: 0.5934 (ttp) REVERT: D 425 ARG cc_start: 0.6506 (ttt180) cc_final: 0.6049 (ttm110) REVERT: H 18 LYS cc_start: 0.6809 (tttt) cc_final: 0.6124 (tmmt) REVERT: H 49 MET cc_start: 0.7480 (mtp) cc_final: 0.6501 (pp-130) REVERT: H 173 LYS cc_start: 0.7575 (mttm) cc_final: 0.7329 (mtmm) REVERT: H 227 MET cc_start: 0.7025 (mmt) cc_final: 0.5906 (ttp) REVERT: H 425 ARG cc_start: 0.6416 (ttt180) cc_final: 0.5985 (ttm110) REVERT: H 429 ILE cc_start: 0.6692 (tp) cc_final: 0.6304 (mm) REVERT: L 14 GLU cc_start: 0.6651 (mt-10) cc_final: 0.6377 (pt0) REVERT: L 30 ASP cc_start: 0.8285 (m-30) cc_final: 0.8070 (m-30) REVERT: L 49 MET cc_start: 0.7572 (mtp) cc_final: 0.6695 (tmm) REVERT: L 227 MET cc_start: 0.7080 (mmt) cc_final: 0.5970 (ttp) REVERT: L 425 ARG cc_start: 0.6530 (ttt180) cc_final: 0.6093 (ttm110) REVERT: Q 14 GLU cc_start: 0.6557 (mt-10) cc_final: 0.6350 (pt0) REVERT: Q 18 LYS cc_start: 0.6930 (tttt) cc_final: 0.6259 (tmmt) REVERT: Q 48 ASP cc_start: 0.7693 (m-30) cc_final: 0.7212 (m-30) REVERT: Q 49 MET cc_start: 0.7433 (mtp) cc_final: 0.6534 (pp-130) REVERT: Q 147 GLU cc_start: 0.7300 (tt0) cc_final: 0.7099 (tt0) REVERT: Q 227 MET cc_start: 0.6995 (mmt) cc_final: 0.6084 (mtp) REVERT: Q 274 LYS cc_start: 0.7352 (mttt) cc_final: 0.7140 (mttp) REVERT: Q 425 ARG cc_start: 0.6545 (ttt180) cc_final: 0.6079 (ttm110) outliers start: 14 outliers final: 7 residues processed: 268 average time/residue: 1.4953 time to fit residues: 449.8736 Evaluate side-chains 267 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 257 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 459 ARG Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 470 MET Chi-restraints excluded: chain R residue 456 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN L 224 GLN ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20730 Z= 0.244 Angle : 0.693 7.795 28250 Z= 0.371 Chirality : 0.050 0.203 3185 Planarity : 0.005 0.053 3485 Dihedral : 9.569 69.891 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 0.90 % Allowed : 6.90 % Favored : 92.19 % 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: 1.62 (0.17), residues: 2505 helix: 1.51 (0.19), residues: 685 sheet: 1.06 (0.18), residues: 795 loop : 0.99 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 423 HIS 0.007 0.002 HIS D 107 PHE 0.021 0.002 PHE L 98 TYR 0.032 0.003 TYR Q 157 ARG 0.009 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 8 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 267 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 252 time to evaluate : 2.263 Fit side-chains REVERT: A 49 MET cc_start: 0.7459 (mtp) cc_final: 0.6649 (pp-130) REVERT: A 227 MET cc_start: 0.6877 (mmt) cc_final: 0.5792 (ttm) REVERT: A 425 ARG cc_start: 0.6475 (ttt180) cc_final: 0.6049 (ttm110) REVERT: D 14 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6462 (tt0) REVERT: D 18 LYS cc_start: 0.6869 (tttt) cc_final: 0.6239 (tmmt) REVERT: D 21 LYS cc_start: 0.6524 (OUTLIER) cc_final: 0.6094 (tppt) REVERT: D 48 ASP cc_start: 0.7723 (m-30) cc_final: 0.7225 (m-30) REVERT: D 49 MET cc_start: 0.7391 (mtp) cc_final: 0.6423 (pp-130) REVERT: D 147 GLU cc_start: 0.7328 (tt0) cc_final: 0.7017 (tt0) REVERT: D 227 MET cc_start: 0.6994 (mmt) cc_final: 0.5986 (ttp) REVERT: D 425 ARG cc_start: 0.6502 (ttt180) cc_final: 0.6041 (ttm110) REVERT: H 18 LYS cc_start: 0.6806 (tttt) cc_final: 0.6117 (tmmt) REVERT: