Starting phenix.real_space_refine on Sat Mar 16 20:03:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmx_0923/03_2024/6lmx_0923.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmx_0923/03_2024/6lmx_0923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmx_0923/03_2024/6lmx_0923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmx_0923/03_2024/6lmx_0923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmx_0923/03_2024/6lmx_0923.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmx_0923/03_2024/6lmx_0923.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 10062 2.51 5 N 2628 2.21 5 O 2745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 133": "OD1" <-> "OD2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 133": "OD1" <-> "OD2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 133": "OD1" <-> "OD2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "D PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 133": "OD1" <-> "OD2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "E PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 133": "OD1" <-> "OD2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "F PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 133": "OD1" <-> "OD2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 133": "OD1" <-> "OD2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "H PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 133": "OD1" <-> "OD2" Residue "H GLU 135": "OE1" <-> "OE2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 80": "OE1" <-> "OE2" Residue "I TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 133": "OD1" <-> "OD2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I GLU 165": "OE1" <-> "OE2" 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: 15588 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1732 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 9, 'TRANS': 230} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 159 Chain: "B" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1732 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 9, 'TRANS': 230} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 159 Chain: "C" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1732 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 9, 'TRANS': 230} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 159 Chain: "D" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1732 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 9, 'TRANS': 230} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 159 Chain: "E" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1732 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 9, 'TRANS': 230} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 159 Chain: "F" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1732 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 9, 'TRANS': 230} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 159 Chain: "G" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1732 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 9, 'TRANS': 230} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 159 Chain: "H" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1732 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 9, 'TRANS': 230} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 159 Chain: "I" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1732 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 9, 'TRANS': 230} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 159 Time building chain proxies: 8.82, per 1000 atoms: 0.57 Number of scatterers: 15588 At special positions: 0 Unit cell: (128.65, 128.65, 101.789, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 153 16.00 O 2745 8.00 N 2628 7.00 C 10062 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 160 " distance=2.01 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 160 " distance=2.01 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 160 " distance=2.01 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 160 " distance=2.01 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 160 " distance=2.01 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 160 " distance=2.01 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 160 " distance=2.01 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 160 " distance=2.01 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 160 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.79 Conformation dependent library (CDL) restraints added in 3.0 seconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4122 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 0 sheets defined 83.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 21 through 37 Processing helix chain 'A' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 51 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 72 through 83 removed outlier: 3.719A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.672A pdb=" N TYR A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 121 Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.712A pdb=" N PHE A 137 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 167 through 200 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR B 50 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 51 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.720A pdb=" N ARG B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 107 removed outlier: 3.672A pdb=" N TYR B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.713A pdb=" N PHE B 137 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 167 through 200 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE B 248 " --> pdb=" O VAL B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 22 through 37 Processing helix chain 'C' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N THR C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 72 through 83 removed outlier: 3.719A pdb=" N ARG C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 107 removed outlier: 3.671A pdb=" N TYR C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 121 Processing helix chain 'C' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.712A pdb=" N PHE C 137 " --> pdb=" O ILE C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 167 through 200 Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 210 through 248 removed outlier: 3.592A pdb=" N PHE C 248 " --> pdb=" O VAL C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N THR D 50 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR D 51 " --> pdb=" O TYR D 47 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 72 through 83 removed outlier: 3.720A pdb=" N ARG D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 107 removed outlier: 3.672A pdb=" N TYR D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 137 removed outlier: 3.712A pdb=" N PHE D 137 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 167 through 200 Processing helix chain 'D' and resid 203 through 208 Processing helix chain 'D' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE D 248 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 258 Processing helix chain 'E' and resid 22 through 37 Processing helix chain 'E' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR E 49 " --> pdb=" O PRO E 45 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR E 50 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 72 through 83 removed outlier: 3.719A pdb=" N ARG E 83 " --> pdb=" O GLU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 107 removed outlier: 3.671A pdb=" N TYR E 97 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.712A pdb=" N PHE E 137 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 167 through 200 Processing helix chain 'E' and resid 203 through 208 Processing helix chain 'E' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE E 248 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 258 Processing helix chain 'F' and resid 22 through 37 Processing helix chain 'F' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR F 49 " --> pdb=" O PRO F 45 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR F 50 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR F 51 " --> pdb=" O TYR F 47 " (cutoff:3.500A) Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 72 through 83 removed outlier: 3.719A pdb=" N ARG F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 107 removed outlier: 3.672A pdb=" N TYR F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 121 Processing helix chain 'F' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER F 129 " --> pdb=" O LEU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 137 removed outlier: 3.712A pdb=" N PHE F 137 " --> pdb=" O ILE F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 167 through 200 Processing helix chain 'F' and resid 203 through 208 Processing helix chain 'F' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE F 248 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 258 Processing helix chain 'G' and resid 22 through 37 Processing helix chain 'G' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR G 49 " --> pdb=" O PRO G 45 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR G 51 " --> pdb=" O TYR G 47 " (cutoff:3.500A) Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 72 through 83 removed outlier: 3.721A pdb=" N ARG G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 107 removed outlier: 3.671A pdb=" N TYR G 97 " --> pdb=" O SER G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 121 Processing helix chain 'G' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER G 129 " --> pdb=" O LEU G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 137 removed outlier: 3.712A pdb=" N PHE G 137 " --> pdb=" O ILE G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 143 Processing helix chain 'G' and resid 147 through 156 Processing helix chain 'G' and resid 167 through 200 Processing helix chain 'G' and resid 203 through 208 Processing helix chain 'G' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE G 248 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 258 Processing helix chain 'H' and resid 22 through 37 Processing helix chain 'H' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR H 49 " --> pdb=" O PRO H 45 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR H 50 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR H 51 " --> pdb=" O TYR H 47 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 72 through 83 removed outlier: 3.719A pdb=" N ARG H 83 " --> pdb=" O GLU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 107 removed outlier: 3.671A pdb=" N TYR H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 121 Processing helix chain 'H' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 137 removed outlier: 3.713A pdb=" N PHE H 137 " --> pdb=" O ILE H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 143 Processing helix chain 'H' and resid 147 through 156 Processing helix chain 'H' and resid 167 through 200 Processing helix chain 'H' and resid 203 through 208 Processing helix chain 'H' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE H 248 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 258 Processing helix chain 'I' and resid 22 through 37 Processing helix chain 'I' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR I 49 " --> pdb=" O PRO I 45 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR I 50 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Proline residue: I 59 - end of helix Processing helix chain 'I' and resid 72 through 83 removed outlier: 3.720A pdb=" N ARG I 83 " --> pdb=" O GLU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 107 removed outlier: 3.671A pdb=" N TYR I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 121 Processing helix chain 'I' and resid 121 through 129 removed outlier: 3.539A pdb=" N SER I 129 " --> pdb=" O LEU I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 137 removed outlier: 3.712A pdb=" N PHE I 137 " --> pdb=" O ILE I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 143 Processing helix chain 'I' and resid 147 through 156 Processing helix chain 'I' and resid 167 through 200 Processing helix chain 'I' and resid 203 through 208 Processing helix chain 'I' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE I 248 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 258 1252 hydrogen bonds defined for protein. 