Starting phenix.real_space_refine on Fri Mar 15 19:19:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxb_16314/03_2024/8bxb_16314.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxb_16314/03_2024/8bxb_16314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxb_16314/03_2024/8bxb_16314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxb_16314/03_2024/8bxb_16314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxb_16314/03_2024/8bxb_16314.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxb_16314/03_2024/8bxb_16314.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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 76 5.16 5 C 8320 2.51 5 N 2032 2.21 5 O 2119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 13": "OD1" <-> "OD2" Residue "A ASP 148": "OD1" <-> "OD2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 13": "OD1" <-> "OD2" Residue "B ASP 148": "OD1" <-> "OD2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 13": "OD1" <-> "OD2" Residue "C ASP 148": "OD1" <-> "OD2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 13": "OD1" <-> "OD2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 13": "OD1" <-> "OD2" Residue "E ASP 148": "OD1" <-> "OD2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 12547 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2496 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "B" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2499 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2493 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "D" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2492 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "E" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2493 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.92, per 1000 atoms: 0.55 Number of scatterers: 12547 At special positions: 0 Unit cell: (91.152, 91.152, 121.536, 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 76 16.00 O 2119 8.00 N 2032 7.00 C 8320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.49 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.49 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.49 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 152 " distance=2.49 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 167 " " NAG B 501 " - " ASN B 167 " " NAG C 501 " - " ASN C 167 " " NAG D 501 " - " ASN D 167 " " NAG E 501 " - " ASN E 167 " Time building additional restraints: 4.71 Conformation dependent library (CDL) restraints added in 2.3 seconds 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3130 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 39.6% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.910A pdb=" N SER A 83 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 95 removed outlier: 3.546A pdb=" N ILE A 95 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 removed outlier: 3.764A pdb=" N ARG A 144 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 225 through 239 Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.640A pdb=" N LYS A 247 " --> pdb=" O PRO A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 279 through 307 removed outlier: 3.600A pdb=" N MET A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 440 Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.911A pdb=" N SER B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 95 removed outlier: 3.545A pdb=" N ILE B 95 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.765A pdb=" N ARG B 144 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 239 Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.640A pdb=" N LYS B 247 " --> pdb=" O PRO B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 279 through 307 removed outlier: 3.601A pdb=" N MET B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 440 Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.911A pdb=" N SER C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.545A pdb=" N ILE C 95 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 145 removed outlier: 3.764A pdb=" N ARG C 144 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 239 Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.641A pdb=" N LYS C 247 " --> pdb=" O PRO C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 279 through 307 removed outlier: 3.601A pdb=" N MET C 307 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 440 Processing helix chain 'D' and resid 13 through 19 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.910A pdb=" N SER D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 removed outlier: 3.546A