Starting phenix.real_space_refine on Thu Nov 16 04:51:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/11_2023/8gmp_40229_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/11_2023/8gmp_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_40229/11_2023/8gmp_40229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/11_2023/8gmp_40229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/11_2023/8gmp_40229_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/11_2023/8gmp_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-1.21rc1-5144/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: 7.50, per 1000 atoms: 0.55 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: 5.58 Conformation dependent library (CDL) restraints added in 2.6 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: 2.18 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: 3.17 Time building geometry restraints manager: 5.87 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: 7656 20.50 - 41.00: 464 41.00 - 61.50: 224 61.50 - 82.00: 32 82.00 - 102.50: 8 Dihedral angle restraints: 8384 sinusoidal: 3288 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 8381 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: 1.510 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: 7.490 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 37.510 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.110 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:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.640 ------------------------------------------------------------------------------- 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 : 16.743 102.504 5008 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 *********************** 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 : 1.500 Fit side-chains outliers start: 40 outliers final: 8 residues processed: 304 average time/residue: 1.1351 time to fit residues: 379.7226 Evaluate side-chains 236 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 228 time to evaluate : 1.495 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1186 time to fit residues: 3.8229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 43 optimal weight: 0.0570 chunk 85 optimal weight: 0.0770 chunk 68 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 152 optimal weight: 0.1980 overall best weight: 0.2294 ------------------------------------------------------------------------------- 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: 0.7738 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13984 Z= 0.178 Angle : 0.659 7.193 18968 Z= 0.346 Chirality : 0.040 0.133 2144 Planarity : 0.006 0.046 2328 Dihedral : 14.590 75.159 2152 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.66 % Allowed : 12.72 % Favored : 84.62 % 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: -4.50 (0.16), residues: 1680 helix: -2.88 (0.11), residues: 1208 sheet: None (None), residues: 0 loop : -2.64 (0.27), residues: 472 *********************** 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 255 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 219 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 227 average time/residue: 1.2401 time to fit residues: 307.7195 Evaluate side-chains 236 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 216 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 8 residues processed: 12 average time/residue: 0.7900 time to fit residues: 12.7362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 126 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 42 optimal weight: 30.0000 chunk 152 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 136 optimal weight: 0.0030 chunk 151 optimal weight: 0.8980 chunk 52 optimal weight: 0.0470 chunk 122 optimal weight: 0.9980 overall best weight: 0.9890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN D 74 ASN F 74 ASN H 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13984 Z= 0.199 Angle : 0.610 6.138 18968 Z= 0.314 Chirality : 0.041 0.120 2144 Planarity : 0.006 0.046 2328 Dihedral : 13.599 76.637 2152 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.96 % Allowed : 14.79 % Favored : 82.25 % 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: -3.11 (0.19), residues: 1680 helix: -1.59 (0.14), residues: 1224 sheet: None (None), residues: 0 loop : -2.97 (0.24), residues: 456 *********************** 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 274 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 234 time to evaluate : 1.700 Fit side-chains outliers start: 40 outliers final: 20 residues processed: 242 average time/residue: 1.2158 time to fit residues: 322.1137 Evaluate side-chains 254 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 234 time to evaluate : 1.487 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 8 residues processed: 12 average time/residue: 0.1286 time to fit residues: 4.6781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.0270 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 overall best weight: 0.9440 ------------------------------------------------------------------------------- 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: 0.7777 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13984 Z= 0.186 Angle : 0.580 6.024 18968 Z= 0.297 Chirality : 0.040 0.117 2144 Planarity : 0.006 0.050 2328 Dihedral : 13.113 76.893 2152 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.29 % Allowed : 16.27 % Favored : 79.44 % 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: -2.58 (0.19), residues: 1680 helix: -1.10 (0.14), residues: 1272 sheet: None (None), residues: 0 loop : -3.28 (0.24), residues: 408 *********************** 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 299 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 241 time to evaluate : 1.593 Fit side-chains outliers start: 58 outliers final: 28 residues processed: 257 average time/residue: 1.2837 time to fit residues: 359.5875 Evaluate side-chains 269 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 241 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 12 residues processed: 16 average time/residue: 0.6859 time to fit residues: 14.5253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 82 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 H 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13984 Z= 0.208 Angle : 0.593 6.038 18968 Z= 0.302 Chirality : 0.041 0.121 2144 Planarity : 0.006 0.053 2328 Dihedral : 13.083 78.667 2152 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.07 % Allowed : 19.01 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.20), residues: 1680 helix: -0.75 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -3.21 (0.25), residues: 408 *********************** 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 295 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 240 time to evaluate : 1.495 Fit side-chains outliers start: 55 outliers final: 27 residues processed: 257 average time/residue: 1.2870 time to fit residues: 360.9058 Evaluate side-chains 267 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 240 time to evaluate : 1.546 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 12 residues processed: 15 average time/residue: 0.8580 time to fit residues: 