Starting phenix.real_space_refine on Wed Jun 11 07:34:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bxb_16314/06_2025/8bxb_16314.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bxb_16314/06_2025/8bxb_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/cci-nas-00/data/ceres_data/8bxb_16314/06_2025/8bxb_16314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bxb_16314/06_2025/8bxb_16314.map" model { file = "/net/cci-nas-00/data/ceres_data/8bxb_16314/06_2025/8bxb_16314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bxb_16314/06_2025/8bxb_16314.cif" } 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. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.65, per 1000 atoms: 0.77 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 - 3.00 Amino acid : True - 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: 3.59 Conformation dependent library (CDL) restraints added in 1.7 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: 2.01 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: 6.76 Time building geometry restraints manager: 4.20 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: 0.00 - 2.24: 17225 2.24 - 4.49: 369 4.49 - 6.73: 41 6.73 - 8.98: 23 8.98 - 11.22: 1 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 3.040 nonbonded pdb=" OD1 ASN D 78 " pdb=" OG SER D 80 " model vdw 2.319 3.040 nonbonded pdb=" OD1 ASN B 78 " pdb=" OG SER B 80 " model vdw 2.319 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 7.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 37.670 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.580 ------------------------------------------------------------------------------- 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 : 0.009 0.463 12877 Z= 0.468 Angle : 0.963 33.763 17682 Z= 0.548 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 5) link_NAG-ASN : angle 0.28934 ( 15) hydrogen bonds : bond 0.15526 ( 580) hydrogen bonds : angle 6.18963 ( 1650) SS BOND : bond 0.46123 ( 4) SS BOND : angle 26.70697 ( 8) covalent geometry : bond 0.00407 (12868) covalent geometry : angle 0.77856 (17659) *********************** 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 to be fit. rotamer outliers: 70 poor density : 294 time to evaluate : 1.420 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: 0.1821 time to fit residues: 101.6171 Evaluate side-chains 237 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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: 0.7980 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 E 58 HIS E 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.141087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112026 restraints weight = 22514.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.115700 restraints weight = 14423.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118278 restraints weight = 10713.286| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12877 Z= 0.143 Angle : 0.560 5.853 17682 Z= 0.286 Chirality : 0.043 0.146 2175 Planarity : 0.004 0.029 2121 Dihedral : 5.237 56.881 1900 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.75 % Allowed : 18.54 % Favored : 76.70 % 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: -1.52 (0.21), residues: 1610 helix: 0.04 (0.21), residues: 540 sheet: -0.76 (0.28), residues: 400 loop : -2.00 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 70 HIS 0.004 0.001 HIS E 58 PHE 0.017 0.001 PHE D 298 TYR 0.016 0.001 TYR B 287 ARG 0.003 0.000 ARG A 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 5) link_NAG-ASN : angle 1.47730 ( 15) hydrogen bonds : bond 0.03937 ( 580) hydrogen bonds : angle 4.51576 ( 1650) SS BOND : bond 0.00253 ( 4) SS BOND : angle 1.90047 ( 8) covalent geometry : bond 0.00321 (12868) covalent geometry : angle 0.55707 (17659) *********************** 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 309 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 249 time to evaluate : 1.635 Fit side-chains REVERT: A 104 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.6858 (p0) REVERT: A 265 MET cc_start: 0.8576 (ttp) cc_final: 0.8305 (ttt) REVERT: A 271 MET cc_start: 0.7733 (tmm) cc_final: 0.7384 (tmm) REVERT: A 275 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8126 (mt) REVERT: B 100 ILE cc_start: 0.9001 (mt) cc_final: 0.8585 (tp) REVERT: B 265 MET cc_start: 0.8446 (ttp) cc_final: 0.8227 (ttp) REVERT: B 271 MET cc_start: 0.7478 (tmm) cc_final: 0.7090 (tmm) REVERT: B 275 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8117 (mt) REVERT: C 21 ILE cc_start: 0.9224 (tp) cc_final: 0.8806 (tt) REVERT: C 87 LYS cc_start: 0.8750 (mtpt) cc_final: 0.8542 (mtpt) REVERT: C 100 ILE cc_start: 0.8899 (mt) cc_final: 0.8511 (tp) REVERT: C 127 MET cc_start: 0.8385 (mtp) cc_final: 0.8089 (mtp) REVERT: C 196 GLN cc_start: 0.8025 (mp10) cc_final: 0.7775 (mp10) REVERT: C 271 MET cc_start: 0.7846 (tmm) cc_final: 0.7643 (tmm) REVERT: C 275 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8074 (mt) REVERT: D 21 ILE cc_start: 0.9293 (tp) cc_final: 0.8911 (tt) REVERT: D 23 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.7891 (t-170) REVERT: D 104 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7798 (p0) REVERT: D 196 GLN cc_start: 0.8045 (mp10) cc_final: 0.7801 (mp10) REVERT: D 275 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8168 (mt) REVERT: D 291 MET cc_start: 0.8732 (tpp) cc_final: 0.8457 (tpp) REVERT: E 17 LEU cc_start: 0.8759 (tp) cc_final: 0.8495 (tp) REVERT: E 21 ILE cc_start: 0.9265 (tp) cc_final: 0.8876 (tt) REVERT: E 23 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7866 (t-170) REVERT: E 239 MET cc_start: 0.8130 (ttp) cc_final: 0.7768 (ttt) REVERT: E 265 MET cc_start: 0.8347 (ttp) cc_final: 0.8048 (ttp) REVERT: E 271 MET cc_start: 0.7538 (tmm) cc_final: 0.7267 (tmm) REVERT: E 287 TYR cc_start: 0.8058 (t80) cc_final: 0.7589 (t80) outliers start: 60 outliers final: 33 residues processed: 281 average time/residue: 0.2587 time to fit residues: 115.7904 Evaluate side-chains 269 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 163 VAL 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 429 LEU 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 275 LEU 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 23 HIS Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ASN 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 E residue 23 HIS 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 275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 67 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.138476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108930 restraints weight = 23073.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112464 restraints weight = 14865.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115015 restraints weight = 11110.317| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12877 Z= 0.158 Angle : 0.566 8.151 17682 Z= 0.285 Chirality : 0.044 0.160 2175 Planarity : 0.003 0.026 2121 Dihedral : 4.250 18.159 1880 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.15 % Allowed : 20.36 % Favored : 74.48 % 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: 0.67 (0.21), residues: 545 sheet: -0.93 (0.25), residues: 475 loop : -1.99 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 185 HIS 0.004 0.001 HIS C 131 PHE 0.015 0.001 PHE D 298 TYR 0.019 0.001 TYR C 287 ARG 0.001 0.000 ARG D 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 5) link_NAG-ASN : angle 1.60308 ( 15) hydrogen bonds : bond 0.03716 ( 580) hydrogen bonds : angle 4.39645 ( 1650) SS BOND : bond 0.00450 ( 4) SS BOND : angle 1.23782 ( 8) covalent geometry : bond 0.00368 (12868) covalent geometry : angle 0.56431 (17659) *********************** 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 305 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 240 time to evaluate : 1.465 Fit side-chains REVERT: A 104 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7959 (p0) REVERT: A 264 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8111 (tt) REVERT: A 265 MET cc_start: 0.8534 (ttp) cc_final: 0.8210 (ttt) REVERT: B 21 ILE cc_start: 0.9298 (tp) cc_final: 0.8876 (tt) REVERT: B 100 ILE cc_start: 0.9090 (mt) cc_final: 0.8699 (tp) REVERT: B 138 CYS cc_start: 0.7848 (p) cc_final: 0.7542 (m) REVERT: B 271 MET cc_start: 0.7646 (tmm) cc_final: 0.7246 (tmm) REVERT: C 21 ILE cc_start: 0.9264 (tp) cc_final: 0.8854 (tt) REVERT: C 87 LYS cc_start: 0.8791 (mtpt) cc_final: 0.8586 (mtpt) REVERT: C 100 ILE cc_start: 0.8998 (mt) cc_final: 0.8625 (tp) REVERT: C 196 GLN cc_start: 0.8083 (mp10) cc_final: 0.7815 (mp10) REVERT: C 271 MET cc_start: 0.7762 (tmm) cc_final: 0.7403 (tmm) REVERT: D 21 ILE cc_start: 0.9343 (tp) cc_final: 0.8962 (tt) REVERT: D 23 HIS cc_start: 0.8214 (OUTLIER) cc_final: 0.7926 (t-170) REVERT: D 100 ILE cc_start: 0.9105 (mt) cc_final: 0.8737 (tp) REVERT: D 104 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7709 (p0) REVERT: D 196 GLN cc_start: 0.8106 (mp10) cc_final: 0.7826 (mp10) REVERT: D 291 MET cc_start: 0.8815 (tpp) cc_final: 0.8594 (tpp) REVERT: E 17 LEU cc_start: 0.8802 (tp) cc_final: 0.8513 (tp) REVERT: E 21 ILE cc_start: 0.9305 (tp) cc_final: 0.8899 (tt) REVERT: E 23 HIS cc_start: 0.8172 (OUTLIER) cc_final: 0.7954 (t-170) REVERT: E 127 MET cc_start: 0.8459 (mtm) cc_final: 0.8205 (mtt) REVERT: E 264 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7948 (tt) REVERT: E 265 