3621 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: 4.46 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2833 1.32 - 1.44: 4009 1.44 - 1.57: 8827 1.57 - 1.69: 0 1.69 - 1.81: 234 Bond restraints: 15903 Sorted by residual: bond pdb=" C CYS I 43 " pdb=" N MET I 44 " ideal model delta sigma weight residual 1.333 1.241 0.091 2.74e-02 1.33e+03 1.11e+01 bond pdb=" C CYS D 43 " pdb=" N MET D 44 " ideal model delta sigma weight residual 1.333 1.242 0.091 2.74e-02 1.33e+03 1.10e+01 bond pdb=" C CYS H 43 " pdb=" N MET H 44 " ideal model delta sigma weight residual 1.333 1.242 0.091 2.74e-02 1.33e+03 1.10e+01 bond pdb=" C CYS C 43 " pdb=" N MET C 44 " ideal model delta sigma weight residual 1.333 1.242 0.091 2.74e-02 1.33e+03 1.10e+01 bond pdb=" C CYS B 43 " pdb=" N MET B 44 " ideal model delta sigma weight residual 1.333 1.242 0.091 2.74e-02 1.33e+03 1.10e+01 ... (remaining 15898 not shown) Histogram of bond angle deviations from ideal: 94.53 - 102.46: 117 102.46 - 110.40: 4159 110.40 - 118.34: 7886 118.34 - 126.27: 9267 126.27 - 134.21: 216 Bond angle restraints: 21645 Sorted by residual: angle pdb=" CG1 ILE I 177 " pdb=" CB ILE I 177 " pdb=" CG2 ILE I 177 " ideal model delta sigma weight residual 110.70 98.65 12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CG1 ILE D 177 " pdb=" CB ILE D 177 " pdb=" CG2 ILE D 177 " ideal model delta sigma weight residual 110.70 98.67 12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CG1 ILE C 177 " pdb=" CB ILE C 177 " pdb=" CG2 ILE C 177 " ideal model delta sigma weight residual 110.70 98.67 12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CG1 ILE G 177 " pdb=" CB ILE G 177 " pdb=" CG2 ILE G 177 " ideal model delta sigma weight residual 110.70 98.68 12.02 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CG1 ILE A 177 " pdb=" CB ILE A 177 " pdb=" CG2 ILE A 177 " ideal model delta sigma weight residual 110.70 98.68 12.02 3.00e+00 1.11e-01 1.60e+01 ... (remaining 21640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 8307 16.91 - 33.83: 1043 33.83 - 50.74: 163 50.74 - 67.66: 36 67.66 - 84.57: 9 Dihedral angle restraints: 9558 sinusoidal: 3231 harmonic: 6327 Sorted by residual: dihedral pdb=" CA LYS E 255 " pdb=" C LYS E 255 " pdb=" N ASP E 256 " pdb=" CA ASP E 256 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA LYS I 255 " pdb=" C LYS I 255 " pdb=" N ASP I 256 " pdb=" CA ASP I 256 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA LYS F 255 " pdb=" C LYS F 255 " pdb=" N ASP F 256 " pdb=" CA ASP F 256 " ideal model delta harmonic sigma weight residual 180.00 157.74 22.26 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 9555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1563 0.054 - 0.107: 781 0.107 - 0.161: 153 0.161 - 0.215: 33 0.215 - 0.268: 35 Chirality restraints: 2565 Sorted by residual: chirality pdb=" CB THR B 174 " pdb=" CA THR B 174 " pdb=" OG1 THR B 174 " pdb=" CG2 THR B 174 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB THR H 174 " pdb=" CA THR H 174 " pdb=" OG1 THR H 174 " pdb=" CG2 THR H 174 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB THR F 174 " pdb=" CA THR F 174 " pdb=" OG1 THR F 174 " pdb=" CG2 THR F 174 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 2562 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 59 " -0.089 5.00e-02 4.00e+02 1.33e-01 2.81e+01 pdb=" N PRO E 60 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 59 " 0.089 5.00e-02 4.00e+02 1.33e-01 2.81e+01 pdb=" N PRO C 60 " -0.229 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO I 59 " 0.089 5.00e-02 4.00e+02 1.32e-01 2.80e+01 pdb=" N PRO I 60 " -0.229 5.00e-02 4.00e+02 pdb=" CA PRO I 60 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO I 60 " 0.072 5.00e-02 4.00e+02 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1435 2.71 - 3.26: 14986 3.26 - 3.80: 24087 3.80 - 4.35: 29294 4.35 - 4.90: 51377 Nonbonded interactions: 121179 Sorted by model distance: nonbonded pdb=" O LEU B 118 " pdb=" OG SER B 181 " model vdw 2.161 2.440 nonbonded pdb=" O LEU F 118 " pdb=" OG SER F 181 " model vdw 2.161 2.440 nonbonded pdb=" O LEU H 118 " pdb=" OG SER H 181 " model vdw 2.161 2.440 nonbonded pdb=" O LEU D 118 " pdb=" OG SER D 181 " model vdw 2.162 2.440 nonbonded pdb=" O LEU I 118 " pdb=" OG SER I 181 " model vdw 2.162 2.440 ... (remaining 121174 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' selection = chain 'I' } 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: 0.410 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: 2.320 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 42.230 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 : 0.019 0.159 15903 Z= 1.208 Angle : 1.321 12.048 21645 Z= 0.753 Chirality : 0.067 0.268 2565 Planarity : 0.013 0.133 2736 Dihedral : 15.243 84.572 5382 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.26 % Allowed : 12.79 % Favored : 85.95 % 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: -6.20 (0.10), residues: 2142 helix: -4.30 (0.05), residues: 1629 sheet: None (None), residues: 0 loop : -2.27 (0.18), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP C 113 PHE 0.047 0.005 PHE I 124 TYR 0.032 0.005 TYR H 176 ARG 0.006 0.001 ARG I 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 282 time to evaluate : 1.639 Fit side-chains REVERT: A 38 GLU cc_start: 0.8114 (pm20) cc_final: 0.7765 (pm20) REVERT: A 96 ARG cc_start: 0.6860 (ptt180) cc_final: 0.6151 (mtt180) REVERT: A 104 GLN cc_start: 0.8142 (mp10) cc_final: 0.7697 (mp10) REVERT: A 157 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7183 (mtm-85) REVERT: A 168 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: B 46 GLU cc_start: 0.8271 (pm20) cc_final: 0.8044 (pm20) REVERT: B 96 ARG cc_start: 0.6558 (ptt180) cc_final: 0.5890 (mtt180) REVERT: B 104 GLN cc_start: 0.8535 (mp10) cc_final: 0.8184 (mp10) REVERT: B 105 ARG cc_start: 0.6521 (ttt90) cc_final: 0.6298 (ttm-80) REVERT: B 120 ASP cc_start: 0.8939 (t0) cc_final: 0.8699 (t0) REVERT: B 133 ASP cc_start: 0.8628 (t0) cc_final: 0.8020 (t0) REVERT: B 157 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7117 (mtm-85) REVERT: B 167 ASN cc_start: 0.8924 (t0) cc_final: 0.8649 (t0) REVERT: B 168 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6510 (tm-30) REVERT: C 38 GLU cc_start: 0.8167 (pm20) cc_final: 0.7916 (pm20) REVERT: C 96 ARG cc_start: 0.6745 (ptt180) cc_final: 0.6052 (mtt180) REVERT: C 104 GLN cc_start: 0.8070 (mp10) cc_final: 0.7232 (mp10) REVERT: C 148 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7437 (mm-30) REVERT: C 165 GLU cc_start: 0.6935 (pm20) cc_final: 0.6702 (pm20) REVERT: C 168 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: D 44 MET cc_start: 0.8809 (mtm) cc_final: 0.8600 (mtm) REVERT: D 96 ARG cc_start: 0.6791 (ptt180) cc_final: 0.5927 (mtt180) REVERT: D 119 MET cc_start: 0.8807 (mmt) cc_final: 0.8521 (mmm) REVERT: D 133 ASP cc_start: 0.8683 (t0) cc_final: 0.8302 (t0) REVERT: D 143 VAL cc_start: 0.8805 (m) cc_final: 0.8452 (t) REVERT: D 146 MET cc_start: 0.6478 (ptp) cc_final: 0.5952 (ptp) REVERT: D 150 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7681 (mt-10) REVERT: D 151 LYS cc_start: 0.7812 (tptt) cc_final: 0.7523 (tptt) REVERT: D 