Starting phenix.real_space_refine on Sat Mar 16 09:34:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/03_2024/8gmp_40229_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/03_2024/8gmp_40229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/03_2024/8gmp_40229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/03_2024/8gmp_40229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/03_2024/8gmp_40229_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/03_2024/8gmp_40229_trim_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.040 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 P 8 5.49 5 S 136 5.16 5 C 9000 2.51 5 N 2216 2.21 5 O 2296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 225": "OD1" <-> "OD2" Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A ASP 121": "OD1" <-> "OD2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 225": "OD1" <-> "OD2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 92": "OD1" <-> "OD2" Residue "D ASP 121": "OD1" <-> "OD2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "E TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 92": "OD1" <-> "OD2" Residue "E ASP 121": "OD1" <-> "OD2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 225": "OD1" <-> "OD2" Residue "F TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 92": "OD1" <-> "OD2" Residue "F ASP 121": "OD1" <-> "OD2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 225": "OD1" <-> "OD2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 92": "OD1" <-> "OD2" Residue "G ASP 121": "OD1" <-> "OD2" Residue "G PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 225": "OD1" <-> "OD2" Residue "H TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H ASP 121": "OD1" <-> "OD2" Residue "H PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 225": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13656 Number of models: 1 Model: "" Number of chains: 16 Chain: "C" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1655 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1655 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1655 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1655 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1655 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1655 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1655 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1655 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.23, per 1000 atoms: 0.53 Number of scatterers: 13656 At special positions: 0 Unit cell: (113.848, 113.848, 98.44, 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) S 136 16.00 P 8 15.00 O 2296 8.00 N 2216 7.00 C 9000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 127 " distance=2.04 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 161 " distance=2.04 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 44 " - pdb=" SG CYS D 161 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 127 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 161 " distance=2.03 Simple disulfide: pdb=" SG CYS F 42 " - pdb=" SG CYS F 127 " distance=2.04 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 161 " distance=2.04 Simple disulfide: pdb=" SG CYS G 42 " - pdb=" SG CYS G 127 " distance=2.03 Simple disulfide: pdb=" SG CYS G 44 " - pdb=" SG CYS G 161 " distance=2.03 Simple disulfide: pdb=" SG CYS H 42 " - pdb=" SG CYS H 127 " distance=2.04 Simple disulfide: pdb=" SG CYS H 44 " - pdb=" SG CYS H 161 " distance=2.03 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.00 Conformation dependent library (CDL) restraints added in 2.2 seconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 0 sheets defined 62.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.599A pdb=" N ALA C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER C 36 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA C 37 " --> pdb=" O GLN C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 69 Proline residue: C 60 - end of helix removed outlier: 3.543A pdb=" N LEU C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 105 removed outlier: 3.816A pdb=" N MET C 103 " --> pdb=" O MET C 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 119 removed outlier: 3.552A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C 115 " --> pdb=" O PRO C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 129 Processing helix chain 'C' and resid 153 through 158 removed outlier: 4.444A pdb=" N ARG C 158 " --> pdb=" O ARG C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 180 through 199 removed outlier: 3.734A pdb=" N GLN C 185 " --> pdb=" O ARG C 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 198 " --> pdb=" O LEU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 203 No H-bonds generated for 'chain 'C' and resid 201 through 203' Processing helix chain 'C' and resid 211 through 235 removed outlier: 3.615A pdb=" N HIS C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 250 removed outlier: 3.845A pdb=" N LYS C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.599A pdb=" N ALA