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7966 (ttp) REVERT: E 271 MET cc_start: 0.7640 (tmm) cc_final: 0.7412 (tmm) outliers start: 65 outliers final: 40 residues processed: 282 average time/residue: 0.1913 time to fit residues: 87.3985 Evaluate side-chains 271 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 ASN 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 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 62 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 210 THR Chi-restraints excluded: chain B residue 289 PHE 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 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 23 HIS Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ASN 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 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 23 HIS 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 210 THR 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 59 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 0.0980 chunk 90 optimal weight: 0.4980 chunk 84 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.143054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114555 restraints weight = 21881.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118066 restraints weight = 14245.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.120539 restraints weight = 10680.230| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12877 Z= 0.118 Angle : 0.542 8.818 17682 Z= 0.273 Chirality : 0.044 0.172 2175 Planarity : 0.003 0.026 2121 Dihedral : 4.079 17.987 1880 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.91 % Allowed : 19.97 % Favored : 75.12 % 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: -0.93 (0.21), residues: 1610 helix: 1.00 (0.21), residues: 545 sheet: -0.63 (0.28), residues: 410 loop : -2.00 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 185 HIS 0.004 0.001 HIS C 131 PHE 0.012 0.001 PHE D 298 TYR 0.019 0.001 TYR C 287 ARG 0.001 0.000 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 5) link_NAG-ASN : angle 1.28284 ( 15) hydrogen bonds : bond 0.03521 ( 580) hydrogen bonds : angle 4.26462 ( 1650) SS BOND : bond 0.00354 ( 4) SS BOND : angle 0.79249 ( 8) covalent geometry : bond 0.00274 (12868) covalent geometry : angle 0.54040 (17659) *********************** 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 299 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 237 time to evaluate : 1.344 Fit side-chains REVERT: A 21 ILE cc_start: 0.9306 (tp) cc_final: 0.8907 (tt) REVERT: A 104 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7856 (p0) REVERT: A 271 MET cc_start: 0.7878 (tmm) cc_final: 0.7552 (tmm) REVERT: B 21 ILE cc_start: 0.9324 (tp) cc_final: 0.9024 (tt) REVERT: B 100 ILE cc_start: 0.9028 (mt) cc_final: 0.8720 (tp) REVERT: B 127 MET cc_start: 0.8652 (mtp) cc_final: 0.8289 (mtm) REVERT: B 271 MET cc_start: 0.7735 (tmm) cc_final: 0.7404 (tmm) REVERT: C 21 ILE cc_start: 0.9285 (tp) cc_final: 0.8917 (tt) REVERT: C 100 ILE cc_start: 0.8960 (mt) cc_final: 0.8670 (tp) REVERT: C 196 GLN cc_start: 0.8110 (mp10) cc_final: 0.7895 (mp10) REVERT: C 271 MET cc_start: 0.7864 (tmm) cc_final: 0.7594 (tmm) REVERT: D 21 ILE cc_start: 0.9322 (tp) cc_final: 0.8985 (tt) REVERT: D 23 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7743 (t-170) REVERT: D 104 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7515 (p0) REVERT: D 196 GLN cc_start: 0.8103 (mp10) cc_final: 0.7866 (mp10) REVERT: E 17 LEU cc_start: 0.8717 (tp) cc_final: 0.8415 (tp) REVERT: E 21 ILE cc_start: 0.9314 (tp) cc_final: 0.8917 (tt) REVERT: E 127 MET cc_start: 0.8505 (mtm) cc_final: 0.8285 (mtm) REVERT: E 264 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8079 (tt) REVERT: E 265 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8202 (ttt) REVERT: E 271 MET cc_start: 0.7699 (tmm) cc_final: 0.7388 (tmm) REVERT: E 291 MET cc_start: 0.8779 (tpp) cc_final: 0.8519 (tpp) outliers start: 62 outliers final: 33 residues processed: 278 average time/residue: 0.1703 time to fit residues: 75.8705 Evaluate side-chains 261 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 ASN 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 273 THR Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 429 LEU 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 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 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 23 HIS Chi-restraints excluded: chain D residue 104 ASN 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 256 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 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 256 LEU 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 5 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 1 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.142496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.114125 restraints weight = 22038.