pdb=" N ILE D 95 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 removed outlier: 3.765A pdb=" N ARG D 144 " --> pdb=" O ASP D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 239 Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.640A pdb=" N LYS D 247 " --> pdb=" O PRO D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 271 Processing helix chain 'D' and resid 279 through 307 removed outlier: 3.600A pdb=" N MET D 307 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 440 Processing helix chain 'E' and resid 13 through 19 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.911A pdb=" N SER E 83 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.545A pdb=" N ILE E 95 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 145 removed outlier: 3.764A pdb=" N ARG E 144 " --> pdb=" O ASP E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 225 Processing helix chain 'E' and resid 225 through 239 Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 243 through 247 removed outlier: 3.639A pdb=" N LYS E 247 " --> pdb=" O PRO E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 279 through 307 removed outlier: 3.600A pdb=" N MET E 307 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 440 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL A 126 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 70 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL A 126 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 70 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL A 59 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP A 52 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N THR A 61 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN A 63 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.780A pdb=" N GLY A 207 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG A 194 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 209 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY A 211 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL B 126 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP B 70 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL B 126 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP B 70 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL B 59 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP B 52 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR B 61 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN B 63 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.780A pdb=" N GLY B 207 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG B 194 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B 209 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 211 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL C 126 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP C 70 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL C 126 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP C 70 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL C 59 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP C 52 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR C 61 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL C 50 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN C 63 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.781A pdb=" N GLY C 207 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG C 194 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE C 209 " --> pdb=" O PRO C 192 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY C 211 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL D 126 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 70 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL D 126 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 70 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL D 59 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP D 52 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR D 61 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN D 63 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 87 through 90 Processing sheet with id=AB7, first strand: chain 'D' and resid 100 through 102 removed outlier: 6.780A pdb=" N GLY D 207 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG D 194 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE D 209 " --> pdb=" O PRO D 192 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY D 211 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 125 through 126 removed outlier: 3.659A pdb=" N VAL E 126 " --> pdb=" O TRP E 70 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 