153 LYS cc_start: 0.8754 (mttt) cc_final: 0.8252 (mttp) REVERT: D 161 LYS cc_start: 0.8347 (mttm) cc_final: 0.8141 (tptp) REVERT: D 168 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6798 (tm-30) REVERT: E 44 MET cc_start: 0.8663 (mtm) cc_final: 0.8421 (mtt) REVERT: E 96 ARG cc_start: 0.6490 (ptt180) cc_final: 0.5465 (mtt-85) REVERT: E 104 GLN cc_start: 0.8257 (mp10) cc_final: 0.7925 (mp10) REVERT: E 119 MET cc_start: 0.8891 (mmt) cc_final: 0.8501 (mmm) REVERT: E 168 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7042 (tm-30) REVERT: F 96 ARG cc_start: 0.6757 (ptt180) cc_final: 0.6175 (mtt180) REVERT: F 104 GLN cc_start: 0.8205 (mp10) cc_final: 0.7870 (mp10) REVERT: F 133 ASP cc_start: 0.8527 (t0) cc_final: 0.8074 (t0) REVERT: F 157 ARG cc_start: 0.7906 (mtm-85) cc_final: 0.7621 (mtp85) REVERT: F 168 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: G 96 ARG cc_start: 0.6288 (ptt180) cc_final: 0.5676 (mtt180) REVERT: G 104 GLN cc_start: 0.7943 (mp10) cc_final: 0.7675 (mp10) REVERT: G 119 MET cc_start: 0.8783 (mmt) cc_final: 0.8328 (mmt) REVERT: G 133 ASP cc_start: 0.8633 (t0) cc_final: 0.8288 (t0) REVERT: G 165 GLU cc_start: 0.5888 (pm20) cc_final: 0.5589 (pm20) REVERT: G 168 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: G 191 MET cc_start: 0.7175 (mmt) cc_final: 0.6878 (mmm) REVERT: H 46 GLU cc_start: 0.8306 (pm20) cc_final: 0.8029 (pm20) REVERT: H 82 LYS cc_start: 0.4291 (OUTLIER) cc_final: 0.4014 (tppp) REVERT: H 96 ARG cc_start: 0.6709 (ptt180) cc_final: 0.5921 (mtt180) REVERT: H 133 ASP cc_start: 0.8669 (t0) cc_final: 0.8422 (t0) REVERT: H 143 VAL cc_start: 0.8815 (m) cc_final: 0.8608 (m) REVERT: H 153 LYS cc_start: 0.8661 (mttt) cc_final: 0.8460 (mtmm) REVERT: H 157 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7453 (mtp85) REVERT: H 168 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: I 38 GLU cc_start: 0.8125 (pm20) cc_final: 0.7852 (pm20) REVERT: I 44 MET cc_start: 0.8832 (mtm) cc_final: 0.8500 (mtm) REVERT: I 96 ARG cc_start: 0.6388 (ptt180) cc_final: 0.5704 (mtt180) REVERT: I 104 GLN cc_start: 0.7912 (mp10) cc_final: 0.7583 (mp10) REVERT: I 143 VAL cc_start: 0.8524 (m) cc_final: 0.8241 (t) REVERT: I 168 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6956 (tm-30) outliers start: 18 outliers final: 0 residues processed: 300 average time/residue: 0.3401 time to fit residues: 139.3208 Evaluate side-chains 277 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 267 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 168 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 196 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 72 ASN B 71 ASN B 72 ASN C 71 ASN C 72 ASN D 71 ASN D 72 ASN E 71 ASN F 71 ASN F 72 ASN G 71 ASN G 72 ASN H 71 ASN H 72 ASN I 71 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15903 Z= 0.193 Angle : 0.599 4.703 21645 Z= 0.331 Chirality : 0.037 0.128 2565 Planarity : 0.008 0.081 2736 Dihedral : 6.249 44.460 2326 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.70 % Allowed : 15.37 % Favored : 80.92 % 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: -2.17 (0.15), residues: 2142 helix: -1.15 (0.10), residues: 1647 sheet: None (None), residues: 0 loop : -1.82 (0.22), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 62 PHE 0.018 0.001 PHE C 197 TYR 0.016 0.002 TYR I 34 ARG 0.002 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 260 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8886 (t80) cc_final: 0.8676 (t80) REVERT: A 104 GLN cc_start: 0.7691 (mp10) cc_final: 0.7016 (mp10) REVERT: B 33 MET cc_start: 0.8098 (ttm) cc_final: 0.7808 (ttm) REVERT: B 38 GLU cc_start: 0.8225 (pm20) cc_final: 0.7746 (pm20) REVERT: B 46 GLU cc_start: 0.8118 (pm20) cc_final: 0.7774 (pm20) REVERT: B 55 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8688 (tp) REVERT: B 133 ASP cc_start: 0.8385 (t0) cc_final: 0.7867 (t0) REVERT: B 157 ARG cc_start: 0.7425 (mtm-85) cc_final: 0.7078 (mtm-85) REVERT: C 33 MET cc_start: 0.8389 (ttm) cc_final: 0.7616 (ttt) REVERT: C 34 TYR cc_start: 0.9020 (t80) cc_final: 0.8723 (t80) REVERT: C 104 GLN cc_start: 0.7740 (mp10) cc_final: 0.7152 (mp10) REVERT: C 161 LYS cc_start: 0.8650 (tptm) cc_final: 0.8309 (tptp) REVERT: C 198 LEU cc_start: 0.8517 (mt) cc_final: 0.8060 (tt) REVERT: D 33 MET cc_start: 0.8518 (ttm) cc_final: 0.8317 (ttt) REVERT: D 38 GLU cc_start: 0.8205 (pm20) cc_final: 0.7926 (pm20) REVERT: D 44 MET cc_start: 0.8436 (mtm) cc_final: 0.8076 (mtm) REVERT: D 143 VAL cc_start: 0.8227 (m) cc_final: 0.7796 (t) REVERT: D 146 MET cc_start: 0.6478 (ptp) cc_final: 0.6225 (ptp) REVERT: D 150 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7592 (mt-10) REVERT: D 151 LYS cc_start: 0.7691 (tptt) cc_final: 0.7321 (tptt) REVERT: D 153 LYS cc_start: 0.8528 (mttt) cc_final: 0.8032 (mttp) REVERT: D 161 LYS cc_start: 0.8411 (mttm) cc_final: 0.8173 (tptp) REVERT: D 198 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7750 (tt) REVERT: E 33 MET cc_start: 0.8207 (ttm) cc_final: 0.7478 (ttm) REVERT: E 104 GLN cc_start: 0.7686 (mp10) cc_final: 0.7218 (mp10) REVERT: E 136 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8622 (mtpp) REVERT: E 153 LYS cc_start: 0.8529 (mtmm) cc_final: 0.8201 (mtmm) REVERT: E 191 MET cc_start: 0.6742 (mmt) cc_final: 0.6493 (mmm) REVERT: F 33 MET cc_start: 0.8199 (ttm) cc_final: 0.7774 (ttt) REVERT: F 38 GLU cc_start: 0.8493 (pm20) cc_final: 0.8251 (pm20) REVERT: F 104 GLN cc_start: 0.7932 (mp10) cc_final: 0.7507 (mp10) REVERT: F 119 MET cc_start: 0.8590 (mmt) cc_final: 0.8309 (mmt) REVERT: F 133 ASP cc_start: 0.7861 (t0) cc_final: 0.7544 (t0) REVERT: F 143 VAL cc_start: 0.8621 (m) cc_final: 0.8416 (t) REVERT: F 157 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7545 (mtp85) REVERT: F 198 LEU cc_start: 0.8313 (mt) cc_final: 0.7968 (tt) REVERT: G 38 GLU cc_start: 0.8304 (pm20) cc_final: 0.7837 (pm20) REVERT: G 133 ASP cc_start: 0.8490 (t0) cc_final: 0.8158 (t0) REVERT: G 143 VAL cc_start: 0.8612 (m) cc_final: 0.8021 (t) REVERT: G 191 MET cc_start: 0.6027 (mmt) cc_final: 0.5715 (mmm) REVERT: G 192 MET cc_start: 0.6488 (ttp) cc_final: 0.6263 (ttp) REVERT: G 198 LEU cc_start: 0.8157 (mt) cc_final: 0.7829 (tt) REVERT: H 33 MET cc_start: 0.8597 (ttm) cc_final: 0.8352 (ttt) REVERT: H 38 GLU cc_start: 0.8125 (pm20) cc_final: 0.7831 (pm20) REVERT: H 44 MET cc_start: 0.8567 (mtm) cc_final: 0.8021 (mtm) REVERT: H 46 GLU cc_start: 0.8142 (pm20) cc_final: 0.7879 (pm20) REVERT: H 104 GLN cc_start: 0.8052 (mp10) cc_final: 0.7658 (mp10) REVERT: H 157 ARG cc_start: 0.7606 (mtm-85) cc_final: 0.7318 (mtp85) REVERT: I 38 GLU cc_start: 0.8224 (pm20) cc_final: 0.8002 (pm20) REVERT: I 49 TYR cc_start: 0.8857 (t80) cc_final: 0.8617 (t80) REVERT: I 191 MET cc_start: 0.6274 (mmt) cc_final: 0.5993 (mmm) outliers start: 53 outliers final: 26 residues processed: 293 average time/residue: 0.3015 time to fit residues: 125.0309 Evaluate side-chains 275 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 247 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 179 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 133 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 196 optimal weight: 0.1980 chunk 212 optimal weight: 30.0000 chunk 175 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 66 optimal weight: 0.0870 chunk 157 optimal weight: 3.