H 49 MET cc_start: 0.7456 (mtp) cc_final: 0.6523 (pp-130) REVERT: H 173 LYS cc_start: 0.7584 (mttm) cc_final: 0.7339 (mtmm) REVERT: H 227 MET cc_start: 0.7079 (mmt) cc_final: 0.5984 (ttp) REVERT: H 425 ARG cc_start: 0.6593 (ttt180) cc_final: 0.6182 (ttm110) REVERT: H 429 ILE cc_start: 0.6704 (tp) cc_final: 0.6302 (mm) REVERT: L 14 GLU cc_start: 0.6628 (mt-10) cc_final: 0.6361 (pt0) REVERT: L 30 ASP cc_start: 0.8261 (m-30) cc_final: 0.8037 (m-30) REVERT: L 49 MET cc_start: 0.7587 (mtp) cc_final: 0.6718 (tmm) REVERT: L 227 MET cc_start: 0.7073 (mmt) cc_final: 0.5960 (ttp) REVERT: L 425 ARG cc_start: 0.6536 (ttt180) cc_final: 0.6101 (ttm110) REVERT: M 458 SER cc_start: 0.5142 (OUTLIER) cc_final: 0.4814 (p) REVERT: Q 14 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6304 (pt0) REVERT: Q 18 LYS cc_start: 0.6915 (tttt) cc_final: 0.6237 (tmmt) REVERT: Q 48 ASP cc_start: 0.7633 (m-30) cc_final: 0.7173 (m-30) REVERT: Q 49 MET cc_start: 0.7433 (mtp) cc_final: 0.6539 (pp-130) REVERT: Q 147 GLU cc_start: 0.7322 (tt0) cc_final: 0.7115 (tt0) REVERT: Q 227 MET cc_start: 0.6982 (mmt) cc_final: 0.6081 (mtp) REVERT: Q 274 LYS cc_start: 0.7337 (mttt) cc_final: 0.7123 (mttp) REVERT: Q 425 ARG cc_start: 0.6663 (ttt180) cc_final: 0.6202 (ttm110) REVERT: R 459 ARG cc_start: 0.4915 (OUTLIER) cc_final: 0.4693 (pmt-80) outliers start: 15 outliers final: 10 residues processed: 260 average time/residue: 1.5378 time to fit residues: 448.4943 Evaluate side-chains 265 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 252 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain O residue 470 MET Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 458 SER Chi-restraints excluded: chain M residue 470 MET Chi-restraints excluded: chain R residue 456 THR Chi-restraints excluded: chain R residue 459 ARG Chi-restraints excluded: chain R residue 470 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 62 optimal weight: 0.0040 chunk 182 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN L 224 GLN Q 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20730 Z= 0.162 Angle : 0.603 7.867 28250 Z= 0.320 Chirality : 0.047 0.219 3185 Planarity : 0.004 0.036 3485 Dihedral : 8.807 65.295 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.71 % Allowed : 7.24 % Favored : 92.05 % 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: 1.88 (0.17), residues: 2505 helix: 1.75 (0.19), residues: 685 sheet: 1.23 (0.18), residues: 785 loop : 1.11 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 423 HIS 0.003 0.001 HIS H 191 PHE 0.015 0.002 PHE H 433 TYR 0.031 0.002 TYR D 299 ARG 0.006 0.001 ARG H 213 *********************** REFINEMENT MACRO_CYCLE 9 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 274 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 263 time to evaluate : 2.520 Fit side-chains REVERT: A 18 LYS cc_start: 0.6817 (tttt) cc_final: 0.6389 (mtpt) REVERT: A 49 MET cc_start: 0.7443 (mtp) cc_final: 0.6623 (pp-130) REVERT: A 227 MET cc_start: 0.6905 (mmt) cc_final: 0.5826 (ttm) REVERT: A 425 ARG cc_start: 0.6412 (ttt180) cc_final: 0.5982 (ttm110) REVERT: D 14 GLU cc_start: 0.6692 (mt-10) cc_final: 0.6327 (tt0) REVERT: D 18 LYS cc_start: 0.6815 (tttt) cc_final: 0.6300 (mtmm) REVERT: D 21 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.6069 (tppt) REVERT: D 48 ASP cc_start: 0.7705 (m-30) cc_final: 0.7214 (m-30) REVERT: D 49 