Starting phenix.real_space_refine on Mon Aug 25 16:56:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qfh_53109/08_2025/9qfh_53109_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qfh_53109/08_2025/9qfh_53109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qfh_53109/08_2025/9qfh_53109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qfh_53109/08_2025/9qfh_53109.map" model { file = "/net/cci-nas-00/data/ceres_data/9qfh_53109/08_2025/9qfh_53109_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qfh_53109/08_2025/9qfh_53109_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 1.744 sd= 1.309 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 175 5.16 5 C 19194 2.51 5 N 4941 2.21 5 O 5315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29625 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6127 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 774, 6105 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 747} Chain breaks: 7 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 774, 6105 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 747} Chain breaks: 7 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 6223 Chain: "B" Number of atoms: 6134 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 776, 6123 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 750} Chain breaks: 7 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Conformer: "B" Number of residues, atoms: 776, 6123 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 750} Chain breaks: 7 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 bond proxies already assigned to first conformer: 6252 Chain: "C" Number of atoms: 6100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 6100 Classifications: {'peptide': 777} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 750} Chain breaks: 7 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 9, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 6100 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 772, 6089 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 746} Chain breaks: 6 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 57 Conformer: "B" Number of residues, atoms: 772, 6089 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 746} Chain breaks: 6 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 57 bond proxies already assigned to first conformer: 6219 Chain: "W" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1292 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1295 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain breaks: 4 Chain: "Y" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1290 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain breaks: 4 Chain: "Z" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1287 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 164} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG A 183 " occ=0.45 ... (20 atoms not shown) pdb=" NH2BARG A 183 " occ=0.55 residue: pdb=" N AARG A 455 " occ=0.63 ... (20 atoms not shown) pdb=" NH2BARG A 455 " occ=0.37 residue: pdb=" N AARG B 184 " occ=0.36 ... (20 atoms not shown) pdb=" NH2BARG B 184 " occ=0.64 residue: pdb=" N AARG D 184 " occ=0.47 ... (20 atoms not shown) pdb=" NH2BARG D 184 " occ=0.53 Time building chain proxies: 11.43, per 1000 atoms: 0.39 Number of scatterers: 29625 At special positions: 0 Unit cell: (127.204, 184.198, 208.978, 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 175 16.00 O 5315 8.00 N 4941 7.00 C 19194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 312 " distance=2.25 Simple disulfide: pdb=" SG CYS A 722 " - pdb=" SG CYS A 777 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 312 " distance=2.23 Simple disulfide: pdb=" SG CYS B 722 " - pdb=" SG CYS B 777 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 312 " distance=2.26 Simple disulfide: pdb=" SG CYS C 722 " - pdb=" SG CYS C 777 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 312 " distance=2.30 Simple disulfide: pdb=" SG CYS D 722 " - pdb=" SG CYS D 777 " distance=2.03 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 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6974 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 36 sheets defined 55.3% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 17 through 32 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 81 through 92 Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.865A pdb=" N PHE A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 209 Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.616A pdb=" N ILE A 227 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 276 through 299 removed outlier: 3.520A pdb=" N ALA A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 removed outlier: 4.476A pdb=" N ASP A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 418 through 421 Processing helix chain 'A' and resid 425 through 438 Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 517 through 521 Processing helix chain 'A' and resid 524 through 548 Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.976A pdb=" N TRP A 553 " --> pdb=" O SER A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 589 Processing helix chain 'A' and resid 599 through 634 Processing helix chain 'A' and resid 639 through 646 Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 668 through 681 Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 710 through 718 removed outlier: 3.574A pdb=" N GLN A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 760 Processing helix chain 'A' and resid 761 through 772 Processing helix chain 'A' and resid 792 through 795 Processing helix chain 'A' and resid 796 through 828 removed outlier: 3.538A pdb=" N PHE A 800 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 32 Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 170 through 184 removed outlier: 3.739A pdb=" N PHE B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 208 Processing helix chain 'B' and resid 224 through 227 removed outlier: 3.689A pdb=" N ILE B 227 " --> pdb=" O PHE B 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 224 through 227' Processing helix chain 'B' and resid 229 through 236 Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 276 through 299 removed outlier: 3.547A pdb=" N ALA B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 331 Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 418 through 421 removed outlier: 3.709A pdb=" N GLU B 421 " --> pdb=" O GLU B 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 421' Processing helix chain 'B' and resid 425 through 438 removed outlier: 3.861A pdb=" N LYS B 436 " --> pdb=" O TYR B 432 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 517 through 521 Processing helix chain 'B' and resid 524 through 548 Processing helix chain 'B' and resid 549 through 554 removed outlier: 3.783A pdb=" N TRP B 553 " --> pdb=" O SER B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 589 Processing helix chain 'B' and resid 599 through 630 Processing helix chain 'B' and resid 639 through 646 removed outlier: 3.567A pdb=" N LEU B 643 " --> pdb=" O SER B 639 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B 646 " --> pdb=" O ASP B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 668 through 680 Processing helix chain 'B' and resid 689 through 700 Processing helix chain 'B' and resid 710 through 718 Processing helix chain 'B' and resid 746 through 760 Processing helix chain 'B' and resid 761 through 772 Processing helix chain 'B' and resid 792 through 795 Processing helix chain 'B' and resid 796 through 828 removed outlier: 3.560A pdb=" N PHE B 800 " --> pdb=" O VAL B 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 32 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 81 through 92 Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 170 through 184 removed outlier: 3.843A pdb=" N PHE C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 209 Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.514A pdb=" N ILE C 227 " --> pdb=" O PHE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'C' and resid 276 through 299 Processing helix chain 'C' and resid 321 through 331 removed outlier: 4.462A pdb=" N ASP C 325 " --> pdb=" O SER C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 421 Processing helix chain 'C' and resid 425 through 438 Processing helix chain 'C' and resid 463 through 471 Processing helix chain 'C' and resid 484 through 489 Processing helix chain 'C' and resid 517 through 521 Processing helix chain 'C' and resid 524 through 548 Processing helix chain 'C' and resid 549 through 554 removed outlier: 3.721A pdb=" N TRP C 553 " --> pdb=" O SER C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 590 Processing helix chain 'C' and resid 599 through 634 Processing helix chain 'C' and resid 639 through 646 removed outlier: 3.686A pdb=" N GLN C 646 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 668 through 681 Processing helix chain 'C' and resid 689 through 700 Processing helix chain 'C' and resid 710 through 