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 71 ASN C 71 ASN D 71 ASN E 71 ASN F 71 ASN G 71 ASN I 71 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15903 Z= 0.162 Angle : 0.505 6.907 21645 Z= 0.272 Chirality : 0.036 0.134 2565 Planarity : 0.006 0.069 2736 Dihedral : 4.471 12.804 2295 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.96 % Allowed : 17.26 % Favored : 80.78 % 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: 0.24 (0.17), residues: 2142 helix: 0.75 (0.12), residues: 1656 sheet: None (None), residues: 0 loop : -1.73 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 62 PHE 0.012 0.001 PHE C 197 TYR 0.011 0.001 TYR D 34 ARG 0.001 0.000 ARG E 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 254 time to evaluate : 1.762 Fit side-chains revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8924 (t80) cc_final: 0.8705 (t80) REVERT: B 33 MET cc_start: 0.8252 (ttm) cc_final: 0.7828 (ttm) REVERT: B 38 GLU cc_start: 0.8211 (pm20) cc_final: 0.7751 (pm20) REVERT: B 55 LEU cc_start: 0.8753 (tp) cc_final: 0.8511 (tp) REVERT: B 133 ASP cc_start: 0.8384 (t0) cc_final: 0.7843 (t0) REVERT: C 33 MET cc_start: 0.8303 (ttm) cc_final: 0.7526 (ttt) REVERT: C 34 TYR cc_start: 0.9029 (t80) cc_final: 0.8761 (t80) REVERT: C 104 GLN cc_start: 0.7932 (mp10) cc_final: 0.7371 (mp10) REVERT: C 161 LYS cc_start: 0.8692 (tptm) cc_final: 0.8339 (tptp) REVERT: D 38 GLU cc_start: 0.8078 (pm20) cc_final: 0.7795 (pm20) REVERT: D 44 MET cc_start: 0.8373 (mtm) cc_final: 0.7911 (mtm) REVERT: D 150 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7607 (mt-10) REVERT: D 153 LYS cc_start: 0.8208 (mttt) cc_final: 0.7742 (mttp) REVERT: D 161 LYS cc_start: 0.8360 (mttm) cc_final: 0.8155 (tptp) REVERT: D 198 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7554 (tt) REVERT: E 33 MET cc_start: 0.8231 (ttm) cc_final: 0.7506 (ttm) REVERT: E 104 GLN cc_start: 0.7959 (mp10) cc_final: 0.7746 (mp10) REVERT: E 129 SER cc_start: 0.8910 (p) cc_final: 0.8405 (t) REVERT: E 136 LYS cc_start: 0.8816 (mtpp) cc_final: 0.8600 (mtpp) REVERT: E 153 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8173 (mtpt) REVERT: E 161 LYS cc_start: 0.8546 (tptm) cc_final: 0.8288 (tptp) REVERT: F 33 MET cc_start: 0.8325 (ttm) cc_final: 0.7975 (ttt) REVERT: F 104 GLN cc_start: 0.8241 (mp10) cc_final: 0.7995 (mp10) REVERT: F 133 ASP cc_start: 0.7835 (t0) cc_final: 0.7549 (t0) REVERT: F 157 ARG cc_start: 0.7639 (mtm-85) cc_final: 0.7395 (mtp85) REVERT: F 191 MET cc_start: 0.6347 (mmm) cc_final: 0.6141 (mmp) REVERT: G 38 GLU cc_start: 0.8236 (pm20) cc_final: 0.7815 (pm20) REVERT: G 133 ASP cc_start: 0.8481 (t0) cc_final: 0.8136 (t0) REVERT: G 192 MET cc_start: 0.6451 (ttp) cc_final: 0.6240 (ttp) REVERT: H 33 MET cc_start: 0.8518 (ttm) cc_final: 0.8305 (ttt) REVERT: H 38 GLU cc_start: 0.8108 (pm20) cc_final: 0.7903 (pm20) REVERT: H 104 GLN cc_start: 0.8242 (mp10) cc_final: 0.7918 (mp10) REVERT: H 157 ARG cc_start: 0.7520 (mtm-85) cc_final: 0.7227 (mtp85) REVERT: I 129 SER cc_start: 0.9007 (p) cc_final: 0.8596 (t) outliers start: 28 outliers final: 14 residues processed: 267 average time/residue: 0.3036 time to fit residues: 115.0839 Evaluate side-chains 253 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 238 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain F residue 153 LYS Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 147 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.0570 chunk 147 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 93 optimal weight: 40.0000 chunk 131 optimal weight: 0.5980 chunk 197 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN D 71 ASN G 71 ASN H 71 ASN I 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15903 Z= 0.250 Angle : 0.563 8.301 21645 Z= 0.295 Chirality : 0.038 0.118 2565 Planarity : 0.006 0.069 2736 Dihedral : 4.393 14.081 2295 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.70 % Allowed : 16.49 % Favored : 79.80 % 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: 0.89 (0.17), residues: 2142 helix: 1.29 (0.12), residues: 1638 sheet: None (None), residues: 0 loop : -1.70 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 62 PHE 0.012 0.001 PHE H 39 TYR 0.017 0.002 TYR G 34 ARG 0.002 0.000 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 261 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8180 (mmp) cc_final: 0.7806 (mmt) REVERT: B 33 MET cc_start: 0.8299 (ttm) cc_final: 0.7852 (ttm) REVERT: B 38 GLU cc_start: 0.8132 (pm20) cc_final: 0.7754 (pm20) REVERT: B 46 GLU cc_start: 0.8064 (pm20) cc_final: 0.7746 (pm20) REVERT: B 133 ASP cc_start: 0.8446 (t0) cc_final: 0.7889 (t0) REVERT: C 33 MET cc_start: 0.8254 (ttm) cc_final: 0.7603 (ttt) REVERT: C 104 GLN cc_start: 0.7873 (mp10) cc_final: 0.7630 (mp10) REVERT: C 161 LYS cc_start: 0.8715 (tptm) cc_final: 0.8420 (tptp) REVERT: D 38 GLU cc_start: 0.8224 (pm20) cc_final: 0.7980 (pm20) REVERT: D 44 MET cc_start: 0.8466 (mtm) cc_final: 0.8021 (mtm) REVERT: D 153 LYS cc_start: 0.8202 (mttt) cc_final: 0.7876 (mttp) REVERT: D 161 LYS cc_start: 0.8460 (mttm) cc_final: 0.8181 (tptp) REVERT: D 165 GLU cc_start: 0.6492 (pm20) cc_final: 0.5945 (pm20) REVERT: D 198 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7514 (tt) REVERT: E 33 MET cc_start: 0.8307 (ttm) cc_final: 0.7598 (ttm) REVERT: E 104 GLN cc_start: 0.8168 (mp10) cc_final: 0.7958 (mp10) REVERT: E 129 SER cc_start: 0.8976 (p) cc_final: 0.8514 (t) REVERT: E 136 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8581 (mtpp) REVERT: E 161 LYS cc_start: 0.8522 (tptm) cc_final: 0.8287 (tptp) REVERT: F 104 GLN cc_start: 0.8227 (mp10) cc_final: 0.7971 (mp10) REVERT: F 133 ASP cc_start: 0.7888 (t0) cc_final: 0.7587 (t0) REVERT: F 157 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7193 (mtm-85) REVERT: G 38 GLU cc_start: 0.8260 (pm20) cc_final: 0.7786 (pm20) REVERT: G 133 ASP cc_start: 0.8449 (t0) cc_final: 0.8144 (t0) REVERT: H 33 MET cc_start: 0.8293 (ttm) cc_final: 0.8051 (ttt) REVERT: H 38 GLU cc_start: 0.7983 (pm20) cc_final: 0.7666 (pm20) REVERT: H 44 MET cc_start: 0.8553 (mtm) cc_final: 0.8184 (mtt) REVERT: H 104 GLN cc_start: 0.8432 (mp10) cc_final: 0.8051 (mp10) REVERT: H 157 ARG cc_start: 0.7513 (mtm-85) cc_final: 0.7197 (mtp85) REVERT: H 165 GLU cc_start: 0.6784 (pm20) cc_final: 0.6369 (pm20) REVERT: I 129 SER cc_start: 0.9044 (p) cc_final: 0.8633 (t) outliers start: 53 outliers final: 38 residues processed: 295 average time/residue: 0.3191 time to fit residues: 136.5604 Evaluate side-chains 300 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 261 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 179 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN D 71 ASN G 71 ASN H 71 ASN I 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15903 Z= 0.360 Angle : 0.621 9.230 21645 Z= 0.324 Chirality : 0.041 0.127 2565 Planarity : 0.006 0.070 2736 Dihedral : 4.468 14.786 2295 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.19 % Allowed : 17.89 % Favored : 77.92 % 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: 0.99 (0.18), residues: 2142 helix: 1.31 (0.12), residues: 1647 sheet: None (None), residues: 0 loop : -1.52 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 62 PHE 0.014 0.002 PHE H 39 TYR 0.024 0.002 TYR A 176 ARG 0.002 0.000 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 256 time to evaluate : 1.666 Fit side-chains revert: symmetry clash REVERT: B 33 MET cc_start: 0.8313 (ttm) cc_final: 0.7559 (ttm) REVERT: B 38 GLU cc_start: 0.8030 (pm20) cc_final: 0.7675 (pm20) REVERT: B 46 GLU cc_start: 0.8056 (pm20) cc_final: 0.7821 (pm20) REVERT: B 133 ASP cc_start: 0.8486 (t0) cc_final: 0.7910 (t0) REVERT: C 104 GLN cc_start: 0.7984 (mp10) cc_final: 0.7718 (mp10) REVERT: C 143 VAL cc_start: 0.8690 (m) cc_final: 0.8350 (t) REVERT: C 161 LYS cc_start: 0.8690 (tptm) cc_final: 0.8355 (tptp) REVERT: D 38 GLU cc_start: 0.8175 (pm20) cc_final: 0.7937 (pm20) REVERT: D 44 MET cc_start: 0.8567 (mtm) cc_final: 0.8115 (mtt) REVERT: D 133 ASP cc_start: 0.8254 (t70) cc_final: 0.7956 (t0) REVERT: D 153 LYS cc_start: 0.8552 (mttt) cc_final: 0.8226 (mttp) REVERT: D 161 LYS cc_start: 0.8469 (mttm) cc_final: 0.8195 (tptp) REVERT: D 165 GLU cc_start: 0.6232 (pm20) cc_final: 0.5670 (pm20) REVERT: D 198 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7520 (tt) REVERT: E 33 MET cc_start: 0.8311 (ttm) cc_final: 0.7715 (ttm) REVERT: E 104 GLN cc_start: 0.8274 (mp10) cc_final: 0.8072 (mp10) REVERT: E 161 LYS cc_start: 0.8532 (tptm) cc_final: 0.8294 (tptp) REVERT: F 104 GLN cc_start: 0.8266 (mp10) cc_final: 0.8000 (mp10) REVERT: F 143 VAL cc_start: 0.8633 (m) cc_final: 0.8392 (t) REVERT: F 157 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7535 (mtp85) REVERT: G 38 GLU cc_start: 0.8227 (pm20) cc_final: 0.7787 (pm20) REVERT: G 133 ASP cc_start: 0.8579 (t0) cc_final: 0.8147 (t0) REVERT: H 33 MET cc_start: 0.8310 (ttm) cc_final: 0.8046 (ttt) REVERT: H 38 GLU cc_start: 0.8008 (pm20) cc_final: 0.7724 (pm20) REVERT: H 44 MET cc_start: 0.8598 (mtm) cc_final: 0.8026 (mtm) REVERT: H 157 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7348 (mtp85) REVERT: H 165 GLU cc_start: 0.6757 (pm20) cc_final: 0.6317 (pm20) outliers start: 60 outliers final: 45 residues processed: 295 average time/residue: 0.2861 time to fit residues: 121.1247 Evaluate side-chains 301 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 255 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 179 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 208 optimal weight: 0.6980 chunk 173 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 109 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN C 71 ASN D 71 ASN E 71 ASN F 71 ASN G 71 ASN H 71 ASN I 71 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15903 Z= 0.170 Angle : 0.508 6.972 21645 Z= 0.267 Chirality : 0.037 0.112 2565 Planarity : 0.006 0.065 2736 Dihedral : 4.109 13.596 2295 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.59 % Allowed : 20.06 % Favored : 77.36 % 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: 1.68 (0.18), residues: 2142 helix: 1.86 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -1.44 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 62 PHE 0.009 0.001 PHE C 197 TYR 0.012 0.001 TYR E 34 ARG 0.001 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 267 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.8033 (mp10) cc_final: 0.7507 (mp10) REVERT: A 119 MET cc_start: 0.8233 (mmp) cc_final: 0.7682 (mmt) REVERT: A 176 TYR cc_start: 0.8315 (t80) cc_final: 0.8092 (t80) REVERT: B 33 MET cc_start: 0.8240 (ttm) cc_final: 0.7732 (ttm) REVERT: B 38 GLU cc_start: 0.8003 (pm20) cc_final: 0.7688 (pm20) REVERT: B 133 ASP cc_start: 0.8413 (t0) cc_final: 0.7890 (t0) REVERT: B 157 ARG cc_start: 0.7649 (mtt90) cc_final: 0.7017 (mtm-85) REVERT: C 104 GLN cc_start: 0.8146 (mp10) cc_final: 0.7051 (mp10) REVERT: C 161 LYS cc_start: 0.8600 (tptm) cc_final: 0.8274 (tptp) REVERT: D 44 MET cc_start: 0.8400 (mtm) cc_final: 0.7956 (mtm) REVERT: D 153 LYS cc_start: 0.8200 (mttt) cc_final: 0.7869 (mttp) REVERT: D 161 LYS cc_start: 0.8427 (mttm) cc_final: 0.8145 (tptp) REVERT: D 198 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7310 (tt) REVERT: E 33 MET cc_start: 0.8273 (ttm) cc_final: 0.7503 (ttm) REVERT: E 104 GLN cc_start: 0.8251 (mp10) cc_final: 0.8022 (mp10) REVERT: E 153 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8203 (mtpt) REVERT: E 161 LYS cc_start: 0.8514 (tptm) cc_final: 0.8308 (tptp) REVERT: F 104 GLN cc_start: 0.8328 (mp10) cc_final: 0.8050 (mp10) REVERT: F 157 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7474 (mtp85) REVERT: G 38 GLU cc_start: 0.8214 (pm20) cc_final: 0.7806 (pm20) REVERT: G 133 ASP cc_start: 0.8471 (t0) cc_final: 0.8128 (t0) REVERT: G 153 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8130 (mttp) REVERT: H 38 GLU cc_start: 0.7955 (pm20) cc_final: 0.7638 (pm20) REVERT: H 104 GLN cc_start: 0.8354 (mp10) cc_final: 0.7865 (mp10) REVERT: H 157 ARG cc_start: 0.7504 (mtm-85) cc_final: 0.7185 (mtp85) REVERT: H 165 GLU cc_start: 0.6777 (pm20) cc_final: 0.6304 (pm20) REVERT: I 104 GLN cc_start: 0.8222 (mp10) cc_final: 0.7918 (mp10) REVERT: I 129 SER cc_start: 0.8878 (p) cc_final: 0.8455 (t) outliers start: 37 outliers final: 33 residues processed: 287 average time/residue: 0.2961 time to fit