A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 69 Proline residue: A 60 - end of helix removed outlier: 3.543A pdb=" N LEU A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 105 removed outlier: 3.815A pdb=" N MET A 103 " --> pdb=" O MET A 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 105 " --> pdb=" O CYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.552A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 129 Processing helix chain 'A' and resid 153 through 158 removed outlier: 4.444A pdb=" N ARG A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 176 No H-bonds generated for 'chain 'A' and resid 173 through 176' Processing helix chain 'A' and resid 180 through 199 removed outlier: 3.734A pdb=" N GLN A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 211 through 235 removed outlier: 3.615A pdb=" N HIS A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 250 removed outlier: 3.846A pdb=" N LYS A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 37 removed outlier: 3.599A pdb=" N ALA B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 69 Proline residue: B 60 - end of helix removed outlier: 3.543A pdb=" N LEU B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 105 removed outlier: 3.816A pdb=" N MET B 103 " --> pdb=" O MET B 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN B 105 " --> pdb=" O CYS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 119 removed outlier: 3.552A pdb=" N VAL B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 129 Processing helix chain 'B' and resid 153 through 158 removed outlier: 4.444A pdb=" N ARG B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 180 through 199 removed outlier: 3.734A pdb=" N GLN B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 211 through 235 removed outlier: 3.615A pdb=" N HIS B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 250 removed outlier: 3.845A pdb=" N LYS B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.599A pdb=" N ALA D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA D 37 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 69 Proline residue: D 60 - end of helix removed outlier: 3.543A pdb=" N LEU D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 105 removed outlier: 3.816A pdb=" N MET D 103 " --> pdb=" O MET D 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 105 " --> pdb=" O CYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.552A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 129 Processing helix chain 'D' and resid 153 through 158 removed outlier: 4.445A pdb=" N ARG D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 176 No H-bonds generated for 'chain 'D' and resid 173 through 176' Processing helix chain 'D' and resid 180 through 199 removed outlier: 3.734A pdb=" N GLN D 185 " --> pdb=" O ARG D 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'D' and resid 211 through 235 removed outlier: 3.615A pdb=" N HIS D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 250 removed outlier: 3.845A pdb=" N LYS D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN D 249 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.599A pdb=" N ALA E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA E 37 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 69 Proline residue: E 60 - end of helix removed outlier: 3.543A pdb=" N LEU E 66 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 105 removed outlier: 3.816A pdb=" N MET E 103 " --> pdb=" O MET E 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN E 105 " --> pdb=" O CYS E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.552A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 129 Processing helix chain 'E' and resid 153 through 158 removed outlier: 4.444A pdb=" N ARG E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 176 No H-bonds generated for 'chain 'E' and resid 173 through 176' Processing helix chain 'E' and resid 180 through 199 removed outlier: 3.734A pdb=" N GLN E 185 " --> pdb=" O ARG E 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E 192 " --> pdb=" O GLY E 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU E 198 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 203 No H-bonds generated for 'chain 'E' and resid 201 through 203' Processing helix chain 'E' and resid 211 through 235 removed outlier: 3.615A pdb=" N HIS E 222 " --> pdb=" O LYS E 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP E 225 " --> pdb=" O SER E 221 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 250 removed outlier: 3.845A pdb=" N LYS E 244 " --> pdb=" O LYS E 240 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN E 248 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN E 249 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.599A pdb=" N ALA F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR F 35 " --> pdb=" O SER F 31 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER F 36 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA F 37 " --> pdb=" O GLN F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 