MET cc_start: 0.7371 (mtp) cc_final: 0.6482 (pp-130) REVERT: D 147 GLU cc_start: 0.7339 (tt0) cc_final: 0.7028 (tt0) REVERT: D 227 MET cc_start: 0.7014 (mmt) cc_final: 0.5974 (ttp) REVERT: D 425 ARG cc_start: 0.6508 (ttt180) cc_final: 0.5883 (mtm-85) REVERT: H 18 LYS cc_start: 0.6790 (tttt) cc_final: 0.6107 (tmmt) REVERT: H 49 MET cc_start: 0.7468 (mtp) cc_final: 0.6589 (pp-130) REVERT: H 173 LYS cc_start: 0.7601 (mttm) cc_final: 0.7364 (mtmm) REVERT: H 227 MET cc_start: 0.7021 (mmt) cc_final: 0.5933 (ttp) REVERT: H 268 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6121 (tt) REVERT: H 425 ARG cc_start: 0.6547 (ttt180) cc_final: 0.6142 (ttm110) REVERT: H 429 ILE cc_start: 0.6764 (tp) cc_final: 0.6399 (mm) REVERT: L 14 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6340 (pt0) REVERT: L 30 ASP cc_start: 0.8219 (m-30) cc_final: 0.7977 (m-30) REVERT: L 49 MET cc_start: 0.7548 (mtp) cc_final: 0.6704 (tmm) REVERT: L 227 MET cc_start: 0.7067 (mmt) cc_final: 0.5958 (ttp) REVERT: L 425 ARG cc_start: 0.6461 (ttt180) cc_final: 0.6027 (ttm110) REVERT: Q 14 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6237 (tt0) REVERT: Q 18 LYS cc_start: 0.6926 (tttt) cc_final: 0.6264 (tmmt) REVERT: Q 48 ASP cc_start: 0.7603 (m-30) cc_final: 0.7164 (m-30) REVERT: Q 49 MET cc_start: 0.7409 (mtp) cc_final: 0.6598 (pp-130) REVERT: Q 147 GLU cc_start: 0.7321 (tt0) cc_final: 0.7087 (tt0) REVERT: Q 227 MET cc_start: 0.6940 (mmt) cc_final: 0.6017 (mtp) REVERT: Q 274 LYS cc_start: 0.7372 (mttt) cc_final: 0.7159 (mttp) REVERT: Q 425 ARG cc_start: 0.6581 (ttt180) cc_final: 0.6127 (ttm110) REVERT: R 459 ARG cc_start: 0.4921 (OUTLIER) cc_final: 0.4594 (pmt-80) outliers start: 11 outliers final: 3 residues processed: 269 average time/residue: 1.5545 time to fit residues: 471.1893 Evaluate side-chains 268 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 262 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain R residue 459 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 148 optimal weight: 0.0970 chunk 224 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN L 224 GLN ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20730 Z= 0.179 Angle : 0.630 9.086 28250 Z= 0.334 Chirality : 0.048 0.222 3185 Planarity : 0.004 0.043 3485 Dihedral : 8.644 63.318 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.62 % Allowed : 7.48 % Favored : 91.90 % 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: 1.85 (0.17), residues: 2505 helix: 1.68 (0.19), residues: 685 sheet: 1.24 (0.18), residues: 785 loop : 1.10 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 423 HIS 0.004 0.001 HIS L 119 PHE 0.017 0.002 PHE A 98 TYR 0.031 0.002 TYR D 299 ARG 0.006 0.001 ARG H 213 ********************** REFINEMENT MACRO_CYCLE 10 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 271 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 262 time to evaluate : 2.452 Fit side-chains REVERT: A 18 LYS cc_start: 0.6816 (tttt) cc_final: 0.6384 (mtpt) REVERT: A 49 MET cc_start: 0.7453 (mtp) cc_final: 0.6675 (pp-130) REVERT: A 227 MET cc_start: 0.6898 (mmt) cc_final: 0.5821 (ttm) REVERT: A 425 ARG cc_start: 0.6432 (ttt180) cc_final: 0.6002 (ttm110) REVERT: D 14 GLU cc_start: 0.6695 (mt-10) cc_final: 0.6409 (tt0) REVERT: D 18 LYS cc_start: 0.6817 (tttt) cc_final: 0.6377 (mtpt) REVERT: D 21 LYS cc_start: 0.6458 (OUTLIER) cc_final: 0.6071 (tppt) REVERT: D 48 ASP cc_start: 0.7696 (m-30) cc_final: 0.7197 (m-30) REVERT: D 49 MET cc_start: 0.7379 (mtp) cc_final: 0.6490 (pp-130) REVERT: D 147 GLU cc_start: 0.7345 (tt0) cc_final: 0.7042 (tt0) REVERT: D 227 MET cc_start: 0.7022 (mmt) cc_final: 0.5982 (ttp) REVERT: D 425 ARG cc_start: 0.6514 (ttt180) cc_final: 0.6048 (ttm110) REVERT: H 18 LYS cc_start: 0.6786 (tttt) cc_final: 0.6101 (tmmt) REVERT: H 49 MET cc_start: 0.7473 (mtp) cc_final: 0.6590 (pp-130) REVERT: H 173 LYS cc_start: 0.7582 (mttm) cc_final: 0.7350 (mtmm) REVERT: H 227 MET cc_start: 0.7081 (mmt) cc_final: 0.5983 (ttp) REVERT: H 268 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.6129 (tt) REVERT: H 425 ARG cc_start: 0.6556 (ttt180) cc_final: 0.6153 (ttm110) REVERT: H 429 ILE cc_start: 0.6780 (tp) cc_final: 0.6414 (mm) REVERT: L 14 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6356 (pt0) REVERT: L 30 ASP cc_start: 0.8216 (m-30) cc_final: 0.7982 (m-30) REVERT: L 49 MET cc_start: 0.7554 (mtp) cc_final: 0.6747 (tmm) REVERT: L 227 MET cc_start: 0.7072 (mmt) cc_final: 0.5960 (ttp) REVERT: L 425 ARG cc_start: 0.6466 (ttt180) cc_final: 0.6037 (ttm110) REVERT: M 458 SER cc_start: 0.4914 (OUTLIER) cc_final: 0.4636 (p) REVERT: Q 14 GLU cc_start: 0.6466 (mt-10) cc_final: 0.6262 (pt0) REVERT: Q 18 LYS cc_start: 0.6906 (tttt) cc_final: 0.6253 (tmmt) REVERT: Q 48 ASP cc_start: 0.7609 (m-30) cc_final: 0.7160 (m-30) REVERT: Q 49 MET cc_start: 0.7418 (mtp) cc_final: 0.6596 (pp-130) REVERT: Q 147 GLU cc_start: 0.7346 (tt0) cc_final: 0.7134 (tt0) REVERT: Q 227 MET cc_start: 0.6943 (mmt) cc_final: 0.6017 (mtp) REVERT: Q 274 LYS cc_start: 0.7357 (mttt) cc_final: 0.7143 (mttp) REVERT: Q 425 ARG cc_start: 0.6483 (ttt180) cc_final: 0.6019 (ttm110) REVERT: R 439 SER cc_start: 0.7727 (m) cc_final: 0.7209 (t) outliers start: 9 outliers final: 5 residues processed: 267 average time/residue: 1.5613 time to fit residues: 467.5129 Evaluate side-chains 268 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 260 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 470 MET Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 458 SER Chi-restraints excluded: chain R residue 470 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 164 optimal weight: 0.0470 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN L 224 GLN Q 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.194313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.147656 restraints weight = 107811.719| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 4.26 r_work: 0.3170 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work: 0.2963 rms_B_bonded: 4.40 restraints_weight: 0.1250 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20730 Z= 0.147 Angle : 0.581 9.002 28250 Z= 0.306 Chirality : 0.046 0.236 3185 Planarity : 0.004 0.036 3485 Dihedral : 8.111 59.117 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.62 % Allowed : 7.67 % Favored : 91.71 % 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: 2.00 (0.17), residues: 2505 helix: 1.84 (0.20), residues: 685 sheet: 1.32 (0.18), residues: 785 loop : 1.17 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 423 HIS 0.002 0.001 HIS A 119 PHE 0.015 0.002 PHE H 433 TYR 0.032 0.002 TYR H 299 ARG 0.006 0.000 ARG H 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10391.46 seconds wall clock time: 183 minutes 10.13 seconds (10990.13 seconds total)