717 Processing helix chain 'C' and resid 746 through 760 Processing helix chain 'C' and resid 761 through 772 Processing helix chain 'C' and resid 792 through 795 Processing helix chain 'C' and resid 796 through 828 removed outlier: 3.631A pdb=" N PHE C 800 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 32 Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 143 through 157 Processing helix chain 'D' and resid 170 through 184 removed outlier: 3.742A pdb=" N PHE D 174 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 224 through 227 removed outlier: 3.709A pdb=" N ILE D 227 " --> pdb=" O PHE D 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 229 through 236 Processing helix chain 'D' and resid 249 through 260 Processing helix chain 'D' and resid 276 through 299 removed outlier: 3.562A pdb=" N ALA D 280 " --> pdb=" O LYS D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 331 Processing helix chain 'D' and resid 418 through 421 removed outlier: 3.737A pdb=" N GLU D 421 " --> pdb=" O GLU D 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 418 through 421' Processing helix chain 'D' and resid 425 through 439 removed outlier: 3.503A pdb=" N ALA D 435 " --> pdb=" O ALA D 431 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS D 436 " --> pdb=" O TYR D 432 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 471 Processing helix chain 'D' and resid 484 through 489 Processing helix chain 'D' and resid 517 through 521 Processing helix chain 'D' and resid 524 through 548 Processing helix chain 'D' and resid 549 through 554 removed outlier: 3.833A pdb=" N TRP D 553 " --> pdb=" O SER D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 589 Processing helix chain 'D' and resid 599 through 630 Processing helix chain 'D' and resid 640 through 646 Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 668 through 681 Processing helix chain 'D' and resid 689 through 700 Processing helix chain 'D' and resid 710 through 718 Processing helix chain 'D' and resid 746 through 760 Processing helix chain 'D' and resid 761 through 772 Processing helix chain 'D' and resid 792 through 795 Processing helix chain 'D' and resid 796 through 828 removed outlier: 3.540A pdb=" N PHE D 800 " --> pdb=" O VAL D 796 " (cutoff:3.500A) Processing helix chain 'W' and resid 7 through 30 Processing helix chain 'W' and resid 95 through 105 Processing helix chain 'W' and resid 105 through 126 removed outlier: 3.837A pdb=" N GLU W 126 " --> pdb=" O ILE W 122 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 161 removed outlier: 3.626A pdb=" N LEU W 136 " --> pdb=" O HIS W 132 " (cutoff:3.500A) Processing helix chain 'W' and resid 177 through 210 removed outlier: 3.541A pdb=" N TYR W 181 " --> pdb=" O GLY W 177 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 30 Processing helix chain 'X' and resid 95 through 105 Processing helix chain 'X' and resid 105 through 128 removed outlier: 4.024A pdb=" N GLU X 126 " --> pdb=" O ILE X 122 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE X 127 " --> pdb=" O ALA X 123 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 161 removed outlier: 3.598A pdb=" N LEU X 136 " --> pdb=" O HIS X 132 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA X 161 " --> pdb=" O ILE X 157 " (cutoff:3.500A) Processing helix chain 'X' and resid 177 through 210 removed outlier: 3.506A pdb=" N TYR X 181 " --> pdb=" O GLY X 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 26 removed outlier: 3.505A pdb=" N ILE Y 26 " --> pdb=" O SER Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 96 through 105 Processing helix chain 'Y' and resid 105 through 128 removed outlier: 3.703A pdb=" N GLU Y 126 " --> pdb=" O ILE Y 122 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE Y 127 " --> pdb=" O ALA Y 123 " (cutoff:3.500A) Processing helix chain 'Y' and resid 132 through 161 Processing helix chain 'Y' and resid 177 through 210 removed outlier: 3.555A pdb=" N TYR Y 181 " --> pdb=" O GLY Y 177 " (cutoff:3.500A) Processing helix chain 'Z' and resid 7 through 30 Processing helix chain 'Z' and resid 94 through 105 Processing helix chain 'Z' and resid 105 through 128 Processing helix chain 'Z' and resid 132 through 161 removed outlier: 3.533A pdb=" N LEU Z 136 " --> pdb=" O HIS Z 132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 177 through 210 removed outlier: 3.601A pdb=" N TYR Z 181 " --> pdb=" O GLY Z 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 49 removed outlier: 3.512A pdb=" N GLY A 10 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N ALA A 72 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N SER A 7 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N PHE A 74 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY A 9 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 73 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 7.119A pdb=" N PHE A 133 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ARG A 163 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR A 135 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LYS A 132 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LEU A 190 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 134 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP A 192 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 136 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR A 189 " --> pdb=" O MET A 218 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE A 242 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 239 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 355 " --> pdb=" O TYR A 370 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR A 370 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 357 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR A 370 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA4, first strand: chain 'A' and resid 443 through 446 removed outlier: 5.892A pdb=" N VAL A 399 " --> pdb=" O SER A 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 410 Processing sheet with id=AA6, first strand: chain 'A' and resid 491 through 493 Processing sheet with id=AA7, first strand: chain 'A' and resid 498 through 500 removed outlier: 3.741A pdb=" N MET A 498 " --> pdb=" O TYR A 736 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 650 through 652 removed outlier: 6.500A pdb=" N ALA A 650 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU A 707 " --> pdb=" O ALA A 650 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY A 652 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N GLU A 709 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N PHE A 704 " --> pdb=" O LYS A 507 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS A 507 " --> pdb=" O PHE A 704 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 504 " --> pdb=" O VAL A 727 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 42 through 49 removed outlier: 10.158A pdb=" N ALA B 72 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N SER B 7 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N PHE B 74 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLY B 9 " --> pdb=" O PHE B 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 164 removed outlier: 6.319A pdb=" N TYR B 135 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 134 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASP B 192 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 136 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR B 189 " --> pdb=" O MET B 218 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA B 220 " --> pdb=" O TYR B 189 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B 191 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N LEU B 222 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE B 242 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASN B 221 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE B 239 " --> pdb=" O MET B 360 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE B 355 " --> pdb=" O TYR B 370 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TYR B 370 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 357 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR B 370 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 335 through 337 removed outlier: 3.766A pdb=" N GLN B 343 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 443 through 446 removed outlier: 5.861A pdb=" N VAL B 399 " --> pdb=" O SER B 445 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 409 through 410 Processing sheet with id=AB5, first strand: chain 'B' and resid 491 through 493 Processing sheet with id=AB6, first strand: chain 'B' and resid 498 through 500 removed outlier: 3.796A pdb=" N MET B 498 " --> pdb=" O TYR B 736 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 650 through 652 removed outlier: 6.539A pdb=" N ALA B 650 " --> pdb=" O ALA B 705 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LEU B 707 " --> pdb=" O ALA B 650 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY B 652 " --> pdb=" O LEU B 707 