70 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 125 through 126 removed outlier: 3.659A pdb=" N VAL E 126 " --> pdb=" O TRP E 70 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 70 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL E 59 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP E 52 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR E 61 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL E 50 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN E 63 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 87 through 90 Processing sheet with id=AC2, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.781A pdb=" N GLY E 207 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG E 194 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE E 209 " --> pdb=" O PRO E 192 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY E 211 " --> pdb=" O VAL E 190 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1650 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 5.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2498 1.33 - 1.45: 3056 1.45 - 1.57: 7181 1.57 - 1.69: 0 1.69 - 1.81: 133 Bond restraints: 12868 Sorted by residual: bond pdb=" N VAL A 113 " pdb=" CA VAL A 113 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.19e-02 7.06e+03 9.95e+00 bond pdb=" N VAL C 114 " pdb=" CA VAL C 114 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.95e+00 bond pdb=" N SER A 109 " pdb=" CA SER A 109 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.27e-02 6.20e+03 7.36e+00 bond pdb=" N ARG A 171 " pdb=" CA ARG A 171 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 6.90e+00 bond pdb=" N VAL C 113 " pdb=" CA VAL C 113 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.64e+00 ... (remaining 12863 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.16: 342 106.16 - 113.12: 7222 113.12 - 120.07: 4387 120.07 - 127.03: 5523 127.03 - 133.99: 185 Bond angle restraints: 17659 Sorted by residual: angle pdb=" N LEU C 285 " pdb=" CA LEU C 285 " pdb=" C LEU C 285 " ideal model delta sigma weight residual 111.82 100.60 11.22 1.16e+00 7.43e-01 9.36e+01 angle pdb=" CA LEU B 285 " pdb=" C LEU B 285 " pdb=" N ALA B 286 " ideal model delta sigma weight residual 118.14 110.15 7.99 1.31e+00 5.83e-01 3.72e+01 angle pdb=" CA LEU E 285 " pdb=" C LEU E 285 " pdb=" N ALA E 286 " ideal model delta sigma weight residual 118.14 110.40 7.74 1.31e+00 5.83e-01 3.49e+01 angle pdb=" N ALA A 286 " pdb=" CA ALA A 286 " pdb=" C ALA A 286 " ideal model delta sigma weight residual 111.82 105.03 6.79 1.16e+00 7.43e-01 3.43e+01 angle pdb=" N ALA E 286 " pdb=" CA ALA E 286 " pdb=" C ALA E 286 " ideal model delta sigma weight residual 112.23 105.08 7.15 1.26e+00 6.30e-01 3.22e+01 ... (remaining 17654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.98: 6503 11.98 - 23.95: 643 23.95 - 35.93: 219 35.93 - 47.90: 112 47.90 - 59.88: 47 Dihedral angle restraints: 7524 sinusoidal: 2679 harmonic: 4845 Sorted by residual: dihedral pdb=" CB CYS C 138 " pdb=" SG CYS C 138 " pdb=" SG CYS C 152 " pdb=" CB CYS C 152 " ideal model delta sinusoidal sigma weight residual 93.00 147.07 -54.07 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 152 " pdb=" CB CYS D 152 " ideal model delta sinusoidal sigma weight residual 93.00 147.05 -54.05 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 147.03 -54.03 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 7521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1651 0.054 - 0.109: 373 0.109 - 0.163: 133 0.163 - 0.217: 12 0.217 - 0.272: 6 Chirality restraints: 2175 Sorted by residual: chirality pdb=" CA VAL E 114 " pdb=" N VAL E 114 " pdb=" C VAL E 114 " pdb=" CB VAL E 114 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL E 288 " pdb=" CA VAL E 288 " pdb=" CG1 VAL E 288 " pdb=" CG2 VAL E 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB VAL A 288 " pdb=" CA VAL A 288 " pdb=" CG1 VAL A 288 " pdb=" CG2 VAL A 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2172 not shown) Planarity restraints: 2126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 285 " 0.027 2.00e-02 2.50e+03 5.83e-02 3.40e+01 pdb=" C LEU B 285 " -0.101 2.00e-02 2.50e+03 pdb=" O LEU B 285 " 0.040 2.00e-02 2.50e+03 pdb=" N ALA B 286 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 286 " 0.028 2.00e-02 2.50e+03 5.74e-02 3.30e+01 pdb=" C ALA D 286 " -0.099 2.00e-02 2.50e+03 pdb=" O ALA D 286 " 0.038 2.00e-02 2.50e+03 pdb=" N TYR D 287 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 285 " -0.026 2.00e-02 2.50e+03 5.58e-02 3.11e+01 