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.117591 restraints weight = 14260.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120109 restraints weight = 10658.122| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12877 Z= 0.121 Angle : 0.546 8.117 17682 Z= 0.276 Chirality : 0.044 0.170 2175 Planarity : 0.003 0.024 2121 Dihedral : 4.032 17.789 1880 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.91 % Allowed : 20.52 % Favored : 74.56 % 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: -0.84 (0.21), residues: 1610 helix: 1.10 (0.22), residues: 545 sheet: -0.56 (0.28), residues: 410 loop : -1.99 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 77 HIS 0.002 0.001 HIS D 68 PHE 0.011 0.001 PHE D 298 TYR 0.014 0.001 TYR A 252 ARG 0.001 0.000 ARG D 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 5) link_NAG-ASN : angle 1.27205 ( 15) hydrogen bonds : bond 0.03478 ( 580) hydrogen bonds : angle 4.29607 ( 1650) SS BOND : bond 0.00344 ( 4) SS BOND : angle 0.79148 ( 8) covalent geometry : bond 0.00281 (12868) covalent geometry : angle 0.54464 (17659) *********************** 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 297 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 235 time to evaluate : 1.441 Fit side-chains REVERT: A 21 ILE cc_start: 0.9276 (tp) cc_final: 0.8890 (tt) REVERT: A 271 MET cc_start: 0.7980 (tmm) cc_final: 0.7690 (tmm) REVERT: B 21 ILE cc_start: 0.9322 (tp) cc_final: 0.9028 (tt) REVERT: B 271 MET cc_start: 0.7744 (tmm) cc_final: 0.7425 (tmm) REVERT: C 21 ILE cc_start: 0.9243 (tp) cc_final: 0.8887 (tt) REVERT: C 100 ILE cc_start: 0.8954 (mt) cc_final: 0.8654 (tp) REVERT: C 196 GLN cc_start: 0.8136 (mp10) cc_final: 0.7925 (mp10) REVERT: C 227 MET cc_start: 0.7693 (tmm) cc_final: 0.6826 (tpp) REVERT: C 271 MET cc_start: 0.7918 (tmm) cc_final: 0.7628 (tmm) REVERT: D 21 ILE cc_start: 0.9313 (tp) cc_final: 0.8993 (tt) REVERT: D 104 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7542 (p0) REVERT: D 196 GLN cc_start: 0.8120 (mp10) cc_final: 0.7882 (mp10) REVERT: E 17 LEU cc_start: 0.8702 (tp) cc_final: 0.8371 (tp) REVERT: E 21 ILE cc_start: 0.9327 (tp) cc_final: 0.8917 (tt) REVERT: E 127 MET cc_start: 0.8528 (mtm) cc_final: 0.8310 (mtm) REVERT: E 264 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8069 (tt) REVERT: E 265 MET cc_start: 0.8452 (ttp) cc_final: 0.8196 (ttp) REVERT: E 271 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7439 (tmm) outliers start: 62 outliers final: 35 residues processed: 280 average time/residue: 0.1875 time to fit residues: 83.0834 Evaluate side-chains 259 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 429 LEU Chi-restraints excluded: chain B residue 62 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 210 THR 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 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 424 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ASN 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 256 LEU Chi-restraints excluded: chain D residue 268 SER 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 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 268 SER Chi-restraints excluded: chain E residue 271 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 136 optimal weight: 0.4980 chunk 29 optimal weight: 0.0670 chunk 98 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** 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 = 0.3763 r_free = 0.3763 target = 0.142404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114047 restraints weight = 22259.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.117552 restraints weight = 14437.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.120117 restraints weight = 10797.835| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12877 Z= 0.124 Angle : 0.565 8.084 17682 Z= 0.283 Chirality : 0.044 0.187 2175 Planarity : 0.003 0.024 2121 Dihedral : 3.984 17.534 1878 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.52 % Allowed : 21.71 % Favored : 73.77 % 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: -0.74 (0.21), residues: 1610 helix: 1.16 (0.21), residues: 545 sheet: -0.49 (0.28), residues: 400 loop : -1.91 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 77 HIS 0.003 0.001 HIS A 58 PHE 0.011 0.001 PHE E 298 TYR 0.015 0.001 TYR C 252 ARG 0.002 0.000 ARG E 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 5) link_NAG-ASN : angle 1.26458 ( 15) hydrogen bonds : bond 0.03450 ( 580) hydrogen bonds : angle 4.28938 ( 1650) SS BOND : bond 0.00345 ( 4) SS BOND : angle 0.77397 ( 8) covalent geometry : bond 0.00291 (12868) covalent geometry : angle 0.56395 (17659) *********************** 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 286 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 229 time to evaluate : 1.491 Fit side-chains REVERT: A 21 ILE cc_start: 0.9275 (tp) cc_final: 0.8896 (tt) REVERT: A 271 MET cc_start: 0.8036 (tmm) cc_final: 0.7777 (tmm) REVERT: B 21 ILE cc_start: 0.9324 (tp) cc_final: 0.9035 (tt) REVERT: B 138 CYS cc_start: 0.7753 (p) cc_final: 0.7370 (m) REVERT: B 271 MET cc_start: 0.7777 (tmm) cc_final: 0.7483 (tmm) REVERT: C 21 ILE cc_start: 0.9248 (tp) cc_final: 0.8901 (tt) REVERT: C 100 ILE cc_start: 0.8929 (mt) cc_final: 0.8653 (tp) REVERT: C 227 MET cc_start: 0.7650 (tmm) cc_final: 0.6907 (tpp) REVERT: C 271 MET cc_start: 0.7944 (tmm) cc_final: 0.7670 (tmm) REVERT: D 21 ILE cc_start: 0.9310 (tp) cc_final: 0.8995 (tt) REVERT: D 104 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7531 (p0) REVERT: D 196 GLN cc_start: 0.8102 (mp10) cc_final: 0.7888 (mp10) REVERT: D 264 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8216 (tt) REVERT: D 291 MET cc_start: 0.8691 (tpp) cc_final: 0.8414 (tpp) REVERT: E 17 LEU cc_start: 0.8679 (tp) cc_final: 0.8342 (tp) REVERT: E 21 ILE cc_start: 0.9320 (tp) cc_final: 0.8924 (tt) REVERT: E 127 MET cc_start: 0.8529 (mtm) cc_final: 0.8314 (mtm) REVERT: E 264 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8209 (tt) REVERT: E 265 MET cc_start: 0.8456 (ttp) cc_final: 0.8247 (ttp) REVERT: E 271 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7511 (tmm) REVERT: E 291 MET cc_start: 0.8768 (tpp) cc_final: 0.8541 (tpp) outliers start: 57 outliers final: 38 residues processed: 271 average time/residue: 0.1811 time to fit residues: 78.4843 Evaluate side-chains 260 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 62 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 210 THR 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 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 424 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ASN 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 188 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 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 268 SER Chi-restraints excluded: chain E residue 271 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 8 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS B 161 HIS C 161 HIS D 161 HIS E 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.139505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110073 restraints weight = 22599.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113358 restraints weight = 15188.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115658 restraints weight = 11656.782| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12877 Z= 0.212 Angle : 0.642 8.572 17682 Z= 0.320 Chirality : 0.046 0.173 2175 Planarity : 0.003 0.024 2121 Dihedral : 4.350 17.402 1878 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.31 % Allowed : 21.79 % Favored : 72.90 % 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: -0.94 (0.21), residues: 1610 helix: 1.04 (0.22), residues: 545 sheet: -0.77 (0.25), residues: 470 loop : -2.03 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 77 HIS 0.003 0.001 HIS A 68 PHE 0.015 0.002 PHE C 103 TYR 0.017 0.001 TYR C 252 ARG 0.002 0.000 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 5) link_NAG-ASN : angle 1.99052 ( 15) hydrogen bonds : bond 0.03822 ( 580) hydrogen bonds : angle 4.62297 ( 1650) SS BOND : bond 0.00517 ( 4) SS BOND : angle 1.01944 ( 8) covalent geometry : bond 0.00506 (12868) covalent geometry : angle 0.63941 (17659) *********************** 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 291 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 224 time to evaluate : 1.504 Fit side-chains REVERT: A 21 ILE cc_start: 0.9273 (tp) cc_final: 0.8899 (tt) REVERT: A 287 TYR cc_start: 0.8206 (t80) cc_final: 0.7973 (t80) REVERT: A 291 MET cc_start: 0.8279 (tpp) cc_final: 0.7961 (tpp) REVERT: B 21 ILE cc_start: 0.9297 (tp) cc_final: 0.8958 (tt) REVERT: B 69 GLU cc_start: 0.7598 (tt0) cc_final: 0.7316 (tt0) REVERT: B 100 ILE cc_start: 0.9203 (mt) cc_final: 0.8860 (tp) REVERT: B 138 CYS cc_start: 0.7864 (p) cc_final: 0.7436 (m) REVERT: B 271 MET cc_start: 0.7945 (tmm) cc_final: 0.7681 (tmm) REVERT: C 21 ILE cc_start: 0.9295 (tp) cc_final: 0.8936 (tt) REVERT: C 69 GLU cc_start: 0.7611 (tt0) cc_final: 0.7358 (tt0) REVERT: C 100 ILE cc_start: 0.9123 (mt) cc_final: 0.8789 (tp) REVERT: C 227 MET cc_start: 0.7733 (tmm) cc_final: 0.7142 (tpp) REVERT: C 271 MET cc_start: 