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N GLU B 709 " --> pdb=" O GLY B 652 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N PHE B 704 " --> pdb=" O LYS B 507 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS B 507 " --> pdb=" O PHE B 704 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 504 " --> pdb=" O VAL B 727 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 42 through 49 removed outlier: 3.535A pdb=" N GLY C 10 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N ALA C 72 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N SER C 7 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N PHE C 74 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY C 9 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE C 73 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 159 through 164 removed outlier: 7.132A pdb=" N PHE C 133 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ARG C 163 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR C 135 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LYS C 132 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N LEU C 190 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL C 134 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP C 192 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU C 136 " --> pdb=" O ASP C 192 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR C 189 " --> pdb=" O MET C 218 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE C 242 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE C 239 " --> pdb=" O MET C 360 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE C 355 " --> pdb=" O TYR C 370 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR C 370 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 357 " --> pdb=" O ALA C 368 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AC2, first strand: chain 'C' and resid 398 through 401 removed outlier: 6.262A pdb=" N VAL C 399 " --> pdb=" O SER C 445 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 409 through 410 Processing sheet with id=AC4, first strand: chain 'C' and resid 477 through 482 removed outlier: 5.076A pdb=" N ALA C 479 " --> pdb=" O GLY C 737 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLY C 737 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 481 " --> pdb=" O GLY C 735 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY C 735 " --> pdb=" O LEU C 481 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 477 through 482 removed outlier: 5.076A pdb=" N ALA C 479 " --> pdb=" O GLY C 737 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLY C 737 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 481 " --> pdb=" O GLY C 735 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY C 735 " --> pdb=" O LEU C 481 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET C 498 " --> pdb=" O TYR C 736 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 650 through 652 removed outlier: 6.693A pdb=" N ALA C 650 " --> pdb=" O ALA C 705 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU C 707 " --> pdb=" O ALA C 650 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY C 652 " --> pdb=" O LEU C 707 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N GLU C 709 " --> pdb=" O GLY C 652 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N PHE C 704 " --> pdb=" O LYS C 507 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS C 507 " --> pdb=" O PHE C 704 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE C 504 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 42 through 49 removed outlier: 4.687A pdb=" N ALA D 72 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 161 through 164 removed outlier: 6.346A pdb=" N TYR D 135 " --> pdb=" O ARG D 163 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL D 134 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP D 192 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU D 136 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR D 189 " --> pdb=" O MET D 218 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA D 220 " --> pdb=" O TYR D 189 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE D 191 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU D 222 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE D 242 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ASN D 221 " --> pdb=" O PHE D 242 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 239 " --> pdb=" O MET D 360 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE D 355 " --> pdb=" O TYR D 370 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR D 370 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL D 357 " --> pdb=" O ALA D 368 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR D 370 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 335 through 337 removed outlier: 3.700A pdb=" N GLN D 343 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 443 through 446 Processing sheet with id=AD2, first strand: chain 'D' and resid 409 through 410 Processing sheet with id=AD3, first strand: chain 'D' and resid 491 through 493 Processing sheet with id=AD4, first strand: chain 'D' and resid 498 through 500 removed outlier: 3.780A pdb=" N MET D 498 " --> pdb=" O TYR D 736 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 650 through 652 removed outlier: 6.590A pdb=" N ALA D 650 " --> pdb=" O ALA D 705 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU D 707 " --> pdb=" O ALA D 650 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY D 652 " --> pdb=" O LEU D 707 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N GLU D 709 " --> pdb=" O GLY D 652 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N PHE D 704 " --> pdb=" O LYS D 507 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS D 507 " --> pdb=" O PHE D 704 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE D 504 " --> pdb=" O VAL D 727 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'W' and resid 77 through 79 Processing sheet with id=AD7, first strand: chain 'X' and resid 77 through 79 removed outlier: 7.776A pdb=" N MET X 58 " --> pdb=" O LEU X 69 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Y' and resid 77 through 79 Processing sheet with id=AD9, first strand: chain 'Z' and resid 77 through 79 removed outlier: 7.426A pdb=" N MET Z 58 " --> pdb=" O LEU Z 69 " (cutoff:3.500A) 1717 hydrogen bonds defined for protein. 4978 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: 7.59 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4670 1.31 - 1.44: 8737 1.44 - 1.56: 16606 1.56 - 1.69: 0 1.69 - 1.81: 298 Bond restraints: 30311 Sorted by residual: bond pdb=" CA SER A 584 " pdb=" CB SER A 584 " ideal model delta sigma weight residual 1.530 1.467 0.063 1.57e-02 4.06e+03 1.63e+01 bond pdb=" CA SER B 596 " pdb=" CB SER B 596 " ideal model delta sigma weight residual 1.536 1.477 0.059 1.46e-02 4.69e+03 1.62e+01 bond pdb=" CA SER A 599 " pdb=" CB SER A 599 " ideal model delta sigma weight residual 1.532 1.475 0.057 1.45e-02 4.76e+03 1.55e+01 bond pdb=" C PRO B 597 " pdb=" O PRO B 597 " ideal model delta sigma weight residual 1.233 1.186 0.047 1.19e-02 7.06e+03 1.54e+01 bond pdb=" CA SER B 584 " pdb=" CB SER B 584 " ideal model delta sigma weight residual 1.530 1.467 0.063 1.63e-02 3.76e+03 1.47e+01 ... (remaining 30306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 40364 2.10 - 4.20: 566 4.20 - 6.31: 74 6.31 - 8.41: 7 8.41 - 10.51: 6 Bond angle restraints: 41017 Sorted by residual: angle pdb=" N ALA D 587 " pdb=" CA ALA D 587 " pdb=" C ALA D 587 " ideal model delta sigma weight residual 111.24 100.73 10.51 1.29e+00 6.01e-01 6.64e+01 angle pdb=" N VAL Y 28 " pdb=" CA VAL Y 28 " pdb=" C VAL Y 28 " ideal model delta sigma weight residual 112.90 105.68 7.22 9.60e-01 1.09e+00 5.66e+01 angle pdb=" N GLY D 592 " pdb=" CA GLY D 592 " pdb=" C GLY D 592 " ideal model delta sigma weight residual 111.85 118.51 -6.66 1.20e+00 6.94e-01 3.08e+01 angle pdb=" CA GLY A 576 " pdb=" C GLY A 576 " pdb=" O GLY A 576 " ideal model delta sigma weight residual 122.47 116.65 5.82 1.08e+00 8.57e-01 2.91e+01 angle pdb=" O GLU D 433 " pdb=" C GLU D 433 " pdb=" N ILE D 434 " ideal model delta sigma weight residual 122.22 115.97 6.25 1.17e+00 7.31e-01 2.85e+01 ... (remaining 41012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 16220 17.67 - 35.34: 1231 35.34 - 53.02: 185 53.02 - 70.69: 48 70.69 - 88.36: 16 Dihedral angle restraints: 17700 sinusoidal: 6826 harmonic: 10874 Sorted by residual: dihedral pdb=" CB CYS C 63 " pdb=" SG CYS C 63 " pdb=" SG CYS C 312 " pdb=" CB CYS C 312 " ideal model delta sinusoidal sigma weight residual -86.00 -137.25 51.25 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " pdb=" SG CYS A 312 " pdb=" CB CYS A 312 " ideal model delta sinusoidal sigma weight residual -86.00 -137.22 51.22 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CA ARG B 632 " pdb=" C ARG B 632 " pdb=" N MET B 633 " pdb=" CA MET B 633 " ideal model delta harmonic sigma weight residual 180.00 -150.91 -29.09 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 