residues: 121.3966 Evaluate side-chains 293 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 259 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 179 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 208 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 71 ASN C 71 ASN D 71 ASN E 71 ASN F 71 ASN G 71 ASN H 71 ASN I 71 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15903 Z= 0.389 Angle : 0.635 9.416 21645 Z= 0.329 Chirality : 0.041 0.162 2565 Planarity : 0.006 0.070 2736 Dihedral : 4.354 14.817 2295 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.33 % Allowed : 19.92 % Favored : 75.75 % 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: 1.42 (0.18), residues: 2142 helix: 1.62 (0.12), residues: 1647 sheet: None (None), residues: 0 loop : -1.37 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 62 PHE 0.014 0.002 PHE C 64 TYR 0.021 0.003 TYR A 176 ARG 0.002 0.000 ARG D 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 251 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8259 (mmp) cc_final: 0.7904 (mmt) REVERT: B 38 GLU cc_start: 0.8132 (pm20) cc_final: 0.7883 (pm20) REVERT: B 133 ASP cc_start: 0.8473 (t0) cc_final: 0.7928 (t0) REVERT: C 104 GLN cc_start: 0.8244 (mp10) cc_final: 0.7548 (mp10) REVERT: C 161 LYS cc_start: 0.8739 (tptm) cc_final: 0.8397 (tptp) REVERT: D 44 MET cc_start: 0.8580 (mtm) cc_final: 0.8178 (mtm) REVERT: D 133 ASP cc_start: 0.8265 (t70) cc_final: 0.7981 (t0) REVERT: D 153 LYS cc_start: 0.8220 (mttt) cc_final: 0.7899 (mttp) REVERT: D 161 LYS cc_start: 0.8469 (mttm) cc_final: 0.8199 (tptp) REVERT: D 198 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7483 (tt) REVERT: E 33 MET cc_start: 0.8332 (ttm) cc_final: 0.7689 (ttm) REVERT: E 119 MET cc_start: 0.8754 (mmt) cc_final: 0.8506 (mmp) REVERT: E 161 LYS cc_start: 0.8551 (tptm) cc_final: 0.8326 (tptp) REVERT: F 104 GLN cc_start: 0.8408 (mp10) cc_final: 0.8115 (mp10) REVERT: F 133 ASP cc_start: 0.8020 (t70) cc_final: 0.7675 (t0) REVERT: F 157 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.7643 (mtp85) REVERT: F 191 MET cc_start: 0.6603 (mmp) cc_final: 0.6278 (mtm) REVERT: G 38 GLU cc_start: 0.8213 (pm20) cc_final: 0.7758 (pm20) REVERT: G 133 ASP cc_start: 0.8598 (t0) cc_final: 0.8173 (t0) REVERT: G 153 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8439 (mttp) REVERT: H 38 GLU cc_start: 0.7928 (pm20) cc_final: 0.7640 (pm20) REVERT: H 44 MET cc_start: 0.8479 (mtm) cc_final: 0.7918 (mtm) REVERT: H 104 GLN cc_start: 0.8233 (mp10) cc_final: 0.7534 (mp10) REVERT: H 157 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7432 (mtp85) REVERT: H 165 GLU cc_start: 0.6776 (pm20) cc_final: 0.6297 (pm20) outliers start: 62 outliers final: 50 residues processed: 289 average time/residue: 0.2898 time to fit residues: 120.1474 Evaluate side-chains 298 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 247 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 179 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 189 optimal weight: 50.0000 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN D 71 ASN G 71 ASN H 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15903 Z= 0.303 Angle : 0.594 8.609 21645 Z= 0.308 Chirality : 0.039 0.138 2565 Planarity : 0.006 0.068 2736 Dihedral : 4.307 14.911 2295 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.12 % Allowed : 19.78 % Favored : 76.10 % 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: 1.63 (0.18), residues: 2142 helix: 1.77 (0.12), residues: 1647 sheet: None (None), residues: 0 loop : -1.29 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 62 PHE 0.010 0.001 PHE D 64 TYR 0.018 0.002 TYR A 176 ARG 0.002 0.000 ARG F 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 244 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.8058 (mp10) cc_final: 0.7587 (mp10) REVERT: B 38 GLU cc_start: 0.8089 (pm20) cc_final: 0.7838 (pm20) REVERT: B 133 ASP cc_start: 0.8466 (t0) cc_final: 0.7935 (t0) REVERT: C 104 GLN cc_start: 0.8189 (mp10) cc_final: 0.7117 (mp10) REVERT: C 161 LYS cc_start: 0.8738 (tptm) cc_final: 0.8365 (tptp) REVERT: D 44 MET cc_start: 0.8530 (mtm) cc_final: 0.8126 (mtm) REVERT: D 133 ASP cc_start: 0.8259 (t70) cc_final: 0.7967 (t0) REVERT: D 153 LYS cc_start: 0.8231 (mttt) cc_final: 0.7910 (mttp) REVERT: D 161 LYS cc_start: 0.8484 (mttm) cc_final: 0.8147 (tptp) REVERT: D 198 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7434 (tt) REVERT: E 33 MET cc_start: 0.8300 (ttm) cc_final: 0.7627 (ttm) REVERT: E 104 GLN cc_start: 0.8016 (mp10) cc_final: 0.7451 (mp10) REVERT: E 161 LYS cc_start: 0.8711 (tptm) cc_final: 0.8458 (tptp) REVERT: F 104 GLN cc_start: 0.8276 (mp10) cc_final: 0.7977 (mp10) REVERT: F 157 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7687 (mtp85) REVERT: F 191 MET cc_start: 0.6686 (mmp) cc_final: 0.6395 (mtm) REVERT: G 38 GLU cc_start: 0.8254 (pm20) cc_final: 0.7830 (pm20) REVERT: G 133 ASP cc_start: 0.8599 (t0) cc_final: 0.8182 (t0) REVERT: G 152 LEU cc_start: 0.8465 (mt) cc_final: 0.8176 (mt) REVERT: G 153 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8432 (mttp) REVERT: H 38 GLU cc_start: 0.7902 (pm20) cc_final: 0.7620 (pm20) REVERT: H 104 GLN cc_start: 0.8363 (mp10) cc_final: 0.7625 (mp10) REVERT: H 157 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7379 (mtp85) REVERT: H 165 GLU cc_start: 0.6152 (pm20) cc_final: 0.5681 (pm20) outliers start: 59 outliers final: 47 residues processed: 280 average time/residue: 0.2918 time to fit residues: 117.4165 Evaluate side-chains 292 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 244 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 179 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 9.9990 chunk 181 optimal weight: 0.7980 chunk 194 optimal weight: 0.0570 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 193 optimal weight: 0.2980 chunk 127 optimal weight: 9.