69 Proline residue: F 60 - end of helix removed outlier: 3.543A pdb=" N LEU F 66 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 removed outlier: 3.816A pdb=" N MET F 103 " --> pdb=" O MET F 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN F 105 " --> pdb=" O CYS F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 119 removed outlier: 3.552A pdb=" N VAL F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL F 115 " --> pdb=" O PRO F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 129 Processing helix chain 'F' and resid 153 through 158 removed outlier: 4.445A pdb=" N ARG F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 176 No H-bonds generated for 'chain 'F' and resid 173 through 176' Processing helix chain 'F' and resid 180 through 199 removed outlier: 3.734A pdb=" N GLN F 185 " --> pdb=" O ARG F 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 192 " --> pdb=" O GLY F 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 198 " --> pdb=" O LEU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 203 No H-bonds generated for 'chain 'F' and resid 201 through 203' Processing helix chain 'F' and resid 211 through 235 removed outlier: 3.615A pdb=" N HIS F 222 " --> pdb=" O LYS F 218 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP F 225 " --> pdb=" O SER F 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 250 removed outlier: 3.846A pdb=" N LYS F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN F 249 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.599A pdb=" N ALA G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER G 36 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA G 37 " --> pdb=" O GLN G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 69 Proline residue: G 60 - end of helix removed outlier: 3.543A pdb=" N LEU G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 105 removed outlier: 3.816A pdb=" N MET G 103 " --> pdb=" O MET G 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN G 105 " --> pdb=" O CYS G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 119 removed outlier: 3.552A pdb=" N VAL G 112 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL G 115 " --> pdb=" O PRO G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 129 Processing helix chain 'G' and resid 153 through 158 removed outlier: 4.444A pdb=" N ARG G 158 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 176 No H-bonds generated for 'chain 'G' and resid 173 through 176' Processing helix chain 'G' and resid 180 through 199 removed outlier: 3.734A pdb=" N GLN G 185 " --> pdb=" O ARG G 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL G 192 " --> pdb=" O GLY G 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU G 198 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 203 No H-bonds generated for 'chain 'G' and resid 201 through 203' Processing helix chain 'G' and resid 211 through 235 removed outlier: 3.616A pdb=" N HIS G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP G 225 " --> pdb=" O SER G 221 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU G 233 " --> pdb=" O LYS G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 250 removed outlier: 3.844A pdb=" N LYS G 244 " --> pdb=" O LYS G 240 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN G 249 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 37 removed outlier: 3.599A pdb=" N ALA H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR H 35 " --> pdb=" O SER H 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER H 36 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA H 37 " --> pdb=" O GLN H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 69 Proline residue: H 60 - end of helix removed outlier: 3.543A pdb=" N LEU H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY H 68 " --> pdb=" O LEU H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.816A pdb=" N MET H 103 " --> pdb=" O MET H 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN H 105 " --> pdb=" O CYS H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 119 removed outlier: 3.552A pdb=" N VAL H 112 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL H 115 " --> pdb=" O PRO H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 129 Processing helix chain 'H' and resid 153 through 158 removed outlier: 4.444A pdb=" N ARG H 158 " --> pdb=" O ARG H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 176 No H-bonds generated for 'chain 'H' and resid 173 through 176' Processing helix chain 'H' and resid 180 through 199 removed outlier: 3.734A pdb=" N GLN H 185 " --> pdb=" O ARG H 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL H 192 " --> pdb=" O GLY H 188 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU H 198 " --> pdb=" O LEU H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 203 No H-bonds generated for 'chain 'H' and resid 201 through 203' Processing helix chain 'H' and resid 211 through 235 removed outlier: 3.616A pdb=" N HIS H 222 " --> pdb=" O LYS H 218 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP H 225 " --> pdb=" O SER H 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU H 233 " --> pdb=" O LYS H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 250 removed outlier: 3.846A pdb=" N LYS H 244 " --> pdb=" O LYS H 240 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL H 245 " --> pdb=" O ALA H 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN H 248 " --> pdb=" O LYS H 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN H 249 " --> pdb=" O VAL H 245 " (cutoff:3.500A) 544 hydrogen bonds defined for protein. 