17697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3725 0.055 - 0.109: 714 0.109 - 0.164: 92 0.164 - 0.219: 16 0.219 - 0.274: 4 Chirality restraints: 4551 Sorted by residual: chirality pdb=" CA ILE B 595 " pdb=" N ILE B 595 " pdb=" C ILE B 595 " pdb=" CB ILE B 595 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ILE C 595 " pdb=" N ILE C 595 " pdb=" C ILE C 595 " pdb=" CB ILE C 595 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ILE D 595 " pdb=" N ILE D 595 " pdb=" C ILE D 595 " pdb=" CB ILE D 595 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 4548 not shown) Planarity restraints: 5149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 598 " 0.501 9.50e-02 1.11e+02 2.25e-01 3.09e+01 pdb=" NE ARG A 598 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 598 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 598 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 598 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 315 " 0.056 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO A 316 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 316 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 316 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 433 " -0.017 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C GLU D 433 " 0.055 2.00e-02 2.50e+03 pdb=" O GLU D 433 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE D 434 " -0.019 2.00e-02 2.50e+03 ... (remaining 5146 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4031 2.75 - 3.29: 28178 3.29 - 3.83: 50652 3.83 - 4.36: 60034 4.36 - 4.90: 103777 Nonbonded interactions: 246672 Sorted by model distance: nonbonded pdb=" O LYS D 210 " pdb=" OH TYR D 217 " model vdw 2.219 3.040 nonbonded pdb=" O LYS B 210 " pdb=" OH TYR B 217 " model vdw 2.220 3.040 nonbonded pdb=" OG SER C 639 " pdb=" OD1 ASP C 642 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR Y 30 " pdb=" OG SER Y 179 " model vdw 2.293 3.040 nonbonded pdb=" O PRO D 522 " pdb=" ND2 ASN D 623 " model vdw 2.301 3.120 ... (remaining 246667 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 2 through 182 or resid 185 through 225 or (resid 226 and ( \ name N or name CA or name C or name O or name CB )) or resid 227 through 229 or \ (resid 230 and (name N or name CA or name C or name O or name CB )) or resid 231 \ through 253 or (resid 254 and (name N or name CA or name C or name O or name CB \ )) or resid 255 through 403 or (resid 404 and (name N or name CA or name C or n \ ame O or name CB )) or resid 405 through 414 or (resid 415 through 416 and (name \ N or name CA or name C or name O or name CB )) or resid 417 or (resid 418 and ( \ name N or name CA or name C or name O or name CB )) or resid 419 through 423 or \ (resid 424 and (name N or name CA or name C or name O or name CB )) or resid 425 \ through 444 or (resid 445 and (name N or name CA or name C or name O or name CB \ )) or resid 446 through 454 or resid 456 through 474 or resid 476 through 551 o \ r (resid 552 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 53 through 593 or (resid 594 and (name N or name CA or name C or name O or name \ CB )) or resid 595 or (resid 596 and (name N or name CA or name C or name O or n \ ame CB )) or resid 597 through 630 or resid 639 through 640 or (resid 641 and (n \ ame N or name CA or name C or name O or name CB )) or resid 642 through 647 or ( \ resid 648 and (name N or name CA or name C or name O or name CB )) or resid 649 \ through 681 or (resid 682 and (name N or name CA or name C or name O or name CB \ )) or resid 683 through 687 or (resid 688 and (name N or name CA or name C or na \ me O or name CB )) or resid 689 through 828)) selection = (chain 'B' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 33 or (resid 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 38 or (resid 39 throug \ h 40 and (name N or name CA or name C or name O or name CB or name CG or name CD \ )) or resid 41 through 182 or resid 185 through 263 or (resid 264 through 265 a \ nd (name N or name CA or name C or name O or name CB )) or resid 266 through 299 \ or (resid 300 and (name N or name CA or name C or name O or name CB )) or resid \ 301 or (resid 302 and (name N or name CA or name C or name O or name CB )) or r \ esid 303 or (resid 304 through 309 and (name N or name CA or name C or name O or \ name CB )) or resid 310 through 358 or (resid 359 and (name N or name CA or nam \ e C or name O or name CB )) or resid 360 or (resid 361 through 363 and (name N o \ r name CA or name C or name O or name CB )) or resid 364 through 403 or (resid 4 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 405 through \ 414 or (resid 415 through 416 and (name N or name CA or name C or name O or nam \ e CB )) or resid 417 or (resid 418 and (name N or name CA or name C or name O or \ name CB )) or resid 419 through 423 or (resid 424 and (name N or name CA or nam \ e C or name O or name CB )) or resid 425 through 444 or (resid 445 and (name N o \ r name CA or name C or name O or name CB )) or resid 446 through 454 or resid 45 \ 6 through 474 or resid 476 through 508 or resid 514 through 551 or (resid 552 an \ d (name N or name CA or name C or name O or name CB )) or resid 553 through 593 \ or (resid 594 and (name N or name CA or name C or name O or name CB )) or resid \ 595 or (resid 596 and (name N or name CA or name C or name O or name CB )) or re \ sid 597 through 630 or resid 639 through 640 or (resid 641 and (name N or name C \ A or name C or name O or name CB )) or resid 642 through 778 or resid 789 throug \ h 828)) selection = (chain 'C' and (resid 2 through 182 or resid 185 through 225 or (resid 226 and ( \ name N or name CA or name C or name O or name CB )) or resid 227 through 229 or \ (resid 230 and (name N or name CA or name C or name O or name CB )) or resid 231 \ through 253 or (resid 254 and (name N or name CA or name C or name O or name CB \ )) or resid 255 through 299 or (resid 300 and (name N or name CA or name C or n \ ame O or name CB )) or resid 301 through 454 or resid 456 through 457 or (resid \ 458 and (name N or name CA or name C or name O or name CB )) or resid 459 throug \ h 508 or resid 514 through 630 or resid 639 through 640 or (resid 641 and (name \ N or name CA or name C or name O or name CB )) or resid 642 through 647 or (resi \ d 648 and (name N or name CA or name C or name O or name CB )) or resid 649 thro \ ugh 681 or (resid 682 and (name N or name CA or name C or name O or name CB )) o \ r resid 683 through 687 or (resid 688 and (name N or name CA or name C or name O \ or name CB )) or resid 689 through 698 or (resid 699 and (name N or name CA or \ name C or name O or name CB )) or resid 700 through 778 or resid 789 through 828 \ )) selection = (chain 'D' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 33 or (resid 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 38 or (resid 39 throug \ h 40 and (name N or name CA or name C or name O or name CB or name CG or name CD \ )) or resid 41 through 182 or resid 185 through 263 or (resid 264 through 265 a \ nd (name N or name CA or name C or name O or name CB )) or resid 266 through 299 \ or (resid 300 and (name N or name CA or name C or name O or name CB )) or resid \ 301 or (resid 302 and (name N or name CA or name C or name O or name CB )) or r \ esid 303 or (resid 304 through 309 and (name N or name CA or name C or name O or \ name CB )) or resid 310 through 358 or (resid 359 and (name N or name CA or nam \ e C or name O or name CB )) or resid 360 or (resid 361 through 363 and (name N o \ r name CA or name C or name O or name CB )) or resid 364 through 403 or (resid 4 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 405 through \ 411 or (resid 412 and (name N or name CA or name C or name O or name CB )) or r \ esid 413 through 414 or (resid 415 through 416 and (name N or name CA or name C \ or name O or name CB )) or resid 417 through 423 or (resid 424 and (name N or na \ me CA or name C or name O or name CB )) or resid 425 through 438 or resid 441 th \ rough 444 or (resid 445 and (name N or name CA or name C or name O or name CB )) \ or resid 446 through 454 or resid 456 through 457 or (resid 458 and (name N or \ name CA or name C or name O or name CB )) or resid 459 through 474 or resid 476 \ through 508 or resid 514 through 551 or (resid 552 and (name N or name CA or nam \ e C or name O or name CB )) or resid 553 through 595 or (resid 596 and (name N o \ r name CA or name C or name O or name CB )) or resid 597 through 647 or (resid 6 \ 48 and (name N or name CA or name C or name O or name CB )) or resid 649 through \ 687 or (resid 688 and (name N or name CA or name C or name O or name CB )) or r \ esid 689 through 698 or (resid 699 and (name N or name CA or name C or name O or \ name CB )) or resid 700 through 778 or resid 789 through 828)) } ncs_group { reference = (chain 'W' and (resid 6 through 70 or (resid 73 through 74 and (name N or name C \ A or name C or name O or name CB )) or resid 75 or (resid 