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 71 ASN E 71 ASN F 71 ASN I 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15903 Z= 0.163 Angle : 0.504 6.173 21645 Z= 0.264 Chirality : 0.037 0.126 2565 Planarity : 0.005 0.065 2736 Dihedral : 4.008 13.767 2295 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.80 % Allowed : 20.96 % Favored : 76.24 % 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: 2.12 (0.18), residues: 2142 helix: 2.12 (0.13), residues: 1665 sheet: None (None), residues: 0 loop : -1.21 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 62 PHE 0.008 0.001 PHE C 197 TYR 0.013 0.001 TYR E 34 ARG 0.001 0.000 ARG F 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 257 time to evaluate : 1.782 Fit side-chains revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7983 (mp10) cc_final: 0.7466 (mp10) REVERT: B 38 GLU cc_start: 0.8019 (pm20) cc_final: 0.7797 (pm20) REVERT: B 133 ASP cc_start: 0.8432 (t0) cc_final: 0.7906 (t0) REVERT: B 157 ARG cc_start: 0.7622 (mtt90) cc_final: 0.6995 (mtm-85) REVERT: B 192 MET cc_start: 0.5982 (ttp) cc_final: 0.5718 (ttp) REVERT: C 34 TYR cc_start: 0.9097 (t80) cc_final: 0.8462 (t80) REVERT: C 104 GLN cc_start: 0.8233 (mp10) cc_final: 0.7160 (mp10) REVERT: C 143 VAL cc_start: 0.8649 (m) cc_final: 0.8425 (t) REVERT: C 161 LYS cc_start: 0.8699 (tptm) cc_final: 0.8352 (tptp) REVERT: D 44 MET cc_start: 0.8397 (mtm) cc_final: 0.7916 (mtm) REVERT: D 104 GLN cc_start: 0.8021 (mp10) cc_final: 0.7704 (mp10) REVERT: D 133 ASP cc_start: 0.8146 (t70) cc_final: 0.7828 (t0) REVERT: D 153 LYS cc_start: 0.8189 (mttt) cc_final: 0.7879 (mttp) REVERT: D 161 LYS cc_start: 0.8410 (mttm) cc_final: 0.8137 (tptp) REVERT: D 198 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7304 (tt) REVERT: E 33 MET cc_start: 0.8342 (ttm) cc_final: 0.7618 (ttm) REVERT: E 104 GLN cc_start: 0.8039 (mp10) cc_final: 0.7475 (mp10) REVERT: E 153 LYS cc_start: 0.8609 (mtmm) cc_final: 0.8198 (mtpt) REVERT: E 161 LYS cc_start: 0.8691 (tptm) cc_final: 0.8448 (tptp) REVERT: F 104 GLN cc_start: 0.8253 (mp10) cc_final: 0.7984 (mp10) REVERT: F 157 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7490 (mtp85) REVERT: G 38 GLU cc_start: 0.8218 (pm20) cc_final: 0.7821 (pm20) REVERT: G 104 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7146 (mp10) REVERT: G 133 ASP cc_start: 0.8565 (t0) cc_final: 0.8151 (t0) REVERT: G 152 LEU cc_start: 0.8377 (mt) cc_final: 0.8144 (mt) REVERT: G 153 LYS cc_start: 0.8272 (mtmt) cc_final: 0.8068 (mttp) REVERT: H 38 GLU cc_start: 0.7873 (pm20) cc_final: 0.7546 (pm20) REVERT: H 104 GLN cc_start: 0.8332 (mp10) cc_final: 0.7584 (mp10) REVERT: H 157 ARG cc_start: 0.7540 (mtm-85) cc_final: 0.7189 (mtp85) REVERT: I 104 GLN cc_start: 0.8340 (mp10) cc_final: 0.7602 (mp10) REVERT: I 129 SER cc_start: 0.8902 (p) cc_final: 0.8446 (t) outliers start: 40 outliers final: 35 residues processed: 279 average time/residue: 0.2961 time to fit residues: 118.4636 Evaluate side-chains 289 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 252 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 97 optimal weight: 0.2980 chunk 142 optimal weight: 8.9990 chunk 215 optimal weight: 50.0000 chunk 198 optimal weight: 6.9990 chunk 171 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7150 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15903 Z= 0.166 Angle : 0.516 8.997 21645 Z= 0.266 Chirality : 0.036 0.131 2565 Planarity : 0.005 0.065 2736 Dihedral : 3.921 13.715 2295 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.94 % Allowed : 21.17 % 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: 2.35 (0.19), residues: 2142 helix: 2.26 (0.13), residues: 1665 sheet: None (None), residues: 0 loop : -1.06 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 62 PHE 0.008 0.001 PHE C 197 TYR 0.013 0.001 TYR E 34 ARG 0.001 0.000 ARG I 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 267 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.8020 (mp10) cc_final: 0.7477 (mp10) REVERT: A 119 MET cc_start: 0.8498 (mmt) cc_final: 0.8239 (mmp) REVERT: B 38 GLU cc_start: 0.8057 (pm20) cc_final: 0.7767 (pm20) REVERT: B 104 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7064 (mp10) REVERT: B 133 ASP cc_start: 0.8428 (t0) cc_final: 0.7875 (t0) REVERT: B 157 ARG cc_start: 0.7660 (mtt90) cc_final: 0.6966 (mtm-85) REVERT: C 34 TYR cc_start: 0.9072 (t80) cc_final: 0.8482 (t80) REVERT: C 44 MET cc_start: 0.8374 (mtm) cc_final: 0.7987 (mtm) REVERT: C 104 GLN cc_start: 0.8294 (mp10) cc_final: 0.7187 (mp10) REVERT: C 151 LYS cc_start: 0.7296 (tptt) cc_final: 0.7004 (tptt) REVERT: C 161 LYS cc_start: 0.8704 (tptm) cc_final: 0.8320 (tptp) REVERT: D 44 MET cc_start: 0.8407 (mtm) cc_final: 0.7853 (mtm) REVERT: D 104 GLN cc_start: 0.8157 (mp10) cc_final: 0.7591 (mp10) REVERT: D 153 LYS cc_start: 0.8160 (mttt) cc_final: 0.7886 (mttp) REVERT: D 161 LYS cc_start: 0.8405 (mttm) cc_final: 0.8118 (tptp) REVERT: D 198 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7420 (tt) REVERT: E 104 GLN cc_start: 0.8090 (mp10) cc_final: 0.7541 (mp10) REVERT: E 153 LYS cc_start: 0.8616 (mtmm) cc_final: 0.8169 (mtpt) REVERT: E 161 LYS cc_start: 0.8677 (tptm) cc_final: 0.8397 (tptp) REVERT: F 104 GLN cc_start: 0.8217 (mp10) cc_final: 0.7404 (mp10) REVERT: F 157 ARG cc_start: 0.7615 (mtm-85) cc_final: 0.7413 (mtp85) REVERT: G 38 GLU cc_start: 0.8219 (pm20) cc_final: 0.7802 (pm20) REVERT: G 104 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: G 133 ASP cc_start: 0.8576 (t0) cc_final: 0.8152 (t0) REVERT: G 153 LYS cc_start: 0.8233 (mtmt) cc_final: 0.8020 (mttp) REVERT: H 38 GLU cc_start: 0.7877 (pm20) cc_final: 0.7544 (pm20) REVERT: H 104 GLN cc_start: 0.8360 (mp10) cc_final: 0.7651 (mp10) REVERT: H 157 ARG cc_start: 0.7580 (mtm-85) cc_final: 0.7189 (mtp85) REVERT: I 104 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7463 (mp10) REVERT: I 129 SER cc_start: 0.8868 (p) cc_final: 0.8476 (t) outliers start: 42 outliers final: 37 residues processed: 289 average time/residue: 0.2901 time to fit residues: 120.6884 Evaluate side-chains 303 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 262 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 104 GLN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 0.8980 chunk 71 optimal weight: 40.0000 chunk 176 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.223344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.169753 restraints weight = 16145.973| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.69 r_work: 0.3234 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15903 Z= 0.184 Angle : 0.525 8.477 21645 Z= 0.272 Chirality : 0.037 0.128 2565 Planarity : 0.005 0.065 2736 Dihedral : 3.933 13.521 2295 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.21 % Allowed : 20.96 % Favored : 75.82 % 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: 2.39 (0.18), residues: 2142 helix: 2.26 (0.13), residues: 1665 sheet: None (None), residues: 0 loop : -0.91 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 62 PHE 0.008 0.001 PHE C 197 TYR 0.014 0.001 TYR D 49 ARG 0.001 0.000 ARG F 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3273.74 seconds wall clock time: 59 minutes 32.94 seconds (3572.94 seconds total)