16.4131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.0170 chunk 146 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 75 optimal weight: 0.0870 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 H 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13984 Z= 0.162 Angle : 0.559 6.679 18968 Z= 0.287 Chirality : 0.039 0.111 2144 Planarity : 0.006 0.053 2328 Dihedral : 12.813 79.211 2152 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.22 % Allowed : 19.90 % Favored : 75.89 % 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: -1.61 (0.20), residues: 1680 helix: -0.38 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -3.01 (0.25), residues: 408 *********************** 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 307 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 250 time to evaluate : 1.649 Fit side-chains outliers start: 57 outliers final: 34 residues processed: 269 average time/residue: 1.2203 time to fit residues: 360.0206 Evaluate side-chains 282 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 248 time to evaluate : 1.426 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 12 residues processed: 22 average time/residue: 0.5638 time to fit residues: 16.8465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 0.2980 chunk 90 optimal weight: 0.0980 chunk 161 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 H 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13984 Z= 0.160 Angle : 0.542 6.010 18968 Z= 0.277 Chirality : 0.038 0.111 2144 Planarity : 0.005 0.052 2328 Dihedral : 12.410 81.444 2152 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.99 % Allowed : 21.45 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1680 helix: 0.11 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -2.65 (0.26), residues: 432 *********************** 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 304 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 250 time to evaluate : 1.335 Fit side-chains outliers start: 54 outliers final: 24 residues processed: 268 average time/residue: 1.2095 time to fit residues: 354.3317 Evaluate side-chains 266 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 242 time to evaluate : 1.456 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 12 residues processed: 12 average time/residue: 0.2023 time to fit residues: 5.7027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.2980 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 0.0020 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 110 optimal weight: 0.0470 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 147 optimal weight: 30.0000 overall best weight: 0.4286 ------------------------------------------------------------------------------- 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 H 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13984 Z= 0.140 Angle : 0.519 5.977 18968 Z= 0.264 Chirality : 0.037 0.105 2144 Planarity : 0.005 0.051 2328 Dihedral : 12.032 83.096 2152 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.03 % Allowed : 23.15 % Favored : 73.82 % 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: -0.30 (0.21), residues: 1680 helix: 0.58 (0.16), residues: 1248 sheet: None (None), residues: 0 loop : -2.44 (0.27), residues: 432 *********************** 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 300 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 259 time to evaluate : 1.474 Fit side-chains outliers start: 41 outliers final: 18 residues processed: 274 average time/residue: 1.2494 time to fit residues: 375.1025 Evaluate side-chains 261 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 243 time to evaluate : 1.571 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 6 average time/residue: 0.6529 time to fit residues: 6.7091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 150 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 136 optimal weight: 0.4980 chunk 142 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN C 74 ASN A 74 ASN B 49 ASN B 74 ASN D 74 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN F 74 ASN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN H 74 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13984 Z= 0.175 Angle : 0.545 6.077 18968 Z= 0.278 Chirality : 0.039 0.119 2144 Planarity : 0.005 0.053 2328 Dihedral : 12.055 84.466 2152 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.85 % Allowed : 22.26 % Favored : 73.89 % 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: -0.15 (0.21), residues: 1680 helix: 0.71 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -2.44 (0.27), residues: 432 *********************** 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 299 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 247 time to evaluate : 1.503 Fit side-chains outliers start: 52 outliers final: 30 residues processed: 263 average time/residue: 1.1754 time to fit residues: 339.3894 Evaluate side-chains 272 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 242 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 15 residues processed: 15 average time/residue: 0.3880 time to fit residues: 9.2078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 30.0000 chunk 141 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN F 74 ASN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN H 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3494 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= 0.182 Angle : 0.550 6.135 18968 Z= 0.282 Chirality : 0.040 0.120 2144 Planarity : 0.006 0.053 2328 Dihedral : 12.084 85.683 2152 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.44 % Allowed : 23.89 % Favored : 73.67 % 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: -0.02 (0.21), residues: 1680 helix: 0.82 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -2.45 (0.27), residues: 432 ********************** 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 268 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 235 time to evaluate : 1.466 Fit side-chains outliers start: 33 outliers final: 19 residues processed: 256 average time/residue: 1.1939 time to fit residues: 335.2309 Evaluate side-chains 253 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 234 time to evaluate : 1.583 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 0.1613 time to fit residues: 3.1120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN F 74 ASN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN H 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.200144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.147235 restraints weight = 13831.785| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.90 r_work: 0.3460 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3542 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= 0.180 Angle : 0.548 6.121 18968 Z= 0.281 Chirality : 0.039 0.121 2144 Planarity : 0.006 0.053 2328 Dihedral : 11.997 87.503 2152 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.00 % Allowed : 24.26 % Favored : 73.74 % 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: 0.17 (0.21), residues: 1680 helix: 0.96 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -2.39 (0.28), residues: 432 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5686.74 seconds wall clock time: 101 minutes 0.42 seconds (6060.42 seconds total)