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 83 or resid 95 through \ 210)) selection = (chain 'X' and (resid 6 through 70 or (resid 73 through 74 and (name N or name C \ A or name C or name O or name CB )) or resid 75 or (resid 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and (n \ ame N or name CA or name C or name O or name CB )) or resid 82 through 83 or res \ id 95 through 210)) selection = (chain 'Y' and (resid 6 through 70 or (resid 73 through 74 and (name N or name C \ A or name C or name O or name CB )) or resid 75 or (resid 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and (n \ ame N or name CA or name C or name O or name CB )) or resid 82 through 210)) selection = (chain 'Z' and (resid 6 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 83 or resid 95 through 210)) } 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=0.36 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.340 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 36.090 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 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 : 0.005 0.266 30319 Z= 0.252 Angle : 0.617 10.558 41033 Z= 0.382 Chirality : 0.044 0.274 4551 Planarity : 0.005 0.225 5149 Dihedral : 12.860 88.362 10702 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.29 % Allowed : 0.29 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.14), residues: 3669 helix: 1.95 (0.12), residues: 1998 sheet: -0.91 (0.24), residues: 441 loop : -0.59 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 603 TYR 0.021 0.001 TYR D 442 PHE 0.029 0.001 PHE B 578 TRP 0.026 0.002 TRP B 320 HIS 0.005 0.001 HIS X 60 Details of bonding type rmsd covalent geometry : bond 0.00395 (30311) covalent geometry : angle 0.61069 (41017) SS BOND : bond 0.16298 ( 8) SS BOND : angle 4.50606 ( 16) hydrogen bonds : bond 0.12623 ( 1715) hydrogen bonds : angle 5.16218 ( 4978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 541 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 TYR cc_start: 0.8172 (t80) cc_final: 0.7687 (t80) REVERT: A 823 ARG cc_start: 0.7581 (ttt90) cc_final: 0.7235 (mtt90) REVERT: B 42 HIS cc_start: 0.7845 (t-90) cc_final: 0.7267 (t70) REVERT: B 257 GLN cc_start: 0.8319 (tt0) cc_final: 0.8083 (tm-30) REVERT: B 589 MET cc_start: 0.9097 (mmt) cc_final: 0.8399 (mmt) REVERT: C 11 LEU cc_start: 0.7623 (mt) cc_final: 0.7392 (mt) REVERT: C 13 MET cc_start: 0.6900 (ptt) cc_final: 0.6340 (ptm) REVERT: C 83 ASN cc_start: 0.7821 (t0) cc_final: 0.7500 (t0) REVERT: C 157 ASN cc_start: 0.8577 (m110) cc_final: 0.8239 (m110) REVERT: C 296 LEU cc_start: 0.7624 (mt) cc_final: 0.7303 (mt) REVERT: C 347 TYR cc_start: 0.7903 (m-80) cc_final: 0.7331 (m-10) REVERT: D 82 MET cc_start: 0.6766 (tmm) cc_final: 0.6535 (tmm) REVERT: D 257 GLN cc_start: 0.7425 (tt0) cc_final: 0.7202 (pp30) REVERT: D 360 MET cc_start: 0.6349 (ttt) cc_final: 0.5975 (ttt) REVERT: Z 131 ARG cc_start: 0.8314 (mtt180) cc_final: 0.7740 (mmm160) outliers start: 6 outliers final: 4 residues processed: 547 average time/residue: 0.7307 time to fit residues: 465.1841 Evaluate side-chains 353 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 349 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain D residue 828 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 0.2980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 336 GLN B 341 ASN B 573 ASN C 65 GLN C 283 HIS C 591 GLN C 768 ASN D 42 HIS D 46 HIS D 221 ASN D 336 GLN D 341 ASN ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 205 HIS X 205 HIS Y 205 HIS Z 205 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.084996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.069452 restraints weight = 183763.351| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.70 r_work: 0.3178 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30319 Z= 0.140 Angle : 0.548 10.841 41033 Z= 0.292 Chirality : 0.041 0.289 4551 Planarity : 0.005 0.122 5149 Dihedral : 4.090 57.232 4096 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.10 % Allowed : 9.77 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.14), residues: 3669 helix: 2.49 (0.11), residues: 2003 sheet: -0.97 (0.23), residues: 459 loop : -0.49 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 828 TYR 0.026 0.001 TYR C 295 PHE 0.017 0.001 PHE A 497 TRP 0.033 0.002 TRP B 320 HIS 0.011 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00304 (30311) covalent geometry : angle 0.54769 (41017) SS BOND : bond 0.00206 ( 8) SS BOND : angle 1.05716 ( 16) hydrogen bonds : bond 0.03775 ( 1715) hydrogen bonds : angle 3.85563 ( 4978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 394 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8491 (mt) cc_final: 0.8206 (mp) REVERT: A 378 VAL cc_start: 0.9193 (p) cc_final: 0.8990 (m) REVERT: A 578 PHE cc_start: 0.7566 (t80) cc_final: 0.7360 (t80) REVERT: A 598 ARG cc_start: 0.8972 (ttm-80) cc_final: 0.8730 (ttp80) REVERT: A 823 ARG cc_start: 0.7538 (ttt90) cc_final: 0.6794 (mtt90) REVERT: B 64 SER cc_start: 0.8461 (m) cc_final: 0.7987 (p) REVERT: B 264 GLU cc_start: 0.8173 (tp30) cc_final: 0.7781 (tp30) REVERT: B 471 TYR cc_start: 0.7148 (m-80) cc_final: 0.6813 (m-80) REVERT: B 589 MET cc_start: 0.9062 (mmt) cc_final: 0.8388 (mmt) REVERT: B 812 MET cc_start: 0.8649 (ttp) cc_final: 0.8347 (ttm) REVERT: C 82 MET cc_start: 0.7596 (tmm) cc_final: 0.7395 (tmm) REVERT: C 374 TYR cc_start: 0.8018 (m-10) cc_final: 0.7724 (m-80) REVERT: C 433 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7941 (mt-10) REVERT: C 725 MET cc_start: 0.9019 (ptp) cc_final: 0.8732 (ppp) REVERT: D 2 PHE cc_start: 0.6237 (t80) cc_final: 0.5873 (t80) REVERT: D 253 GLN cc_start: 0.7928 (mt0) cc_final: 0.7564 (mt0) REVERT: W 73 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.5887 (p90) REVERT: X 204 ARG cc_start: 0.7913 (mmm-85) cc_final: 0.7669 (mtt-85) REVERT: Y 73 PHE cc_start: 0.6744 (OUTLIER) cc_final: 0.6220 (m-10) REVERT: Z 58 MET cc_start: 0.8082 (tpt) cc_final: 0.7818 (tpt) REVERT: Z 131 ARG cc_start: 0.8108 (mtt180) cc_final: 0.6988 (mmm160) outliers start: 62 outliers final: 16 residues processed: 421 average time/residue: 0.6588 time to fit residues: 322.7978 Evaluate side-chains 349 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 330 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 73 PHE Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain Y residue 73 PHE Chi-restraints excluded: chain Y residue 130 THR Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain Z residue 207 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 358 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 242 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 319 optimal weight: 4.9990 chunk 320 optimal weight: 0.5980 chunk 255 optimal weight: 0.7980 chunk 316 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 336 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 437 HIS B 573 ASN C 299 GLN C 591 GLN D 42 HIS D 221 ASN D 243 GLN W 205 HIS X 205 HIS Z 160 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.077514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.061603 restraints weight = 190223.528| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.58 r_work: 0.2987 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30319 Z= 0.131 Angle : 0.528 24.202 41033 Z= 0.275 Chirality : 0.040 0.221 4551 Planarity : 0.004 0.052 5149 Dihedral : 3.645 17.368 4086 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.10 % Allowed : 10.77 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.14), residues: 3669 helix: 2.72 (0.11), residues: 2009 sheet: -0.90 (0.23), residues: 448 loop : -0.45 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 664 TYR 0.021 0.001 TYR D 127 PHE 0.025 0.001 PHE D 62 TRP 0.032 0.001 TRP D 320 HIS 0.009 0.001 HIS D 42 Details of bonding type rmsd covalent geometry : bond 0.00300 (30311) covalent geometry : angle 0.52783 (41017) SS BOND : bond 0.00166 ( 8) SS BOND : angle 1.13932 ( 16) hydrogen bonds : bond 0.03925 ( 1715) hydrogen bonds : angle 3.73215 ( 4978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 355 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7827 (mtp) REVERT: A 328 ARG cc_start: 0.8382 (tmm-80) cc_final: 0.8095 (ttm-80) REVERT: A 366 ARG cc_start: 0.8407 (ttp80) cc_final: 0.8142 (ptm160) REVERT: A 598 ARG cc_start: 0.9044 (ttm-80) cc_final: 0.8747 (ttp80) REVERT: A 823 ARG cc_start: 0.7657 (ttt90) cc_final: 0.6893 (mtt90) REVERT: B 264 GLU cc_start: 0.8290 (tp30) cc_final: 0.7945 (tp30) REVERT: B 360 MET cc_start: 0.8695 (ttt) cc_final: 0.8403 (tpp) REVERT: B 812 MET cc_start: 0.8832 (ttp) cc_final: 0.8562 (ttm) REVERT: C 258 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7544 (mpp80) REVERT: C 725 MET cc_start: 0.9110 (ptp) cc_final: 0.8830 (ppp) REVERT: D 29 LEU cc_start: 0.7978 (mt) cc_final: 0.7764 (mt) REVERT: D 253 GLN cc_start: 0.8327 (mt0) cc_final: 0.7990 (mt0) REVERT: W 73 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.5906 (p90) REVERT: Y 73 PHE cc_start: 0.6658 (OUTLIER) cc_final: 0.6345 (m-80) REVERT: Y 204 ARG cc_start: 0.8381 (mtt-85) cc_final: 0.8139 (mtp85) REVERT: Z 58 MET cc_start: 0.8196 (tpt) cc_final: 0.7867 (tpt) REVERT: Z 78 LYS cc_start: 0.6923 (mttt) cc_final: 0.6619 (mttt) REVERT: Z 131 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7002 (mmm160) REVERT: Z 205 HIS cc_start: 0.8324 (OUTLIER) cc_final: 0.8053 (m90) outliers start: 62 outliers final: 16 residues processed: 383 average time/residue: 0.7485 time to fit residues: 330.8637 Evaluate side-chains 345 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 324 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 67 CYS Chi-restraints excluded: chain W residue 73 PHE Chi-restraints excluded: chain Y residue 73 PHE Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 205 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 146 optimal weight: 0.7980 chunk 276 optimal weight: 0.0470 chunk 316 optimal weight: 1.9990 chunk 348 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 293 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 294 optimal weight: 6.9990 chunk 335 optimal weight: 5.9990 overall best weight: 0.