1632 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: 3.28 Time building geometry restraints manager: 5.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2056 1.31 - 1.44: 3792 1.44 - 1.57: 7936 1.57 - 1.70: 16 1.70 - 1.83: 184 Bond restraints: 13984 Sorted by residual: bond pdb=" C TRP H 109 " pdb=" O TRP H 109 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.31e-02 5.83e+03 1.95e+01 bond pdb=" C TRP G 109 " pdb=" O TRP G 109 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.31e-02 5.83e+03 1.95e+01 bond pdb=" C TRP C 109 " pdb=" O TRP C 109 " ideal model delta sigma weight residual 1.237 1.179 0.057 1.31e-02 5.83e+03 1.92e+01 bond pdb=" C TRP B 109 " pdb=" O TRP B 109 " ideal model delta sigma weight residual 1.237 1.179 0.057 1.31e-02 5.83e+03 1.92e+01 bond pdb=" C TRP E 109 " pdb=" O TRP E 109 " ideal model delta sigma weight residual 1.237 1.179 0.057 1.31e-02 5.83e+03 1.92e+01 ... (remaining 13979 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.84: 496 106.84 - 113.63: 7728 113.63 - 120.43: 5386 120.43 - 127.22: 5174 127.22 - 134.02: 184 Bond angle restraints: 18968 Sorted by residual: angle pdb=" C ASN H 41 " pdb=" N CYS H 42 " pdb=" CA CYS H 42 " ideal model delta sigma weight residual 124.01 104.03 19.98 1.84e+00 2.95e-01 1.18e+02 angle pdb=" C ASN F 41 " pdb=" N CYS F 42 " pdb=" CA CYS F 42 " ideal model delta sigma weight residual 124.01 104.06 19.95 1.84e+00 2.95e-01 1.18e+02 angle pdb=" C ASN G 41 " pdb=" N CYS G 42 " pdb=" CA CYS G 42 " ideal model delta sigma weight residual 124.01 104.07 19.94 1.84e+00 2.95e-01 1.17e+02 angle pdb=" C ASN B 41 " pdb=" N CYS B 42 " pdb=" CA CYS B 42 " ideal model delta sigma weight residual 124.01 104.07 19.94 1.84e+00 2.95e-01 1.17e+02 angle pdb=" C ASN C 41 " pdb=" N CYS C 42 " pdb=" CA CYS C 42 " ideal model delta sigma weight residual 124.01 104.07 19.94 1.84e+00 2.95e-01 1.17e+02 ... (remaining 18963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.50: 7664 20.50 - 41.00: 480 41.00 - 61.50: 248 61.50 - 82.00: 32 82.00 - 102.50: 8 Dihedral angle restraints: 8432 sinusoidal: 3336 harmonic: 5096 Sorted by residual: dihedral pdb=" CA ALA H 176 " pdb=" C ALA H 176 " pdb=" N VAL H 177 " pdb=" CA VAL H 177 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ALA G 176 " pdb=" C ALA G 176 " pdb=" N VAL G 177 " pdb=" CA VAL G 177 " ideal model delta harmonic sigma weight residual 180.00 159.23 20.77 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ALA C 176 " pdb=" C ALA C 176 " pdb=" N VAL C 177 " pdb=" CA VAL C 177 " ideal model delta harmonic sigma weight residual 180.00 159.23 20.77 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 8429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1941 0.066 - 0.133: 171 0.133 - 0.199: 24 0.199 - 0.266: 0 0.266 - 0.332: 8 Chirality restraints: 2144 Sorted by residual: chirality pdb=" CA TRP H 109 " pdb=" N TRP H 109 " pdb=" C TRP H 109 " pdb=" CB TRP H 109 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA TRP E 109 " pdb=" N TRP E 109 " pdb=" C TRP E 109 " pdb=" CB TRP E 109 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA TRP B 109 " pdb=" N TRP B 109 " pdb=" C TRP B 109 " pdb=" CB TRP B 109 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 2141 not shown) Planarity restraints: 2328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 60 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.79e+00 pdb=" N PRO F 61 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO F 61 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 61 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO H 60 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO H 61 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 61 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 61 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 60 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.75e+00 pdb=" N PRO B 61 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 61 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 61 " 0.034 5.00e-02 4.00e+02 ... (remaining 2325 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4632 2.87 - 3.37: 12547 3.37 - 3.88: 19467 3.88 - 4.39: 24182 4.39 - 4.90: 40965 Nonbonded interactions: 101793 Sorted by model distance: nonbonded pdb=" O ASN H 41 " pdb=" CA CYS H 42 " model vdw 2.357 2.776 nonbonded pdb=" O ASN A 41 " pdb=" CA CYS A 42 " model vdw 2.357 2.776 nonbonded pdb=" O ASN F 41 " pdb=" CA CYS F 42 " model vdw 2.357 2.776 nonbonded pdb=" O ASN G 41 " pdb=" CA CYS G 42 " model vdw 2.358 2.776 nonbonded