0.8048 (tmm) cc_final: 0.7778 (tmm) REVERT: D 21 ILE cc_start: 0.9359 (tp) cc_final: 0.9030 (tt) REVERT: D 69 GLU cc_start: 0.7710 (tt0) cc_final: 0.7391 (tt0) REVERT: D 104 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7476 (p0) REVERT: D 151 MET cc_start: 0.8109 (ptp) cc_final: 0.7770 (ptm) REVERT: D 264 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8327 (tt) REVERT: D 291 MET cc_start: 0.8819 (tpp) cc_final: 0.8562 (tpp) REVERT: E 17 LEU cc_start: 0.8791 (tp) cc_final: 0.8406 (tp) REVERT: E 21 ILE cc_start: 0.9329 (tp) cc_final: 0.8910 (tt) REVERT: E 69 GLU cc_start: 0.7738 (tt0) cc_final: 0.7459 (tt0) REVERT: E 100 ILE cc_start: 0.9246 (mt) cc_final: 0.8893 (tp) REVERT: E 127 MET cc_start: 0.8603 (mtm) cc_final: 0.8300 (mtm) REVERT: E 264 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8084 (tt) REVERT: E 265 MET cc_start: 0.8599 (ttp) cc_final: 0.8232 (ttp) REVERT: E 271 MET cc_start: 0.7969 (tmm) cc_final: 0.7699 (tmm) REVERT: E 291 MET cc_start: 0.8870 (tpp) cc_final: 0.8639 (tpp) outliers start: 67 outliers final: 40 residues processed: 268 average time/residue: 0.1789 time to fit residues: 76.8404 Evaluate side-chains 259 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 160 THR Chi-restraints excluded: chain A residue 163 VAL 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 289 PHE Chi-restraints excluded: chain A residue 417 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 289 PHE Chi-restraints excluded: chain C residue 62 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 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 D residue 62 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 119 VAL 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 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 117 LEU 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 264 LEU Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 125 optimal weight: 6.9990 chunk 86 optimal weight: 0.1980 chunk 126 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** 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 = 0.3742 r_free = 0.3742 target = 0.140072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110847 restraints weight = 22537.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114199 restraints weight = 14937.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.116607 restraints weight = 11377.899| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12877 Z= 0.178 Angle : 0.639 11.699 17682 Z= 0.317 Chirality : 0.045 0.175 2175 Planarity : 0.003 0.025 2121 Dihedral : 4.226 17.120 1878 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.68 % Allowed : 22.74 % 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: -0.98 (0.21), residues: 1610 helix: 1.04 (0.22), residues: 545 sheet: -0.54 (0.25), residues: 430 loop : -2.27 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 77 HIS 0.004 0.001 HIS C 161 PHE 0.014 0.001 PHE D 298 TYR 0.021 0.001 TYR C 252 ARG 0.003 0.000 ARG D 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 5) link_NAG-ASN : angle 1.67870 ( 15) hydrogen bonds : bond 0.03665 ( 580) hydrogen bonds : angle 4.61455 ( 1650) SS BOND : bond 0.00446 ( 4) SS BOND : angle 0.90256 ( 8) covalent geometry : bond 0.00427 (12868) covalent geometry : angle 0.63713 (17659) *********************** 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 279 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 220 time to evaluate : 1.517 Fit side-chains REVERT: A 21 ILE cc_start: 0.9269 (tp) cc_final: 0.8920 (tt) REVERT: A 291 MET cc_start: 0.8272 (tpp) cc_final: 0.7884 (tpp) REVERT: B 21 ILE cc_start: 0.9220 (tp) cc_final: 0.8897 (tt) REVERT: B 69 GLU cc_start: 0.7595 (tt0) cc_final: 0.7261 (tt0) REVERT: B 100 ILE cc_start: 0.9133 (mt) cc_final: 0.8800 (tp) REVERT: B 138 CYS cc_start: 0.7817 (p) cc_final: 0.7465 (m) REVERT: B 269 ASP cc_start: 0.7523 (m-30) cc_final: 0.7309 (t0) REVERT: B 271 MET cc_start: 0.7984 (tmm) cc_final: 0.7737 (tmm) REVERT: C 21 ILE cc_start: 0.9311 (tp) cc_final: 0.8970 (tt) REVERT: C 69 GLU cc_start: 0.7596 (tt0) cc_final: 0.7357 (tt0) REVERT: C 100 ILE cc_start: 0.9093 (mt) cc_final: 0.8771 (tp) REVERT: C 227 MET cc_start: 0.7702 (tmm) cc_final: 0.7232 (tpp) REVERT: C 271 MET cc_start: 0.8084 (tmm) cc_final: 0.7871 (tmm) REVERT: C 275 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7886 (mm) REVERT: D 21 ILE cc_start: 0.9344 (tp) cc_final: 0.9031 (tt) REVERT: D 104 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7710 (p0) REVERT: D 151 MET cc_start: 0.8105 (ptp) cc_final: 0.7748 (ptt) REVERT: D 291 MET cc_start: 0.8846 (tpp) cc_final: 0.8547 (tpp) REVERT: E 17 LEU cc_start: 0.8773 (tp) cc_final: 0.8401 (tp) REVERT: E 21 ILE