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN C 65 GLN C 591 GLN D 147 GLN D 246 ASN ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 205 HIS X 205 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.073563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.057680 restraints weight = 163748.831| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.30 r_work: 0.2897 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30319 Z= 0.125 Angle : 0.493 9.437 41033 Z= 0.262 Chirality : 0.040 0.216 4551 Planarity : 0.004 0.101 5149 Dihedral : 3.617 16.219 4086 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.58 % Allowed : 12.25 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.14), residues: 3669 helix: 2.78 (0.11), residues: 2018 sheet: -0.80 (0.24), residues: 441 loop : -0.44 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 14 TYR 0.021 0.001 TYR C 295 PHE 0.018 0.001 PHE A 377 TRP 0.026 0.001 TRP B 259 HIS 0.006 0.001 HIS X 205 Details of bonding type rmsd covalent geometry : bond 0.00287 (30311) covalent geometry : angle 0.49294 (41017) SS BOND : bond 0.00959 ( 8) SS BOND : angle 1.06621 ( 16) hydrogen bonds : bond 0.03572 ( 1715) hydrogen bonds : angle 3.62545 ( 4978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 337 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 ILE cc_start: 0.8769 (mm) cc_final: 0.8545 (mp) REVERT: A 328 ARG cc_start: 0.8477 (tmm-80) cc_final: 0.8245 (ttm-80) REVERT: A 444 LEU cc_start: 0.8710 (mm) cc_final: 0.8477 (mp) REVERT: A 574 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8488 (mm-30) REVERT: A 823 ARG cc_start: 0.7719 (ttt90) cc_final: 0.7063 (mtt90) REVERT: B 264 GLU cc_start: 0.8293 (tp30) cc_final: 0.7839 (tp30) REVERT: B 471 TYR cc_start: 0.7793 (m-80) cc_final: 0.7546 (m-80) REVERT: B 633 MET cc_start: 0.8463 (tpp) cc_final: 0.7659 (ttt) REVERT: B 812 MET cc_start: 0.8784 (ttp) cc_final: 0.8516 (ttm) REVERT: C 258 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8114 (mpp80) REVERT: C 313 LEU cc_start: 0.7847 (mp) cc_final: 0.7568 (mm) REVERT: C 374 TYR cc_start: 0.8283 (m-80) cc_final: 0.7968 (m-80) REVERT: C 433 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: C 641 GLU cc_start: 0.8264 (mp0) cc_final: 0.7952 (mp0) REVERT: C 725 MET cc_start: 0.9165 (ptp) cc_final: 0.8884 (ppp) REVERT: W 73 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.5829 (p90) REVERT: W 131 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7243 (mmm160) REVERT: W 207 GLN cc_start: 0.8302 (tp40) cc_final: 0.7978 (mt0) REVERT: X 78 LYS cc_start: 0.5392 (mptt) cc_final: 0.4936 (ptpt) REVERT: X 203 ASP cc_start: 0.8439 (t0) cc_final: 0.8034 (t0) REVERT: X 207 GLN cc_start: 0.8408 (tm-30) cc_final: 0.7808 (tm-30) REVERT: Y 73 PHE cc_start: 0.6613 (OUTLIER) cc_final: 0.6301 (m-80) REVERT: Y 204 ARG cc_start: 0.8394 (mtt-85) cc_final: 0.8156 (mtp85) REVERT: Y 205 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7602 (m90) REVERT: Z 58 MET cc_start: 0.8268 (tpt) cc_final: 0.7930 (tpt) REVERT: Z 78 LYS cc_start: 0.6939 (mttt) cc_final: 0.6731 (mttt) REVERT: Z 131 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7072 (mmm160) REVERT: Z 207 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.8000 (mt0) outliers start: 46 outliers final: 15 residues processed: 364 average time/residue: 0.7809 time to fit residues: 325.7743 Evaluate side-chains 326 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 305 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 67 CYS Chi-restraints excluded: chain W residue 73 PHE Chi-restraints excluded: chain X residue 11 LEU Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain X residue 68 CYS Chi-restraints excluded: chain Y residue 73 PHE Chi-restraints excluded: chain Y residue 205 HIS Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain Z residue 207 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 70 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 269 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 332 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 355 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN C 315 ASN C 591 GLN ** D 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 713 ASN W 205 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.067346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.051284 restraints weight = 178267.186| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.41 r_work: 0.2673 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30319 Z= 0.218 Angle : 0.570 9.066 41033 Z= 0.302 Chirality : 0.042 0.169 4551 Planarity : 0.004 0.053 5149 Dihedral : 3.968 19.610 4086 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.64 % Allowed : 12.64 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.14), residues: 3669 helix: 2.58 (0.11), residues: 2005 sheet: -1.03 (0.23), residues: 448 loop : -0.51 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 14 TYR 0.018 0.002 TYR A 77 PHE 0.025 0.002 PHE A 377 TRP 0.032 0.002 TRP D 320 HIS 0.010 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00519 (30311) covalent geometry : angle 0.56987 (41017) SS BOND : bond 0.00666 ( 8) SS BOND : angle 1.32529 ( 16) hydrogen bonds : bond 0.04778 ( 1715) hydrogen bonds : angle 3.88552 ( 4978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 688 LYS cc_start: 0.8958 (mptt) cc_final: 0.8710 (mppt) REVERT: A 823 ARG cc_start: 0.7985 (ttt90) cc_final: 0.7594 (tpp-160) REVERT: B 264 GLU cc_start: 0.8424 (tp30) cc_final: 0.8079 (tm-30) REVERT: B 633 MET cc_start: 0.8426 (tpp) cc_final: 0.8089 (ttt) REVERT: B 812 MET cc_start: 0.8811 (ttp) cc_final: 0.8604 (ttm) REVERT: C 65 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: C 131 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: C 258 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8520 (mpp80) REVERT: C 641 GLU cc_start: 0.8378 (mp0) cc_final: 0.8071 (mp0) REVERT: D 147 GLN cc_start: 0.8673 (mt0) cc_final: 0.8407 (tt0) REVERT: D 725 MET cc_start: 0.9011 (ptm) cc_final: 0.8755 (ptt) REVERT: W 73 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.5986 (p90) REVERT: W 131 ARG cc_start: 0.8350 (mtt180) cc_final: 0.7515 (mmm160) REVERT: W 207 GLN cc_start: 0.8518 (tp40) cc_final: 0.8279 (mt0) REVERT: X 129 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8490 (mtmt) REVERT: X 131 ARG cc_start: 0.8772 (mtp85) cc_final: 0.7787 (mmp-170) REVERT: X 203 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8330 (m-30) REVERT: Y 204 ARG cc_start: 0.8472 (mtt-85) cc_final: 0.8228 (mtp85) REVERT: Z 78 LYS cc_start: 0.6949 (mttt) cc_final: 0.6675 (mttt) REVERT: Z 131 ARG cc_start: 0.8273 (mtt180) cc_final: 0.7236 (mmm160) REVERT: Z 207 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8019 (mt0) outliers start: 48 outliers final: 17 residues processed: 348 average time/residue: 0.7483 time to fit residues: 298.5844 Evaluate side-chains 316 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 293 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 67 CYS Chi-restraints excluded: chain W residue 73 PHE Chi-restraints excluded: chain X residue 68 CYS Chi-restraints excluded: chain X residue 203 ASP Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain Z residue 207 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 28 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 270 optimal weight: 7.9990 chunk 246 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 256 optimal weight: 0.9980 chunk 269 optimal weight: 0.8980 chunk 307 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 HIS ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN C 591 GLN X 205 HIS X 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.068472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.052406 restraints weight = 169623.902| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.35 r_work: 0.2738 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30319 Z= 0.133 Angle : 0.491 10.848 