pdb=" O ASN C 41 " pdb=" CA CYS C 42 " model vdw 2.358 2.776 ... (remaining 101788 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.010 Extract box with map and model: 7.460 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 35.300 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.006 0.086 13984 Z= 0.406 Angle : 1.086 19.983 18968 Z= 0.577 Chirality : 0.046 0.332 2144 Planarity : 0.007 0.060 2328 Dihedral : 17.177 102.504 5056 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.96 % Allowed : 4.14 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.76 (0.13), residues: 1680 helix: -4.65 (0.06), residues: 1232 sheet: None (None), residues: 0 loop : -3.04 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP H 109 HIS 0.002 0.001 HIS H 238 PHE 0.010 0.001 PHE A 125 TYR 0.009 0.001 TYR D 179 ARG 0.003 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 276 time to evaluate : 1.438 Fit side-chains REVERT: C 74 ASN cc_start: 0.7605 (m110) cc_final: 0.7168 (t0) REVERT: C 77 MET cc_start: 0.6827 (mtt) cc_final: 0.6621 (mtt) REVERT: C 100 PHE cc_start: 0.6993 (t80) cc_final: 0.6664 (t80) REVERT: A 74 ASN cc_start: 0.7516 (m110) cc_final: 0.6999 (t0) REVERT: A 100 PHE cc_start: 0.6955 (t80) cc_final: 0.6698 (t80) REVERT: B 74 ASN cc_start: 0.7610 (m110) cc_final: 0.7168 (t0) REVERT: B 77 MET cc_start: 0.6829 (mtt) cc_final: 0.6626 (mtt) REVERT: B 100 PHE cc_start: 0.6994 (t80) cc_final: 0.6666 (t80) REVERT: D 74 ASN cc_start: 0.7519 (m110) cc_final: 0.6997 (t0) REVERT: D 100 PHE cc_start: 0.6960 (t80) cc_final: 0.6701 (t80) REVERT: E 74 ASN cc_start: 0.7607 (m110) cc_final: 0.7162 (t0) REVERT: E 77 MET cc_start: 0.6829 (mtt) cc_final: 0.6625 (mtt) REVERT: E 100 PHE cc_start: 0.6994 (t80) cc_final: 0.6665 (t80) REVERT: F 74 ASN cc_start: 0.7518 (m110) cc_final: 0.6996 (t0) REVERT: F 100 PHE cc_start: 0.6958 (t80) cc_final: 0.6700 (t80) REVERT: G 74 ASN cc_start: 0.7606 (m110) cc_final: 0.7162 (t0) REVERT: G 77 MET cc_start: 0.6829 (mtt) cc_final: 0.6623 (mtt) REVERT: G 100 PHE cc_start: 0.6994 (t80) cc_final: 0.6666 (t80) REVERT: H 74 ASN cc_start: 0.7515 (m110) cc_final: 0.6997 (t0) REVERT: H 100 PHE cc_start: 0.6953 (t80) cc_final: 0.6695 (t80) outliers start: 40 outliers final: 8 residues processed: 304 average time/residue: 1.0550 time to fit residues: 353.6934 Evaluate side-chains 236 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 228 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain H residue 131 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.8980 chunk 127 optimal weight: 0.0170 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.0570 chunk 85 optimal weight: 0.0770 chunk 68 optimal weight: 0.0570 chunk 131 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 overall best weight: 0.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 GLN A 105 GLN B 105 GLN D 105 GLN E 105 GLN F 105 GLN G 105 GLN H 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13984 Z= 0.171 Angle : 0.647 6.802 18968 Z= 0.335 Chirality : 0.041 0.129 2144 Planarity : 0.006 0.046 2328 Dihedral : 15.319 74.663 2208 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.25 % Allowed : 12.43 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.16), residues: 1680 helix: -2.92 (0.11), residues: 1208 sheet: None (None), residues: 0 loop : -2.68 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 169 HIS 0.001 0.001 HIS H 222 PHE 0.012 0.001 PHE B 209 TYR 0.012 0.001 TYR B 98 ARG 0.002 0.000 ARG G 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 228 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 MET cc_start: 0.6864 (mtt) cc_final: 0.6645 (mtt) REVERT: C 154 ARG cc_start: 0.7813 (ttm110) cc_final: 0.7356 (ttm-80) REVERT: C 229 LYS cc_start: 0.8054 (mttp) cc_final: 0.7794 (ttmm) REVERT: A 100 PHE cc_start: 0.6821 (t80) cc_final: 0.6595 (t80) REVERT: B 77 MET cc_start: 0.6865 (mtt) cc_final: 0.6646 (mtt) REVERT: B 154 ARG cc_start: 0.7818 (ttm110) cc_final: 0.7358 (ttm-80) REVERT: B 229 LYS cc_start: 0.8053 (mttp) cc_final: 0.7797 (ttmm) REVERT: D 100 PHE cc_start: 0.6824 (t80) cc_final: 0.6597 (t80) REVERT: E 77 MET cc_start: 0.6862 (mtt) cc_final: 0.6645 (mtt) REVERT: E 154 ARG cc_start: 0.7819 (ttm110) cc_final: 0.7359 (ttm-80) REVERT: E 229 LYS cc_start: 0.8048 (mttp) cc_final: 0.7793 (ttmm) REVERT: F 100 PHE cc_start: 0.6830 (t80) cc_final: 0.6602 (t80) REVERT: G 77 MET cc_start: 0.6911 (mtt) cc_final: 0.6690 (mtt) REVERT: G 154 ARG cc_start: 0.7819 (ttm110) cc_final: 0.7359 (ttm-80) REVERT: G 229 LYS cc_start: 0.8049 (mttp) cc_final: 0.7790 (ttmm) REVERT: H 100 PHE cc_start: 0.6819 (t80) cc_final: 0.6590 (t80) outliers start: 44 outliers final: 28 residues processed: 240 average time/residue: 1.1620 time to fit residues: 305.7789 Evaluate side-chains 255 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 227 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 254 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 0.3980 chunk 126 optimal weight: 30.0000 chunk 103 optimal weight: 7.9990 chunk 42 optimal weight: 30.0000 chunk 152 optimal weight: 0.3980 chunk 165 optimal weight: 3.9990 chunk 136 optimal weight: 0.0870 chunk 151 optimal weight: 0.5980 chunk 52 optimal weight: 0.0670 chunk 122 optimal weight: 4.