Starting phenix.real_space_refine (version: dev) on Tue Feb 21 19:53:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmx_0923/02_2023/6lmx_0923.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmx_0923/02_2023/6lmx_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_0923/02_2023/6lmx_0923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmx_0923/02_2023/6lmx_0923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmx_0923/02_2023/6lmx_0923.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmx_0923/02_2023/6lmx_0923.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 9.03, per 1000 atoms: 0.58 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: 6.23 Conformation dependent library (CDL) restraints added in 2.6 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: 0.64 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: 4.50 Time building geometry restraints manager: 6.70 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 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. 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: 0.430 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: 3.040 Check model and map are aligned: 0.240 Process input model: 40.930 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 % 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 *********************** 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 : 1.753 Fit side-chains outliers start: 18 outliers final: 0 residues processed: 300 average time/residue: 0.3649 time to fit residues: 149.2079 Evaluate side-chains 266 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.915 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 196 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7576 moved from start: 0.2377 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= 0.194 Angle : 0.616 5.445 21645 Z= 0.341 Chirality : 0.037 0.124 2565 Planarity : 0.009 0.082 2736 Dihedral : 5.376 16.863 2295 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 3.98 % 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: -2.30 (0.14), residues: 2142 helix: -1.25 (0.10), residues: 1647 sheet: None (None), residues: 0 loop : -1.83 (0.22), residues: 495 *********************** 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 309 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 252 time to evaluate : 1.735 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 29 residues processed: 285 average time/residue: 0.3025 time to fit residues: 123.6793 Evaluate side-chains 274 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 245 time to evaluate : 1.748 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1706 time to fit residues: 10.9465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 163 optimal weight: 30.0000 chunk 133 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 196 optimal weight: 0.4980 chunk 212 optimal weight: 30.0000 chunk 175 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 15903 Z= 0.344 Angle : 0.646 8.398 21645 Z= 0.344 Chirality : 0.041 0.141 2565 Planarity : 0.007 0.077 2736 Dihedral : 4.978 13.805 2295 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.17), residues: 2142 helix: 0.32 (0.12), residues: 1647 sheet: None (None), residues: 0 loop : -1.73 (0.23), residues: 495 *********************** 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 283 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 256 time to evaluate : 1.685 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 269 average time/residue: 0.3058 time to fit residues: 117.4714 Evaluate side-chains 267 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 255 time to evaluate : 1.677 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1475 time to fit residues: 5.5860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.9980 chunk 147 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 93 optimal weight: 50.0000 chunk 131 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 186 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7533 moved from start: 0.3174 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= 0.175 Angle : 0.524 5.560 21645 Z= 0.279 Chirality : 0.037 0.111 2565 Planarity : 0.006 0.067 2736 Dihedral : 4.466 13.586 2295 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.18), residues: 2142 helix: 1.33 (0.13), residues: 1647 sheet: None (None), residues: 0 loop : -1.57 (0.26), residues: 495 *********************** 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 290 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 264 time to evaluate : 1.821 Fit side-chains outliers start: 26 outliers final: 16 residues processed: 270 average time/residue: 0.3131 time to fit residues: 120.4818 Evaluate side-chains 268 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 252 time to evaluate : 1.897 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1930 time to fit residues: 7.8280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 3 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 15903 Z= 0.370 Angle : 0.645 9.518 21645 Z= 0.335 Chirality : 0.041 0.132 2565 Planarity : 0.006 0.071 2736 Dihedral : 4.590 14.443 2295 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.18), residues: 2142 helix: 1.27 (0.12), residues: 1647 sheet: None (None), residues: 0 loop : -1.50 (0.26), residues: 495 *********************** 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 287 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 249 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 24 residues processed: 275 average time/residue: 0.2995 time to fit residues: 117.9681 Evaluate side-chains 272 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 248 time to evaluate : 1.835 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1409 time to fit residues: 8.8838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 122 optimal weight: 0.0040 chunk 51 optimal weight: 0.7980 chunk 208 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 109 optimal weight: 0.0060 overall best weight: 0.5408 ------------------------------------------------------------------------------- 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 