41033 Z= 0.261 Chirality : 0.040 0.191 4551 Planarity : 0.004 0.052 5149 Dihedral : 3.728 17.326 4086 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.29 % Allowed : 13.38 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.14), residues: 3669 helix: 2.85 (0.11), residues: 1995 sheet: -0.94 (0.24), residues: 448 loop : -0.48 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 14 TYR 0.019 0.001 TYR W 174 PHE 0.014 0.001 PHE A 377 TRP 0.023 0.001 TRP B 259 HIS 0.005 0.001 HIS C 211 Details of bonding type rmsd covalent geometry : bond 0.00312 (30311) covalent geometry : angle 0.49051 (41017) SS BOND : bond 0.00263 ( 8) SS BOND : angle 1.21563 ( 16) hydrogen bonds : bond 0.03891 ( 1715) hydrogen bonds : angle 3.69808 ( 4978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 302 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8757 (mmm) cc_final: 0.8528 (mtp) REVERT: A 181 MET cc_start: 0.9107 (mmt) cc_final: 0.8897 (mmt) REVERT: A 574 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8512 (mm-30) REVERT: A 688 LYS cc_start: 0.8918 (mptt) cc_final: 0.8649 (mppt) REVERT: A 823 ARG cc_start: 0.7938 (ttt90) cc_final: 0.7581 (tpp-160) REVERT: B 181 MET cc_start: 0.9050 (mmm) cc_final: 0.8794 (mmp) REVERT: B 259 TRP cc_start: 0.9219 (OUTLIER) cc_final: 0.8838 (t-100) REVERT: B 264 GLU cc_start: 0.8368 (tp30) cc_final: 0.7990 (tm-30) REVERT: B 633 MET cc_start: 0.8451 (tpp) cc_final: 0.8227 (ttt) REVERT: C 78 ASP cc_start: 0.8783 (m-30) cc_final: 0.8512 (m-30) REVERT: C 258 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8390 (mtt90) REVERT: C 641 GLU cc_start: 0.8353 (mp0) cc_final: 0.8077 (mp0) REVERT: D 147 GLN cc_start: 0.8615 (mt0) cc_final: 0.8350 (tt0) REVERT: D 359 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8075 (pt0) REVERT: D 725 MET cc_start: 0.8991 (ptm) cc_final: 0.8719 (ptt) REVERT: W 131 ARG cc_start: 0.8289 (mtt180) cc_final: 0.7385 (mmm160) REVERT: W 207 GLN cc_start: 0.8515 (tp40) cc_final: 0.8314 (mt0) REVERT: X 78 LYS cc_start: 0.5858 (mptt) cc_final: 0.5655 (pttt) REVERT: X 129 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8530 (mtmt) REVERT: X 131 ARG cc_start: 0.8758 (mtp85) cc_final: 0.7694 (mmm160) REVERT: Y 204 ARG cc_start: 0.8450 (mtt-85) cc_final: 0.8212 (mtp85) REVERT: Z 9 GLN cc_start: 0.8230 (mt0) cc_final: 0.7910 (mt0) REVERT: Z 131 ARG cc_start: 0.8221 (mtt180) cc_final: 0.7193 (mmm160) REVERT: Z 207 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7996 (mt0) outliers start: 37 outliers final: 18 residues processed: 329 average time/residue: 0.8764 time to fit residues: 329.1286 Evaluate side-chains 314 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 293 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 259 TRP Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 67 CYS Chi-restraints excluded: chain W residue 79 GLN Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 207 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 200 optimal weight: 0.7980 chunk 339 optimal weight: 3.9990 chunk 359 optimal weight: 6.9990 chunk 257 optimal weight: 0.0670 chunk 148 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 351 optimal weight: 1.9990 chunk 346 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN X 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.068107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.052224 restraints weight = 159304.435| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.27 r_work: 0.2732 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30319 Z= 0.136 Angle : 0.489 8.300 41033 Z= 0.259 Chirality : 0.039 0.158 4551 Planarity : 0.004 0.061 5149 Dihedral : 3.643 16.642 4086 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.29 % Allowed : 13.80 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.14), residues: 3669 helix: 2.88 (0.11), residues: 2002 sheet: -0.88 (0.24), residues: 448 loop : -0.51 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 14 TYR 0.020 0.001 TYR W 174 PHE 0.015 0.001 PHE C 62 TRP 0.022 0.001 TRP B 259 HIS 0.005 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00321 (30311) covalent geometry : angle 0.48814 (41017) SS BOND : bond 0.00246 ( 8) SS BOND : angle 1.08044 ( 16) hydrogen bonds : bond 0.03861 ( 1715) hydrogen bonds : angle 3.66423 ( 4978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 306 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 688 LYS cc_start: 0.8940 (mptt) cc_final: 0.8719 (mppt) REVERT: A 823 ARG cc_start: 0.7970 (ttt90) cc_final: 0.7597 (tpp-160) REVERT: A 827 LYS cc_start: 0.7712 (mttt) cc_final: 0.7384 (mptm) REVERT: B 181 MET cc_start: 0.9027 (mmm) cc_final: 0.8779 (mmp) REVERT: B 259 TRP cc_start: 0.9198 (OUTLIER) cc_final: 0.8810 (t-100) REVERT: B 264 GLU cc_start: 0.8414 (tp30) cc_final: 0.8076 (tm-30) REVERT: B 633 MET cc_start: 0.8433 (tpp) cc_final: 0.8114 (ttt) REVERT: C 78 ASP cc_start: 0.8689 (m-30) cc_final: 0.8452 (m-30) REVERT: C 258 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8428 (mtt90) REVERT: C 295 TYR cc_start: 0.8698 (t80) cc_final: 0.8286 (t80) REVERT: C 313 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8366 (mp) REVERT: C 641 GLU cc_start: 0.8350 (mp0) cc_final: 0.8079 (mp0) REVERT: C 647 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8923 (m) REVERT: C 811 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8694 (mtm) REVERT: D 147 GLN cc_start: 0.8640 (mt0) cc_final: 0.8369 (tt0) REVERT: D 359 GLU cc_start: 0.8584 (mt-10) cc_final: 0.7966 (pt0) REVERT: W 73 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6099 (p90) REVERT: W 131 ARG cc_start: 0.8347 (mtt180) cc_final: 0.7494 (mmm160) REVERT: X 31 ASP cc_start: 0.8517 (m-30) cc_final: 0.8299 (m-30) REVERT: X 129 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8591 (mtmt) REVERT: X 131 ARG cc_start: 0.8791 (mtp85) cc_final: 0.7638 (mmm160) REVERT: Z 9 GLN cc_start: 0.8171 (mt0) cc_final: 0.7860 (mt0) REVERT: Z 131 ARG cc_start: 0.8216 (mtt180) cc_final: 0.7159 (mmm160) REVERT: Z 207 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8074 (mt0) outliers start: 38 outliers final: 18 residues processed: 332 average time/residue: 0.8741 time to fit residues: 331.7432 Evaluate side-chains 316 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 291 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain B residue 259 TRP Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 811 MET Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 67 CYS Chi-restraints excluded: chain W residue 73 PHE Chi-restraints excluded: chain W residue 79 GLN Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 207 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 7.9990 chunk 320 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 333 optimal weight: 7.9990 chunk 355 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 HIS ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN X 160 ASN X 207 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.066154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.050314 restraints weight = 175619.599| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.30 r_work: 0.2674 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 30319 Z= 0.244 Angle : 0.566 8.703 41033 Z= 0.300 Chirality : 0.043 0.165 4551 Planarity : 0.004 0.065 5149 Dihedral : 3.943 19.201 4086 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.52 % Allowed : 13.99 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.14), residues: 3669 helix: 2.65 (0.11), residues: 2005 sheet: -1.02 (0.23), residues: 449 loop : -0.60 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 14 TYR 0.021 0.002 TYR Y 174 PHE 0.022 0.002 PHE A 497 TRP 0.028 0.002 TRP B 259 HIS 0.012 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00586 (30311) covalent geometry : angle 0.56549 (41017) SS BOND : bond 0.00340 ( 8) SS BOND : angle 1.30116 ( 16) hydrogen bonds : bond 0.04695 ( 1715) hydrogen bonds : angle 3.87528 ( 4978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 688 LYS cc_start: 0.9078 (mptt) cc_final: 0.8774 (mppt) REVERT: A 823 ARG cc_start: 0.8014 (ttt90) cc_final: 0.7645 (tpp-160) REVERT: A 827 LYS cc_start: 0.7813 (mttt) cc_final: 0.7502 (mptt) REVERT: B 181 MET cc_start: 0.9053 (mmm) cc_final: 0.8841 (mmp) REVERT: B 264 GLU cc_start: 0.8370 (tp30) cc_final: 0.8018 (tm-30) REVERT: C 78 ASP cc_start: 0.8770 (m-30) cc_final: 0.8511 (m-30) REVERT: C 641 GLU cc_start: 0.8436 (mp0) cc_final: 0.8153 (mp0) REVERT: C 664 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8576 (ttp80) REVERT: D 147 GLN cc_start: 0.8676 (mt0) cc_final: 0.8383 (tt0) REVERT: D 264 GLU cc_start: 0.8140 (tp30) cc_final: 0.7579 (tp30) REVERT: D 359 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8106 (pt0) REVERT: W 73 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.6145 (p90) REVERT: W 131 ARG cc_start: 0.8322 (mtt180) cc_final: 0.7517 (mmm160) REVERT: X 129 LYS cc_start: 0.9025 (mtpt) cc_final: 0.8696 (mtmt) REVERT: X 131 ARG cc_start: 0.8840 (mtp85) cc_final: 0.7623 (mmm160) REVERT: Z 9 GLN cc_start: 0.8314 (mt0) cc_final: 0.7978 (mt0) REVERT: Z 131 ARG cc_start: 0.8314 (mtt180) cc_final: 0.7313 (mmm160) REVERT: Z 207 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7983 (mp10) outliers start: 44 outliers final: 21 residues processed: 321 average time/residue: 0.8376 time to fit residues: 306.1318 Evaluate side-chains 305 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 281 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 664 ARG Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 67 CYS Chi-restraints excluded: chain W residue 73 PHE Chi-restraints excluded: chain X residue 68 CYS Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain Z residue 207 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 106 optimal weight: 0.9990 chunk 344 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 275 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 chunk 368 optimal weight: 0.6980 chunk 160 optimal weight: 0.5980 chunk 256 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 HIS ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN Z 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.067484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.051766 restraints weight = 161775.956| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.22 r_work: 0.2729 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.6397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30319 Z= 0.117 Angle : 0.491 10.254 41033 Z= 0.262 Chirality : 0.039 0.162 4551 Planarity : 0.004 0.060 5149 Dihedral : 3.692 17.446 4086 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.77 % Allowed : 14.96 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.14), residues: 3669 helix: 2.90 (0.11), residues: 2004 sheet: -0.92 (0.23), residues: 451 loop : -0.53 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 14 TYR 0.020 0.001 TYR W 174 PHE 0.013 0.001 PHE C 62 TRP 0.021 0.001 TRP A 259 HIS 0.005 0.001 HIS Y 205 Details of bonding type rmsd covalent geometry : bond 0.00268 (30311) covalent geometry : angle 0.49089 (41017) SS BOND : bond 0.00206 ( 8) SS BOND : angle 1.13951 ( 16) hydrogen bonds : bond 0.03825 ( 1715) hydrogen bonds : angle 3.68739 ( 4978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 300 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.8568 (ttp) cc_final: 0.8338 (mtp) REVERT: A 452 TYR cc_start: 0.7887 (m-10) cc_final: 0.7676 (m-10) REVERT: A 688 LYS cc_start: 0.9091 (mptt) cc_final: 0.8829 (mppt) REVERT: A 823 ARG cc_start: 0.7996 (ttt90) cc_final: 0.7645 (tpp-160) REVERT: A 827 LYS cc_start: 0.7773 (mttt) cc_final: 0.7406 (mptm) REVERT: B 181 MET cc_start: 0.9050 (mmm) cc_final: 0.8816 (mmp) REVERT: B 264 GLU cc_start: 0.8342 (tp30) cc_final: 0.8028 (tm-30) REVERT: C 78 ASP cc_start: 0.8681 (m-30) cc_final: 0.8444 (m-30) REVERT: C 634 VAL cc_start: 0.9017 (p) cc_final: 0.8587 (m) REVERT: C 641 GLU cc_start: 0.8414 (mp0) cc_final: 0.8110 (mp0) REVERT: D 147 GLN cc_start: 0.8624 (mt0) cc_final: 0.8347 (tt0) REVERT: D 264 GLU cc_start: 0.7965 (tp30) cc_final: 0.7497 (tp30) REVERT: D 359 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8098 (pt0) REVERT: W 73 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6131 (p90) REVERT: W 131 ARG cc_start: 0.8373 (mtt180) cc_final: 0.7577 (mmm160) REVERT: X 31 ASP cc_start: 0.8518 (m-30) cc_final: 0.8101 (m-30) REVERT: X 129 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8685 (mtmt) REVERT: X 131 ARG cc_start: 0.8882 (mtp85) cc_final: 0.7681 (mmm160) REVERT: Z 9 GLN cc_start: 0.8176 (mt0) cc_final: 0.7862 (mt0) REVERT: Z 131 ARG cc_start: 0.8243 (mtt180) cc_final: 0.7220 (mmm160) REVERT: Z 207 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8020 (mp10) outliers start: 22 outliers final: 11 residues processed: 315 average time/residue: 0.9416 time to fit residues: 336.5593 Evaluate side-chains 303 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 290 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 67 CYS Chi-restraints excluded: chain W residue 73 PHE Chi-restraints excluded: chain Y residue 59 THR Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 207 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 169 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 170 optimal weight: 0.1980 chunk 25 optimal weight: 0.0980 chunk 231 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 61 optimal weight: 0.0040 chunk 236 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 HIS ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN X 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.068253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.052587 restraints weight = 169598.226| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.27 r_work: 0.2754 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.6455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30319 Z= 0.105 Angle : 0.469 9.753 41033 Z= 0.251 Chirality : 0.039 0.172 4551 Planarity : 0.004 0.061 5149 Dihedral : 3.496 16.668 4086 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.58 % Allowed : 15.22 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.14), residues: 3669 helix: 3.01 (0.11), residues: 2000 sheet: -0.84 (0.24), residues: 437 loop : -0.53 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 14 TYR 0.024 0.001 TYR D 677 PHE 0.011 0.001 PHE C 62 TRP 0.020 0.001 TRP B 259 HIS 0.005 0.001 HIS Y 205 Details of bonding type rmsd covalent geometry : bond 0.00239 (30311) covalent geometry : angle 0.46897 (41017) SS BOND : bond 0.00137 ( 8) SS BOND : angle 0.76381 ( 16) hydrogen bonds : bond 0.03499 ( 1715) hydrogen bonds : angle 3.57751 ( 4978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 301 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 688 LYS cc_start: 0.9115 (mptt) cc_final: 0.8862 (mppt) REVERT: A 740 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8547 (m) REVERT: A 823 ARG cc_start: 0.8000 (ttt90) cc_final: 0.7651 (tpp-160) REVERT: A 827 LYS cc_start: 0.7781 (mttt) cc_final: 0.7428 (mptm) REVERT: B 264 GLU cc_start: 0.8295 (tp30) cc_final: 0.8055 (tm-30) REVERT: C 78 ASP cc_start: 0.8661 (m-30) cc_final: 0.8015 (m-30) REVERT: C 641 GLU cc_start: 0.8386 (mp0) cc_final: 0.8083 (mp0) REVERT: D 147 GLN cc_start: 0.8614 (mt0) cc_final: 0.8357 (tt0) REVERT: D 359 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8146 (pt0) REVERT: W 31 ASP cc_start: 0.8329 (m-30) cc_final: 0.8092 (m-30) REVERT: W 65 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.7873 (mtm-85) REVERT: W 73 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.6102 (p90) REVERT: W 130 THR cc_start: 0.8822 (m) cc_final: 0.8541 (t) REVERT: W 131 ARG cc_start: 0.8379 (mtt180) cc_final: 0.7494 (mmm160) REVERT: X 31 ASP cc_start: 0.8459 (m-30) cc_final: 0.8193 (m-30) REVERT: X 129 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8643 (mtmt) REVERT: X 131 ARG cc_start: 0.8893 (mtp85) cc_final: 0.7677 (mmm160) REVERT: Z 9 GLN cc_start: 0.8199 (mt0) cc_final: 0.7898 (mt0) REVERT: Z 131 ARG cc_start: 0.8242 (mtt180) cc_final: 0.7206 (mmm160) REVERT: Z 207 GLN cc_start: 0.8367 (tp40) cc_final: 0.8139 (mt0) outliers start: 16 outliers final: 8 residues processed: 316 average time/residue: 0.8997 time to fit residues: 323.8690 Evaluate side-chains 299 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 289 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 73 PHE Chi-restraints excluded: chain Y residue 59 THR Chi-restraints excluded: chain Z residue 8 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 126 optimal weight: 0.0170 chunk 285 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 346 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 312 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 337 optimal weight: 0.6980 chunk 218 optimal weight: 0.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 HIS ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN C 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.068107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.052259 restraints weight = 172455.971| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.32 r_work: 0.2741 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30319 Z= 0.118 Angle : 0.480 11.985 41033 Z= 0.254 Chirality : 0.039 0.175 4551 Planarity : 0.004 0.064 5149 Dihedral : 3.477 16.772 4086 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.71 % Allowed : 15.47 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.14), residues: 3669 helix: 3.01 (0.11), residues: 2007 sheet: -0.79 (0.24), residues: 438 loop : -0.53 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 14 TYR 0.014 0.001 TYR W 128 PHE 0.020 0.001 PHE D 686 TRP 0.021 0.001 TRP B 259 HIS 0.004 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00278 (30311) covalent geometry : angle 0.47927 (41017) SS BOND : bond 0.00125 ( 8) SS BOND : angle 1.20589 ( 16) hydrogen bonds : bond 0.03568 ( 1715) hydrogen bonds : angle 3.57624 ( 4978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11464.54 seconds wall clock time: 195 minutes 54.98 seconds (11754.98 seconds total)