pdb=" C LEU E 285 " 0.096 2.00e-02 2.50e+03 pdb=" O LEU E 285 " -0.038 2.00e-02 2.50e+03 pdb=" N ALA E 286 " -0.033 2.00e-02 2.50e+03 ... (remaining 2123 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2836 2.78 - 3.31: 10902 3.31 - 3.84: 20960 3.84 - 4.37: 22511 4.37 - 4.90: 39189 Nonbonded interactions: 96398 Sorted by model distance: nonbonded pdb=" CD1 LEU D 170 " pdb=" O ARG D 171 " model vdw 2.256 3.460 nonbonded pdb=" CD1 LEU C 170 " pdb=" O ARG C 171 " model vdw 2.259 3.460 nonbonded pdb=" OD1 ASN A 78 " pdb=" OG SER A 80 " model vdw 2.318 2.440 nonbonded pdb=" OD1 ASN D 78 " pdb=" OG SER D 80 " model vdw 2.319 2.440 nonbonded pdb=" OD1 ASN B 78 " pdb=" OG SER B 80 " model vdw 2.319 2.440 ... (remaining 96393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 304 or (resid 305 and (name N or n \ ame CA or name C or name O or name CB )) or resid 306 through 443 or resid 501)) \ selection = (chain 'B' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 269 or (resid 270 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name NE )) or res \ id 271 through 306 or (resid 307 and (name N or name CA or name C or name O or n \ ame CB )) or resid 414 through 443 or resid 501)) selection = (chain 'C' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 443 or resid 501)) selection = chain 'D' selection = (chain 'E' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 443 or resid 501)) } 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 group one per residue 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: 12.800 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: 0.000 Extract box with map and model: 18.710 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 34.450 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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 : 0.004 0.045 12868 Z= 0.267 Angle : 0.779 11.225 17659 Z= 0.477 Chirality : 0.055 0.272 2175 Planarity : 0.006 0.098 2121 Dihedral : 13.499 59.880 4382 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.85 % Favored : 96.09 % Rotamer: Outliers : 5.55 % Allowed : 14.10 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.59 (0.19), residues: 1610 helix: -1.63 (0.18), residues: 535 sheet: -1.19 (0.28), residues: 410 loop : -1.98 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 159 HIS 0.005 0.001 HIS C 131 PHE 0.012 0.001 PHE B 289 TYR 0.014 0.002 TYR A 287 ARG 0.006 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 294 time to evaluate : 1.410 Fit side-chains REVERT: A 104 ASN cc_start: 0.7295 (OUTLIER) cc_final: 0.6791 (p0) REVERT: A 264 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8195 (tt) REVERT: A 265 MET cc_start: 0.8529 (ttp) cc_final: 0.8269 (ttt) REVERT: A 271 MET cc_start: 0.7761 (tmm) cc_final: 0.7490 (tmm) REVERT: B 17 LEU cc_start: 0.8255 (tp) cc_final: 0.7926 (tp) REVERT: B 264 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8260 (mt) REVERT: B 265 MET cc_start: 0.8577 (ttp) cc_final: 0.8194 (ttp) REVERT: B 271 MET cc_start: 0.7555 (tmm) cc_final: 0.7317 (tmm) REVERT: C 21 ILE cc_start: 0.9029 (tp) cc_final: 0.8672 (tt) REVERT: C 87 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8433 (mtpt) REVERT: C 271 MET cc_start: 0.7734 (tmm) cc_final: 0.7467 (tmm) REVERT: D 21 ILE cc_start: 0.9018 (tp) cc_final: 0.8720 (tt) REVERT: D 104 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.6775 (p0) REVERT: D 264 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8191 (mt) REVERT: D 265 MET cc_start: 0.8430 (ttp) cc_final: 0.8105 (ttm) REVERT: D 271 MET cc_start: 0.7810 (tmm) cc_final: 0.7499 (tmm) REVERT: E 21 ILE cc_start: 0.9084 (tp) cc_final: 0.8711 (tt) REVERT: E 239 MET cc_start: 0.7409 (ttp) cc_final: 0.7156 (ttt) REVERT: E 264 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8254 (mt) REVERT: E 265 MET cc_start: 0.8441 (ttp) cc_final: 0.8111 (ttp) REVERT: E 271 MET cc_start: 0.7560 (tmm) cc_final: 0.7199 (tmm) outliers start: 70 outliers final: 8 residues processed: 354 average time/residue: 0.1787 time to fit residues: 99.5134 Evaluate side-chains 237 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 223 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 264 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 0.0770 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 93 optimal weight: 0.2980 chunk 145 optimal weight: 4.