cc_start: 0.9327 (tp) cc_final: 0.8930 (tt) REVERT: E 69 GLU cc_start: 0.7769 (tt0) cc_final: 0.7465 (tt0) REVERT: E 100 ILE cc_start: 0.9180 (mt) cc_final: 0.8830 (tp) REVERT: E 127 MET cc_start: 0.8578 (mtm) cc_final: 0.8294 (mtm) REVERT: E 264 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8081 (tt) REVERT: E 265 MET cc_start: 0.8577 (ttp) cc_final: 0.8204 (ttp) REVERT: E 271 MET cc_start: 0.8003 (tmm) cc_final: 0.7745 (tmm) REVERT: E 291 MET cc_start: 0.8876 (tpp) cc_final: 0.8657 (tpp) outliers start: 59 outliers final: 39 residues processed: 257 average time/residue: 0.1798 time to fit residues: 74.3757 Evaluate side-chains 252 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 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 289 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 429 LEU 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 254 ILE 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 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 104 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 119 VAL 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 117 LEU 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 264 LEU Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 429 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 40 optimal weight: 0.0770 chunk 151 optimal weight: 0.4980 chunk 111 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** 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 = 0.3766 r_free = 0.3766 target = 0.142052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113326 restraints weight = 22197.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.116683 restraints weight = 14653.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119134 restraints weight = 11092.089| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12877 Z= 0.129 Angle : 0.627 9.982 17682 Z= 0.311 Chirality : 0.045 0.254 2175 Planarity : 0.003 0.023 2121 Dihedral : 4.070 15.878 1878 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.49 % Allowed : 24.01 % Favored : 72.50 % 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: -0.96 (0.21), residues: 1610 helix: 1.04 (0.22), residues: 545 sheet: -0.48 (0.28), residues: 355 loop : -2.11 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 77 HIS 0.004 0.001 HIS B 161 PHE 0.012 0.001 PHE A 234 TYR 0.019 0.001 TYR C 252 ARG 0.001 0.000 ARG D 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 5) link_NAG-ASN : angle 1.32866 ( 15) hydrogen bonds : bond 0.03564 ( 580) hydrogen bonds : angle 4.51739 ( 1650) SS BOND : bond 0.00306 ( 4) SS BOND : angle 0.70993 ( 8) covalent geometry : bond 0.00308 (12868) covalent geometry : angle 0.62648 (17659) *********************** 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 254 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 1.360 Fit side-chains REVERT: A 21 ILE cc_start: 0.9254 (tp) cc_final: 0.8921 (tt) REVERT: A 305 MET cc_start: 0.7823 (ptp) cc_final: 0.7538 (tpt) REVERT: B 21 ILE cc_start: 0.9211 (tp) cc_final: 0.8879 (tt) REVERT: B 138 CYS cc_start: 0.7792 (p) cc_final: 0.7360 (m) REVERT: B 271 MET cc_start: 0.7968 (tmm) cc_final: 0.7760 (tmm) REVERT: C 21 ILE cc_start: 0.9289 (tp) cc_final: 0.8965 (tt) REVERT: C 100 ILE cc_start: 0.8965 (mt) cc_final: 0.8668 (tp) REVERT: C 227 MET cc_start: 0.7628 (tmm) cc_final: 0.7172 (tpp) REVERT: C 271 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7859 (tmm) REVERT: D 21 ILE cc_start: 0.9327 (tp) cc_final: 0.9025 (tt) REVERT: D 151 MET cc_start: 0.8058 (ptp) cc_final: 0.7705 (ptt) REVERT: D 291 MET cc_start: 0.8826 (tpp) cc_final: 0.8538 (tpp) REVERT: D 416 LEU cc_start: 0.8698 (tp) cc_final: 0.8490 (tt) REVERT: E 21 ILE cc_start: 0.9285 (tp) cc_final: 0.8905 (tt) REVERT: E 127 MET cc_start: 0.8553 (mtm) cc_final: 0.8302 (mtm) REVERT: E 271 MET cc_start: 0.7994 (tmm) cc_final: 0.7748 (tmm) REVERT: E 291 MET cc_start: 0.8847 (tpp) cc_final: 0.8389 (tpp) outliers start: 44 outliers final: 35 residues processed: 238 average time/residue: 0.1745 time to fit residues: 66.4801 Evaluate side-chains 240 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 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 273 THR Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 417 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 254 ILE 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 245 LEU Chi-restraints excluded: chain C residue 271 MET 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 163 VAL 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 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 268 SER Chi-restraints excluded: chain E residue 429 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 129 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 54 optimal weight: 0.0770 chunk 125 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 0.0170 chunk 65 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.143129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114029 restraints weight = 22019.