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13984 Z= 0.141 Angle : 0.556 6.209 18968 Z= 0.284 Chirality : 0.038 0.138 2144 Planarity : 0.005 0.042 2328 Dihedral : 13.786 76.479 2208 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.70 % Allowed : 15.46 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.19), residues: 1680 helix: -1.49 (0.14), residues: 1264 sheet: None (None), residues: 0 loop : -2.97 (0.25), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 114 HIS 0.000 0.000 HIS G 238 PHE 0.015 0.001 PHE B 100 TYR 0.009 0.001 TYR C 98 ARG 0.002 0.000 ARG G 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 240 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 ARG cc_start: 0.7748 (ttm110) cc_final: 0.7257 (ttm-80) REVERT: A 100 PHE cc_start: 0.6827 (t80) cc_final: 0.6625 (t80) REVERT: A 103 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7296 (ttt) REVERT: B 154 ARG cc_start: 0.7750 (ttm110) cc_final: 0.7259 (ttm-80) REVERT: D 100 PHE cc_start: 0.6815 (t80) cc_final: 0.6603 (t80) REVERT: D 103 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7278 (ttt) REVERT: E 154 ARG cc_start: 0.7750 (ttm110) cc_final: 0.7257 (ttm-80) REVERT: F 100 PHE cc_start: 0.6804 (t80) cc_final: 0.6595 (t80) REVERT: F 103 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7274 (ttt) REVERT: G 154 ARG cc_start: 0.7751 (ttm110) cc_final: 0.7258 (ttm-80) REVERT: H 100 PHE cc_start: 0.6805 (t80) cc_final: 0.6600 (t80) REVERT: H 103 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7283 (ttt) outliers start: 23 outliers final: 13 residues processed: 248 average time/residue: 1.1716 time to fit residues: 317.8627 Evaluate side-chains 245 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 228 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 103 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 ASN G 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13984 Z= 0.276 Angle : 0.647 6.454 18968 Z= 0.331 Chirality : 0.044 0.148 2144 Planarity : 0.006 0.053 2328 Dihedral : 14.110 75.936 2200 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.25 % Allowed : 17.31 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.19), residues: 1680 helix: -1.23 (0.14), residues: 1264 sheet: None (None), residues: 0 loop : -3.11 (0.24), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 189 HIS 0.001 0.000 HIS B 238 PHE 0.010 0.002 PHE C 125 TYR 0.010 0.001 TYR G 98 ARG 0.003 0.000 ARG C 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 235 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6746 (ttm) REVERT: A 100 PHE cc_start: 0.6818 (t80) cc_final: 0.6614 (t80) REVERT: D 100 PHE cc_start: 0.6835 (t80) cc_final: 0.6625 (t80) REVERT: F 71 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6747 (ttm) REVERT: F 100 PHE cc_start: 0.6831 (t80) cc_final: 0.6621 (t80) REVERT: H 71 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6746 (ttm) REVERT: H 100 PHE cc_start: 0.6812 (t80) cc_final: 0.6608 (t80) outliers start: 71 outliers final: 42 residues processed: 251 average time/residue: 1.1804 time to fit residues: 324.6103 Evaluate side-chains 280 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 235 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 228 ARG Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 228 ARG Chi-restraints excluded: chain H residue 251 PHE Chi-restraints excluded: chain H residue 254 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 82 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN B 49 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13984 Z= 0.298 Angle : 0.668 7.220 18968 Z= 0.340 Chirality : 0.044 0.155 2144 Planarity : 0.006 0.057 2328 Dihedral : 14.301 77.888 2200 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.40 % Allowed : 18.34 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.19), residues: 1680 helix: -1.10 (0.14), residues: 1272 sheet: None (None), residues: 0 loop : -3.28 (0.25), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 169 HIS 0.001 0.000 HIS A 238 PHE 0.010 0.002 PHE E 125 TYR 0.011 0.002 TYR C 98 ARG 0.002 0.000 ARG E 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 224 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 MET cc_start: 0.7249 (mtp) cc_final: 0.6702 (ttm) outliers start: 73 outliers final: 40 residues processed: 252 average time/residue: 1.3005 time to fit residues: 356.1224 Evaluate side-chains 264 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 224 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 228 ARG Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 228 ARG Chi-restraints excluded: chain H residue 251 PHE Chi-restraints excluded: chain H residue 254 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.0020 chunk 146 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13984 Z= 0.185 Angle : 0.571 6.215 18968 Z= 0.292 Chirality : 0.039 