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 HIS C 58 HIS D 58 HIS D 74 GLN E 58 HIS E 74 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12868 Z= 0.169 Angle : 0.523 5.684 17659 Z= 0.267 Chirality : 0.043 0.144 2175 Planarity : 0.003 0.027 2121 Dihedral : 5.203 56.600 1900 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.23 % Allowed : 19.10 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.47 (0.21), residues: 1610 helix: 0.10 (0.21), residues: 540 sheet: -0.71 (0.28), residues: 400 loop : -1.99 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 70 HIS 0.004 0.001 HIS D 58 PHE 0.016 0.001 PHE D 298 TYR 0.015 0.001 TYR B 287 ARG 0.001 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 245 time to evaluate : 1.472 Fit side-chains REVERT: A 265 MET cc_start: 0.8673 (ttp) cc_final: 0.8365 (ttt) REVERT: A 271 MET cc_start: 0.7741 (tmm) cc_final: 0.7482 (tmm) REVERT: A 275 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7726 (mt) REVERT: B 17 LEU cc_start: 0.8314 (tp) cc_final: 0.8092 (tp) REVERT: B 265 MET cc_start: 0.8655 (ttp) cc_final: 0.8334 (ttp) REVERT: C 21 ILE cc_start: 0.9129 (tp) cc_final: 0.8722 (tt) REVERT: C 127 MET cc_start: 0.8514 (mtp) cc_final: 0.8200 (mtp) REVERT: C 275 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7724 (mt) REVERT: D 21 ILE cc_start: 0.9104 (tp) cc_final: 0.8764 (tt) REVERT: D 127 MET cc_start: 0.8442 (mtp) cc_final: 0.8156 (mtp) REVERT: D 275 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7750 (mt) REVERT: E 17 LEU cc_start: 0.8310 (tp) cc_final: 0.8059 (tp) REVERT: E 21 ILE cc_start: 0.9156 (tp) cc_final: 0.8799 (tt) REVERT: E 239 MET cc_start: 0.7645 (ttp) cc_final: 0.7321 (ttt) REVERT: E 265 MET cc_start: 0.8563 (ttp) cc_final: 0.8244 (ttp) REVERT: E 287 TYR cc_start: 0.7686 (t80) cc_final: 0.7254 (t80) outliers start: 66 outliers final: 38 residues processed: 279 average time/residue: 0.1863 time to fit residues: 81.9088 Evaluate side-chains 267 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 226 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 74 GLN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 436 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7889 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12868 Z= 0.280 Angle : 0.572 8.475 17659 Z= 0.288 Chirality : 0.044 0.147 2175 Planarity : 0.003 0.022 2121 Dihedral : 4.343 21.688 1876 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.23 % Allowed : 20.76 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.02 (0.21), residues: 1610 helix: 0.79 (0.21), residues: 545 sheet: -0.34 (0.29), residues: 375 loop : -2.11 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 185 HIS 0.005 0.001 HIS B 68 PHE 0.015 0.002 PHE D 298 TYR 0.021 0.001 TYR C 287 ARG 0.001 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 233 time to evaluate : 1.425 Fit side-chains REVERT: A 265 MET cc_start: 0.8729 (ttp) cc_final: 0.8363 (ttt) REVERT: A 271 MET cc_start: 0.7776 (tmm) cc_final: 0.7550 (tmm) REVERT: B 17 LEU cc_start: 0.8347 (tp) cc_final: 0.8031 (tp) REVERT: B 21 ILE cc_start: 0.9257 (tp) cc_final: 0.8844 (tt) REVERT: B 271 MET cc_start: 0.7686 (tmm) cc_final: 0.7452 (tmm) REVERT: C 21 ILE cc_start: 0.9236 (tp) cc_final: 0.8793 (tt) REVERT: D 21 ILE cc_start: 0.9236 (tp) cc_final: 0.8831 (tt) REVERT: E 17 LEU cc_start: 0.8443 (tp) cc_final: 0.8106 (tp) REVERT: E 21 ILE cc_start: 0.9227 (tp) cc_final: 0.8823 (tt) REVERT: E 264 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8258 (tt) REVERT: E 265 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8212 (ttp) outliers start: 66 outliers final: 42 residues processed: 278 average time/residue: 0.1851 time to fit residues: 83.2870 Evaluate side-chains 264 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 220 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.0270 chunk 109 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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: 0.7865 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12868 Z= 0.195 Angle : 0.539 8.340 17659 Z= 0.269 Chirality : 0.044 0.211 2175 Planarity : 0.002 0.024 2121 Dihedral : 4.132 18.965 1876 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.15 % Allowed : 20.92 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.87 (0.21), residues: 1610 helix: 1.14 (0.22), residues: 545 sheet: -0.49 (0.28), residues: 390 loop : -2.11 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 185 HIS 0.005 0.001 HIS C 131 PHE 0.013 0.001 PHE D 298 TYR 0.016 0.001 TYR C 287 ARG 0.001 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 232 time to evaluate : 1.464 Fit side-chains REVERT: A 21 ILE cc_start: 0.9198 (tp) cc_final: 0.8809 (tt) REVERT: A 265 MET cc_start: 0.8590 (ttp) cc_final: 0.8369 (ttp) REVERT: A 271 MET cc_start: 