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117396 restraints weight = 14661.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119874 restraints weight = 11169.954| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12877 Z= 0.129 Angle : 0.639 11.859 17682 Z= 0.315 Chirality : 0.045 0.259 2175 Planarity : 0.003 0.027 2121 Dihedral : 3.990 14.283 1876 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.01 % Allowed : 24.25 % Favored : 72.74 % 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: -0.96 (0.21), residues: 1610 helix: 1.14 (0.22), residues: 545 sheet: -0.85 (0.28), residues: 375 loop : -2.00 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 77 HIS 0.004 0.001 HIS B 161 PHE 0.011 0.001 PHE A 234 TYR 0.019 0.001 TYR C 252 ARG 0.001 0.000 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 5) link_NAG-ASN : angle 1.26216 ( 15) hydrogen bonds : bond 0.03508 ( 580) hydrogen bonds : angle 4.48062 ( 1650) SS BOND : bond 0.00311 ( 4) SS BOND : angle 0.69012 ( 8) covalent geometry : bond 0.00308 (12868) covalent geometry : angle 0.63824 (17659) ********************** 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 253 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 1.465 Fit side-chains REVERT: A 21 ILE cc_start: 0.9245 (tp) cc_final: 0.8942 (tt) REVERT: A 265 MET cc_start: 0.7955 (ttt) cc_final: 0.7626 (ttt) REVERT: A 305 MET cc_start: 0.8013 (ptp) cc_final: 0.7586 (tpt) REVERT: B 21 ILE cc_start: 0.9203 (tp) cc_final: 0.8891 (tt) REVERT: B 127 MET cc_start: 0.8505 (mtm) cc_final: 0.8255 (mtt) REVERT: B 138 CYS cc_start: 0.7933 (p) cc_final: 0.7445 (m) REVERT: C 21 ILE cc_start: 0.9267 (tp) cc_final: 0.8959 (tt) REVERT: C 100 ILE cc_start: 0.8930 (mt) cc_final: 0.8639 (tp) REVERT: C 227 MET cc_start: 0.7637 (tmm) cc_final: 0.7167 (tpp) REVERT: C 275 LEU cc_start: 0.8163 (mm) cc_final: 0.7787 (mm) REVERT: D 21 ILE cc_start: 0.9318 (tp) cc_final: 0.9024 (tt) REVERT: D 151 MET cc_start: 0.8038 (ptp) cc_final: 0.7690 (ptt) REVERT: D 291 MET cc_start: 0.8828 (tpp) cc_final: 0.8559 (tpp) REVERT: E 21 ILE cc_start: 0.9278 (tp) cc_final: 0.8907 (tt) REVERT: E 127 MET cc_start: 0.8552 (mtm) cc_final: 0.8297 (mtm) REVERT: E 271 MET cc_start: 0.8019 (tmm) cc_final: 0.7761 (tmm) outliers start: 38 outliers final: 31 residues processed: 241 average time/residue: 0.1781 time to fit residues: 68.4578 Evaluate side-chains 236 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 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 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 254 ILE 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 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 163 VAL 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 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 268 SER Chi-restraints excluded: chain E residue 429 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 9 optimal weight: 1.9990 chunk 94 optimal weight: 0.0970 chunk 108 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** 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 = 0.3771 r_free = 0.3771 target = 0.142362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113210 restraints weight = 22196.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.116608 restraints weight = 14756.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.119054 restraints weight = 11210.513| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12877 Z= 0.144 Angle : 0.647 11.618 17682 Z= 0.318 Chirality : 0.045 0.284 2175 Planarity : 0.003 0.025 2121 Dihedral : 4.022 14.530 1876 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.01 % Allowed : 24.41 % 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: -0.95 (0.21), residues: 1610 helix: 1.19 (0.22), residues: 545 sheet: -0.90 (0.28), residues: 375 loop : -1.99 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 77 HIS 0.005 0.001 HIS E 161 PHE 0.020 0.001 PHE B 137 TYR 0.020 0.001 TYR C 252 ARG 0.001 0.000 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 5) link_NAG-ASN : angle 1.37979 ( 15) hydrogen bonds : bond 0.03547 ( 580) hydrogen bonds : angle 4.52076 ( 1650) SS BOND : bond 0.00351 ( 4) SS BOND : angle 0.75670 ( 8) covalent geometry : bond 0.00347 (12868) covalent geometry : angle 0.64635 (17659) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4071.01 seconds wall clock time: 72 minutes 3.39 seconds (4323.39 seconds total)