0.126 2144 Planarity : 0.006 0.055 2328 Dihedral : 13.815 77.501 2200 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.85 % Allowed : 19.75 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1680 helix: -0.57 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -3.07 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 114 HIS 0.001 0.000 HIS A 238 PHE 0.018 0.001 PHE D 100 TYR 0.009 0.001 TYR G 98 ARG 0.001 0.000 ARG C 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 221 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 44 residues processed: 241 average time/residue: 1.2881 time to fit residues: 337.7300 Evaluate side-chains 265 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 221 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 228 ARG Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 228 ARG Chi-restraints excluded: chain H residue 251 PHE Chi-restraints excluded: chain H residue 254 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 136 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN A 74 ASN B 74 ASN D 74 ASN E 74 ASN F 74 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13984 Z= 0.172 Angle : 0.552 5.998 18968 Z= 0.283 Chirality : 0.039 0.120 2144 Planarity : 0.006 0.054 2328 Dihedral : 13.431 78.888 2200 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.44 % Allowed : 19.75 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1680 helix: -0.16 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -2.85 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 114 HIS 0.001 0.000 HIS E 238 PHE 0.009 0.001 PHE C 100 TYR 0.011 0.001 TYR G 98 ARG 0.001 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 236 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 ARG cc_start: 0.7821 (ttm110) cc_final: 0.7356 (ttm-80) REVERT: A 71 MET cc_start: 0.7315 (mtp) cc_final: 0.6741 (ttm) REVERT: A 99 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7804 (mtp) REVERT: B 154 ARG cc_start: 0.7821 (ttm110) cc_final: 0.7372 (ttm-80) REVERT: D 71 MET cc_start: 0.7160 (mtp) cc_final: 0.6590 (ttm) REVERT: D 99 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7806 (mtp) REVERT: E 154 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7355 (ttm-80) REVERT: F 71 MET cc_start: 0.7242 (mtp) cc_final: 0.6665 (ttm) REVERT: F 99 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7801 (mtp) REVERT: G 154 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7353 (ttm-80) REVERT: H 71 MET cc_start: 0.7315 (mtp) cc_final: 0.6740 (ttm) REVERT: H 99 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7806 (mtp) outliers start: 60 outliers final: 35 residues processed: 258 average time/residue: 1.1526 time to fit residues: 325.9035 Evaluate side-chains 275 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 236 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 99 MET Chi-restraints excluded: chain F residue 228 ARG Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 228 ARG Chi-restraints excluded: chain H residue 251 PHE Chi-restraints excluded: chain H residue 254 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.8980 chunk 64 optimal weight: 0.0970 chunk 96 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 110 optimal weight: 0.0670 chunk 80 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 147 optimal weight: 30.0000 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13984 Z= 0.140 Angle : 0.518 5.958 18968 Z= 0.264 Chirality : 0.037 0.107 2144 Planarity : 0.006 0.053 2328 Dihedral : 13.096 80.790 2200 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.96 % Allowed : 21.01 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.21), residues: 1680 helix: 0.46 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -2.41 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 114 HIS 0.000 0.000 HIS A 238 PHE 0.012 0.001 PHE D 100 TYR 0.018 0.001 TYR H 98 ARG 0.001 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 255 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7238 (m-40) cc_final: 0.6467 (t0) REVERT: C 154 ARG cc_start: 0.7663 (ttm110) cc_final: 0.7109 (ttm-80) REVERT: A 74 ASN cc_start: 0.7143 (m-40) cc_final: 0.6533 (t0) REVERT: B 74 ASN cc_start: 0.7235 (m-40) cc_final: 0.6461 (t0) REVERT: B 154 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7108 (ttm-80) REVERT: D 74 ASN cc_start: 0.7111 (m-40) cc_final: 0.6510 (t0) REVERT: E 74 ASN cc_start: 0.7238 (m-40) cc_final: 0.6458 (t0) REVERT: E 154 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7111 (ttm-80) REVERT: F 74 ASN cc_start: 0.7140 (m-40) cc_final: 0.6539 (t0) REVERT: G 154 ARG cc_start: 0.7667 (ttm110) cc_final: 0.7118 (ttm-80) REVERT: H 74 ASN cc_start: 0.7142 (m-40) cc_final: 0.6529 (t0) outliers start: 40 outliers final: 19 residues processed: 271 average time/residue: 1.1786 time to fit residues: 349.4982 Evaluate side-chains 252 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 233 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 251 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 142 optimal weight: 0.0870 