0.7829 (tmm) cc_final: 0.7605 (tmm) REVERT: B 17 LEU cc_start: 0.8386 (tp) cc_final: 0.8066 (tp) REVERT: B 21 ILE cc_start: 0.9242 (tp) cc_final: 0.8974 (tt) REVERT: C 21 ILE cc_start: 0.9200 (tp) cc_final: 0.8839 (tt) REVERT: C 227 MET cc_start: 0.7453 (tmm) cc_final: 0.6850 (tpp) REVERT: D 21 ILE cc_start: 0.9209 (tp) cc_final: 0.8856 (tt) REVERT: E 17 LEU cc_start: 0.8436 (tp) cc_final: 0.8092 (tp) REVERT: E 21 ILE cc_start: 0.9202 (tp) cc_final: 0.8798 (tt) REVERT: E 127 MET cc_start: 0.8250 (mtt) cc_final: 0.7899 (mtt) REVERT: E 264 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8305 (tt) REVERT: E 265 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8271 (ttt) REVERT: E 287 TYR cc_start: 0.7795 (t80) cc_final: 0.7441 (t80) outliers start: 65 outliers final: 35 residues processed: 277 average time/residue: 0.1769 time to fit residues: 77.8123 Evaluate side-chains 256 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 219 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 265 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 2 optimal weight: 0.0000 chunk 115 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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: 0.7868 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12868 Z= 0.186 Angle : 0.541 8.346 17659 Z= 0.268 Chirality : 0.044 0.166 2175 Planarity : 0.002 0.021 2121 Dihedral : 4.043 16.455 1876 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.55 % Allowed : 21.32 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.75 (0.21), residues: 1610 helix: 1.25 (0.22), residues: 545 sheet: -0.24 (0.29), residues: 375 loop : -2.14 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 77 HIS 0.003 0.001 HIS B 68 PHE 0.011 0.001 PHE D 298 TYR 0.013 0.001 TYR A 252 ARG 0.001 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 234 time to evaluate : 1.471 Fit side-chains REVERT: A 21 ILE cc_start: 0.9169 (tp) cc_final: 0.8791 (tt) REVERT: B 17 LEU cc_start: 0.8390 (tp) cc_final: 0.8081 (tp) REVERT: B 21 ILE cc_start: 0.9239 (tp) cc_final: 0.8983 (tt) REVERT: C 21 ILE cc_start: 0.9175 (tp) cc_final: 0.8835 (tt) REVERT: C 227 MET cc_start: 0.7391 (tmm) cc_final: 0.6902 (tpp) REVERT: D 21 ILE cc_start: 0.9205 (tp) cc_final: 0.8884 (tt) REVERT: D 264 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8405 (tt) REVERT: E 21 ILE cc_start: 0.9200 (tp) cc_final: 0.8811 (tt) REVERT: E 127 MET cc_start: 0.8150 (mtt) cc_final: 0.7896 (mtm) REVERT: E 227 MET cc_start: 0.7553 (tmm) cc_final: 0.7281 (tpt) REVERT: E 264 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8354 (tt) REVERT: E 265 MET cc_start: 0.8628 (ttp) cc_final: 0.8345 (ttt) REVERT: E 287 TYR cc_start: 0.7795 (t80) cc_final: 0.7462 (t80) outliers start: 70 outliers final: 47 residues processed: 282 average time/residue: 0.1802 time to fit residues: 80.4986 Evaluate side-chains 271 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 222 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 436 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 154 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7884 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12868 Z= 0.202 Angle : 0.550 8.165 17659 Z= 0.272 Chirality : 0.044 0.169 2175 Planarity : 0.002 0.021 2121 Dihedral : 4.035 15.061 1876 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.31 % Allowed : 22.11 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.77 (0.21), residues: 1610 helix: 1.24 (0.22), residues: 545 sheet: -0.28 (0.29), residues: 375 loop : -2.15 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 77 HIS 0.003 0.001 HIS D 68 PHE 0.011 0.001 PHE E 298 TYR 0.015 0.001 TYR A 252 ARG 0.002 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 230 time to evaluate : 1.578 Fit side-chains REVERT: A 21 ILE cc_start: 0.9172 (tp) cc_final: 0.8807 (tt) REVERT: A 291 MET cc_start: 0.8152 (tpp) cc_final: 0.7884 (tpp) REVERT: B 17 LEU cc_start: 0.8372 (tp) cc_final: 0.8078 (tp) REVERT: B 21 ILE cc_start: 0.9217 (tp) cc_final: 0.8961 (tt) REVERT: B 127 MET cc_start: 0.8544 (mtm) cc_final: 0.8280 (mtt) REVERT: B 291 MET cc_start: 0.8567 (tpp) cc_final: 0.8351 (tpp) REVERT: C 21 ILE cc_start: 0.9174 (tp) cc_final: 0.8834 (tt) REVERT: C 227 MET cc_start: 0.7389 (tmm) cc_final: 0.7000 (tpp) REVERT: D 21 ILE cc_start: 0.9215 (tp) cc_final: 0.8901 (tt) REVERT: E 21 ILE cc_start: 0.9202 (tp) cc_final: 0.8812 (tt) REVERT: E 127 MET cc_start: 0.8317 (mtt) cc_final: 0.7958 (mtt) REVERT: E 227 MET cc_start: 0.7558 (tmm) cc_final: 0.7335 (tpt) REVERT: E 264 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8366 (tt) REVERT: E 265 MET cc_start: 0.8607 (ttp) cc_final: 0.8394 (ttp) outliers start: 67 outliers final: 50 residues processed: 277 average time/residue: 0.1808 time to fit residues: 79.4000 Evaluate side-chains 269 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 218 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 436 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 0.0570 chunk 130 optimal weight: 0.3980 chunk 86 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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: 0.7856 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12868 Z= 0.164 Angle : 0.551 9.640 17659 Z= 0.269 Chirality : 0.043 0.161 2175 Planarity : 0.002 0.021 2121 Dihedral : 3.946 15.592 1876 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.07 % Allowed : 23.06 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.67 (0.21), residues: 1610 helix: 1.26 (0.22), residues: 545 sheet: -0.18 (0.29), residues: 365 loop : -2.03 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 77 HIS 0.002 0.001 HIS C 131 PHE 0.010 0.001 PHE E 298 TYR 0.016 0.001 TYR A 252 ARG 0.002 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 232 time to evaluate : 1.452 Fit side-chains REVERT: A 21 ILE cc_start: 0.9136 (tp) cc_final: 0.8798 (tt) REVERT: B 17 LEU cc_start: 0.8341 (tp) cc_final: 0.8069 (tp) REVERT: B 21 ILE cc_start: 0.9154 (tp) cc_final: 0.8889 (tt) REVERT: B 127 MET cc_start: 0.8508 (mtm) cc_final: 0.8251 (mtt) REVERT: B 138 CYS cc_start: 0.7344 (p) cc_final: 0.7011 (m) REVERT: C 21 ILE cc_start: 0.9153 (tp) cc_final: 0.8839 (tt) REVERT: C 227 MET cc_start: 0.7349 (tmm) cc_final: 0.6995 (tpp) REVERT: D 21 ILE cc_start: 0.9205 (tp) cc_final: 0.8906 (tt) REVERT: D 264 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8375 (tt) REVERT: E 21 ILE cc_start: 0.9188 (tp) cc_final: 0.8829 (tt) REVERT: E 127 MET cc_start: 0.8284 (mtt) cc_final: 0.7941 (mtt) REVERT: E 264 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8340 (tt) REVERT: E 265 MET cc_start: 0.8613 (ttp) cc_final: 0.8274 (ttp) outliers start: 64 outliers final: 47 residues processed: 278 average time/residue: 0.1970 time to fit residues: 87.0129 Evaluate side-chains 267 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 218 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 436 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.8054 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 12868 Z= 0.511 Angle : 0.767 11.556 17659 Z= 0.378 Chirality : 0.049 0.157 2175 Planarity : 0.004 0.028 2121 Dihedral : 4.922 21.491 1876 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 6.18 % Allowed : 21.63 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.20 (0.21), residues: 1610 helix: 0.85 (0.22), residues: 545 sheet: -0.66 (0.26), residues: 410 loop : -2.33 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 128 HIS 0.005 0.002 HIS C 68 PHE 0.022 0.002 PHE B 103 TYR 0.024 0.002 TYR C 287 ARG 0.003 0.001 ARG C 194 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 219 time to evaluate : 1.547 Fit side-chains REVERT: A 21 ILE cc_start: 0.9227 (tp) cc_final: 0.8852 (tt) REVERT: A 69 GLU cc_start: 0.7602 (tt0) cc_final: 0.7375 (tt0) REVERT: B 21 ILE cc_start: 0.9244 (tp) cc_final: 0.8942 (tt) REVERT: C 21 ILE cc_start: 0.9315 (tp) cc_final: 0.8952 (tt) REVERT: C 69 GLU cc_start: 0.7511 (tt0) cc_final: 0.7301 (tt0) REVERT: C 227 MET cc_start: 0.7455 (tmm) cc_final: 0.7250 (tpp) REVERT: D 21 ILE cc_start: 0.9263 (tp) cc_final: 0.8926 (tt) REVERT: E 21 ILE cc_start: 0.9230 (tp) cc_final: 0.8830 (tt) REVERT: E 69 GLU cc_start: 0.7599 (tt0) cc_final: 0.7349 (tt0) REVERT: E 127 MET cc_start: 0.8506 (mtt) cc_final: 0.8106 (mtt) REVERT: E 291 MET cc_start: 0.8665 (tpp) cc_final: 0.8434 (tpp) outliers start: 78 outliers final: 58 residues processed: 279 average time/residue: 0.1779 time to fit residues: 79.0002 Evaluate side-chains 261 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 203 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 417 THR Chi-restraints excluded: chain E residue 436 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 0.0980 chunk 134 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7927 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12868 Z= 0.214 Angle : 0.636 12.956 17659 Z= 0.308 Chirality : 0.046 0.266 2175 Planarity : 0.002 0.020 2121 Dihedral : 4.330 17.584 1876 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.36 % Allowed : 23.30 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.00 (0.21), residues: 1610 