E 71 ASN G 71 ASN H 71 ASN I 71 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 15903 Z= 0.159 Angle : 0.514 6.092 21645 Z= 0.272 Chirality : 0.037 0.131 2565 Planarity : 0.006 0.064 2736 Dihedral : 4.203 13.602 2295 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.18), residues: 2142 helix: 1.83 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -1.40 (0.28), residues: 504 *********************** 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 280 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 262 time to evaluate : 1.956 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 268 average time/residue: 0.3022 time to fit residues: 116.3118 Evaluate side-chains 261 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 251 time to evaluate : 1.811 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1428 time to fit residues: 5.1831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 119 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 208 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 ASN E 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: 0.7587 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 15903 Z= 0.330 Angle : 0.614 8.732 21645 Z= 0.318 Chirality : 0.040 0.128 2565 Planarity : 0.006 0.068 2736 Dihedral : 4.340 14.651 2295 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 1.54 % 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: 1.51 (0.18), residues: 2142 helix: 1.68 (0.12), residues: 1647 sheet: None (None), residues: 0 loop : -1.31 (0.28), residues: 495 *********************** 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 264 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 242 time to evaluate : 1.907 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 17 residues processed: 253 average time/residue: 0.3199 time to fit residues: 114.7894 Evaluate side-chains 257 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 240 time to evaluate : 1.823 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1649 time to fit residues: 7.4881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 189 optimal weight: 30.0000 overall best weight: 2.6984 ------------------------------------------------------------------------------- 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 H 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 15903 Z= 0.392 Angle : 0.658 9.808 21645 Z= 0.341 Chirality : 0.041 0.134 2565 Planarity : 0.006 0.070 2736 Dihedral : 4.547 16.418 2295 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.18), residues: 2142 helix: 1.57 (0.12), residues: 1620 sheet: None (None), residues: 0 loop : -1.43 (0.26), residues: 522 *********************** 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 260 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 243 time to evaluate : 1.659 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 251 average time/residue: 0.3116 time to fit residues: 111.3401 Evaluate side-chains 252 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 243 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1401 time to fit residues: 4.9173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.2980 chunk 181 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.7547 moved from start: 0.3606 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= 0.204 Angle : 0.555 7.526 21645 Z= 0.290 Chirality : 0.037 0.124 2565 Planarity : 0.006 0.066 2736 Dihedral : 4.252 18.449 2295 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.49 % 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: 1.89 (0.18), residues: 2142 helix: 1.91 (0.13), residues: 1674 sheet: None (None), residues: 0 loop : -1.19 (0.29), residues: 468 *********************** 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 252 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 245 time to evaluate : 1.838 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 249 average time/residue: 0.2973 time to fit residues: 106.8478 Evaluate side-chains 242 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 1.761 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1293 time to fit residues: 2.8612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 0.7548 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 15903 Z= 0.219 Angle : 0.563 8.630 21645 Z= 0.292 Chirality : 0.038 0.124 2565 Planarity : 0.006 0.066 2736 Dihedral : 4.195 16.725 2295 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.14 % 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: 2.02 (0.18), residues: 2142 helix: 2.00 (0.13), residues: 1674 sheet: None (None), residues: 0 loop : -1.13 (0.29), residues: 468 ********************** 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 250 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 248 time to evaluate : 1.697 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 248 average time/residue: 0.3053 time to fit residues: 108.9425 Evaluate side-chains 247 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 245 time to evaluate : 1.868 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1420 time to fit residues: 2.9892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 71 optimal weight: 0.0020 chunk 176 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN D 71 ASN E 71 ASN F 71 ASN G 71 ASN I 71 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.222787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.172132 restraints weight = 16102.475| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.66 r_work: 0.3254 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 15903 Z= 0.200 Angle : 0.556 8.300 21645 Z= 0.288 Chirality : 0.037 0.136 2565 Planarity : 0.005 0.066 2736 Dihedral : 4.135 19.662 2295 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.42 % 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: 2.19 (0.19), residues: 2142 helix: 2.15 (0.13), residues: 1665 sheet: None (None), residues: 0 loop : -1.13 (0.29), residues: 477 =============================================================================== Job complete usr+sys time: 3155.29 seconds wall clock time: 57 minutes 34.66 seconds (3454.66 seconds total)