chunk 99 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13984 Z= 0.196 Angle : 0.562 6.089 18968 Z= 0.287 Chirality : 0.040 0.124 2144 Planarity : 0.006 0.055 2328 Dihedral : 13.167 81.943 2200 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.11 % Allowed : 22.26 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.21), residues: 1680 helix: 0.49 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -2.50 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 189 HIS 0.001 0.000 HIS B 238 PHE 0.018 0.001 PHE A 209 TYR 0.016 0.001 TYR D 98 ARG 0.001 0.000 ARG F 173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 233 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7245 (m-40) cc_final: 0.6490 (t0) REVERT: C 154 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7310 (ttm-80) REVERT: A 71 MET cc_start: 0.7165 (mtp) cc_final: 0.6600 (ttm) REVERT: A 74 ASN cc_start: 0.7169 (m-40) cc_final: 0.6546 (t0) REVERT: A 77 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.6226 (mtp) REVERT: B 74 ASN cc_start: 0.7241 (m-40) cc_final: 0.6488 (t0) REVERT: B 154 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7309 (ttm-80) REVERT: D 74 ASN cc_start: 0.7164 (m-40) cc_final: 0.6559 (t0) REVERT: D 77 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.6242 (mtt) REVERT: E 74 ASN cc_start: 0.7238 (m-40) cc_final: 0.6486 (t0) REVERT: E 154 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7311 (ttm-80) REVERT: F 71 MET cc_start: 0.7151 (mtp) cc_final: 0.6585 (ttm) REVERT: F 74 ASN cc_start: 0.7168 (m-40) cc_final: 0.6553 (t0) REVERT: F 77 MET cc_start: 0.6565 (OUTLIER) cc_final: 0.6224 (mtp) REVERT: G 74 ASN cc_start: 0.7393 (m-40) cc_final: 0.6625 (t0) REVERT: G 154 ARG cc_start: 0.7786 (ttm110) cc_final: 0.7194 (ttm-80) REVERT: H 71 MET cc_start: 0.7165 (mtp) cc_final: 0.6598 (ttm) REVERT: H 74 ASN cc_start: 0.7169 (m-40) cc_final: 0.6540 (t0) REVERT: H 77 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6236 (mtp) outliers start: 42 outliers final: 29 residues processed: 256 average time/residue: 1.0983 time to fit residues: 309.5665 Evaluate side-chains 269 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 236 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 77 MET Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 251 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 105 optimal weight: 30.0000 chunk 141 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13984 Z= 0.180 Angle : 0.551 6.137 18968 Z= 0.281 Chirality : 0.039 0.122 2144 Planarity : 0.006 0.055 2328 Dihedral : 13.134 83.943 2200 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.81 % Allowed : 22.41 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.21), residues: 1680 helix: 0.67 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -2.48 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 114 HIS 0.001 0.000 HIS H 238 PHE 0.023 0.001 PHE B 209 TYR 0.014 0.001 TYR D 98 ARG 0.001 0.000 ARG E 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 226 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7220 (m-40) cc_final: 0.6426 (t0) REVERT: A 74 ASN cc_start: 0.7166 (m-40) cc_final: 0.6528 (t0) REVERT: A 77 MET cc_start: 0.6585 (OUTLIER) cc_final: 0.6213 (mtp) REVERT: B 74 ASN cc_start: 0.7216 (m-40) cc_final: 0.6421 (t0) REVERT: D 74 ASN cc_start: 0.7166 (m-40) cc_final: 0.6518 (t0) REVERT: D 77 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.6264 (mtp) REVERT: E 74 ASN cc_start: 0.7212 (m-40) cc_final: 0.6422 (t0) REVERT: F 74 ASN cc_start: 0.7163 (m-40) cc_final: 0.6522 (t0) REVERT: F 77 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.6251 (mtp) REVERT: G 74 ASN cc_start: 0.7307 (m-40) cc_final: 0.6518 (t0) REVERT: H 74 ASN cc_start: 0.7168 (m-40) cc_final: 0.6526 (t0) REVERT: H 77 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.6252 (mtp) outliers start: 38 outliers final: 26 residues processed: 250 average time/residue: 1.0982 time to fit residues: 301.9319 Evaluate side-chains 256 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 226 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 77 MET Chi-restraints excluded: chain H residue 251 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.196659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142071 restraints weight = 13778.600| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.95 r_work: 0.3279 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13984 Z= 0.256 Angle : 0.610 6.571 18968 Z= 0.312 Chirality : 0.043 0.143 2144 Planarity : 0.006 0.057 2328 Dihedral : 13.392 84.611 2200 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.77 % Allowed : 21.15 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1680 helix: 0.49 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -2.69 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 189 HIS 0.001 0.000 HIS H 238 PHE 0.016 0.002 PHE A 209 TYR 0.013 0.001 TYR D 98 ARG 0.002 0.000 ARG E 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5358.10 seconds wall clock time: 94 minutes 33.09 seconds (5673.09 seconds total)