helix: 1.04 (0.21), residues: 545 sheet: -0.46 (0.29), residues: 330 loop : -2.15 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 77 HIS 0.003 0.001 HIS B 131 PHE 0.018 0.001 PHE B 137 TYR 0.022 0.001 TYR C 252 ARG 0.003 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 224 time to evaluate : 1.573 Fit side-chains REVERT: A 21 ILE cc_start: 0.9157 (tp) cc_final: 0.8835 (tt) REVERT: A 69 GLU cc_start: 0.7611 (tt0) cc_final: 0.7369 (tt0) REVERT: A 127 MET cc_start: 0.8732 (mtp) cc_final: 0.8506 (mtm) REVERT: B 21 ILE cc_start: 0.9151 (tp) cc_final: 0.8843 (tt) REVERT: B 127 MET cc_start: 0.8437 (mtp) cc_final: 0.8234 (mtt) REVERT: B 138 CYS cc_start: 0.7336 (p) cc_final: 0.6913 (m) REVERT: B 275 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7734 (mm) REVERT: C 21 ILE cc_start: 0.9228 (tp) cc_final: 0.8914 (tt) REVERT: C 275 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7684 (mm) REVERT: D 21 ILE cc_start: 0.9214 (tp) cc_final: 0.8925 (tt) REVERT: D 127 MET cc_start: 0.8414 (mtp) cc_final: 0.8052 (mtp) REVERT: D 416 LEU cc_start: 0.8206 (tp) cc_final: 0.7931 (tt) REVERT: E 21 ILE cc_start: 0.9197 (tp) cc_final: 0.8824 (tt) REVERT: E 127 MET cc_start: 0.8454 (mtt) cc_final: 0.8043 (mtt) outliers start: 55 outliers final: 44 residues processed: 263 average time/residue: 0.1783 time to fit residues: 74.3467 Evaluate side-chains 256 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 210 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.0570 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 146 optimal weight: 0.4980 chunk 126 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 0.3980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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: 0.7888 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12868 Z= 0.192 Angle : 0.648 13.170 17659 Z= 0.309 Chirality : 0.045 0.222 2175 Planarity : 0.003 0.023 2121 Dihedral : 4.100 14.680 1876 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.09 % Allowed : 24.80 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.04 (0.21), residues: 1610 helix: 1.16 (0.22), residues: 545 sheet: -1.02 (0.27), residues: 370 loop : -2.03 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 77 HIS 0.005 0.001 HIS A 131 PHE 0.017 0.001 PHE C 137 TYR 0.022 0.001 TYR A 110 ARG 0.002 0.000 ARG B 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 219 time to evaluate : 1.620 Fit side-chains REVERT: A 21 ILE cc_start: 0.9147 (tp) cc_final: 0.8838 (tt) REVERT: B 21 ILE cc_start: 0.9160 (tp) cc_final: 0.8859 (tt) REVERT: B 127 MET cc_start: 0.8396 (mtp) cc_final: 0.8149 (mtt) REVERT: B 138 CYS cc_start: 0.7371 (p) cc_final: 0.6868 (m) REVERT: C 21 ILE cc_start: 0.9200 (tp) cc_final: 0.8902 (tt) REVERT: C 127 MET cc_start: 0.8310 (mtm) cc_final: 0.8110 (mtm) REVERT: C 275 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7661 (mm) REVERT: D 21 ILE cc_start: 0.9238 (tp) cc_final: 0.8928 (tt) REVERT: D 127 MET cc_start: 0.8377 (mtp) cc_final: 0.8018 (mtp) REVERT: E 21 ILE cc_start: 0.9191 (tp) cc_final: 0.8830 (tt) REVERT: E 127 MET cc_start: 0.8437 (mtt) cc_final: 0.8164 (mtt) outliers start: 39 outliers final: 36 residues processed: 247 average time/residue: 0.1806 time to fit residues: 71.0482 Evaluate side-chains 242 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 205 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 4.9990 chunk 38 optimal weight: 0.0670 chunk 117 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.0270 chunk 111 optimal weight: 0.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.143049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.114163 restraints weight = 22306.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117407 restraints weight = 14962.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.119805 restraints weight = 11448.159| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12868 Z= 0.188 Angle : 0.660 12.388 17659 Z= 0.310 Chirality : 0.045 0.311 2175 Planarity : 0.003 0.018 2121 Dihedral : 4.026 14.567 1876 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.41 % Allowed : 25.44 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.98 (0.21), residues: 1610 helix: 1.22 (0.22), residues: 540 sheet: -1.15 (0.27), residues: 380 loop : -1.88 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 77 HIS 0.003 0.001 HIS A 131 PHE 0.020 0.002 PHE A 156 TYR 0.016 0.001 TYR A 112 ARG 0.003 0.000 ARG B 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2621.79 seconds wall clock time: 51 minutes 13.05 seconds (3073.05 seconds total)