Starting phenix.real_space_refine on Thu Mar 5 19:52:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wae_32383/03_2026/7wae_32383.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wae_32383/03_2026/7wae_32383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wae_32383/03_2026/7wae_32383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wae_32383/03_2026/7wae_32383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wae_32383/03_2026/7wae_32383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wae_32383/03_2026/7wae_32383.map" } resolution = 2.64 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= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 11 5.21 5 S 88 5.16 5 C 15578 2.51 5 N 4357 2.21 5 O 4792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24850 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 877, 6683 Classifications: {'peptide': 877} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 841} Chain: "B" Number of atoms: 6683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 877, 6683 Classifications: {'peptide': 877} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 841} Chain: "C" Number of atoms: 5510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5510 Classifications: {'peptide': 724} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 695} Chain: "D" Number of atoms: 5510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5510 Classifications: {'peptide': 724} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 695} Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 3, 'ASP%COO:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 3, 'ASP%COO:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 3, 'ASP%COO:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 3, 'ASP%COO:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'AGS': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'AGS': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 74 Unusual residues: {' MG': 3, 'AGS': 2} Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Chain: "J" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "K" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "M" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Time building chain proxies: 5.70, per 1000 atoms: 0.23 Number of scatterers: 24850 At special positions: 0 Unit cell: (165.17, 164.34, 125.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 24 15.00 Mg 11 11.99 O 4792 8.00 N 4357 7.00 C 15578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ASP_CG-ANY_N " ASP J 3 " - " ARG J 101 " " ASP J 5 " - " ARG J 102 " " ASP K 3 " - " ARG K 101 " " ASP K 5 " - " ARG K 102 " " ASP L 3 " - " ARG L 101 " " ASP L 5 " - " ARG L 102 " " ASP M 3 " - " ARG M 101 " " ASP M 5 " - " ARG M 102 " Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5814 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 26 sheets defined 43.5% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 76 through 92 removed outlier: 3.773A pdb=" N VAL A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 140 removed outlier: 3.863A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 164 through 177 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 219 through 230 Processing helix chain 'A' and resid 244 through 254 removed outlier: 4.509A pdb=" N ASP A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.786A pdb=" N ALA A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 4.618A pdb=" N GLU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.917A pdb=" N ILE A 408 " --> pdb=" O THR A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 409 through 424 Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 498 through 513 removed outlier: 3.677A pdb=" N THR A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 548 removed outlier: 4.192A pdb=" N LEU A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 removed outlier: 3.525A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 608 removed outlier: 3.831A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 627 removed outlier: 3.585A pdb=" N MET A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 682 through 686 Processing helix chain 'A' and resid 690 through 707 removed outlier: 3.676A pdb=" N GLN A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 721 Processing helix chain 'A' and resid 749 through 761 removed outlier: 3.575A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 793 Processing helix chain 'A' and resid 810 through 826 Processing helix chain 'A' and resid 841 through 852 Processing helix chain 'A' and resid 865 through 876 removed outlier: 3.846A pdb=" N ALA A 869 " --> pdb=" O SER A 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 76 through 92 removed outlier: 3.722A pdb=" N VAL B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 140 removed outlier: 3.827A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 164 through 177 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'B' and resid 219 through 230 Processing helix chain 'B' and resid 244 through 254 removed outlier: 4.583A pdb=" N ASP B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.653A pdb=" N ALA B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 345 removed outlier: 4.520A pdb=" N GLU B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 373 Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.905A pdb=" N ILE B 408 " --> pdb=" O THR B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 409 through 424 Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 498 through 513 removed outlier: 3.703A pdb=" N THR B 513 " --> pdb=" O ILE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 548 removed outlier: 4.206A pdb=" N LEU B 545 " --> pdb=" O GLN B 541 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 546 " --> pdb=" O SER B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.514A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 608 removed outlier: 3.786A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 627 through 629 No H-bonds generated for 'chain 'B' and resid 627 through 629' Processing helix chain 'B' and resid 644 through 653 Processing helix chain 'B' and resid 682 through 686 Processing helix chain 'B' and resid 690 through 707 removed outlier: 3.644A pdb=" N GLN B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 721 Processing helix chain 'B' and resid 749 through 761 removed outlier: 3.610A pdb=" N PHE B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 793 Processing helix chain 'B' and resid 810 through 826 Processing helix chain 'B' and resid 841 through 852 Processing helix chain 'B' and resid 865 through 876 removed outlier: 3.880A pdb=" N ALA B 869 " --> pdb=" O SER B 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 65 through 74 Processing helix chain 'C' and resid 76 through 92 removed outlier: 3.922A pdb=" N VAL C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 140 removed outlier: 3.809A pdb=" N VAL C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 Processing helix chain 'C' and resid 164 through 177 Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'C' and resid 219 through 230 Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 245 through 254 removed outlier: 3.500A pdb=" N VAL C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 Processing helix chain 'C' and resid 335 through 345 removed outlier: 4.704A pdb=" N GLU C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 374 removed outlier: 3.996A pdb=" N GLY C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 384 removed outlier: 3.897A pdb=" N GLY C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 381 through 384' Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.831A pdb=" N ILE C 408 " --> pdb=" O THR C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 409 through 424 Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 498 through 513 removed outlier: 4.113A pdb=" N THR C 513 " --> pdb=" O ILE C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 548 removed outlier: 4.128A pdb=" N LEU C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 568 removed outlier: 3.560A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 608 removed outlier: 3.780A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 627 through 629 No H-bonds generated for 'chain 'C' and resid 627 through 629' Processing helix chain 'C' and resid 644 through 653 Processing helix chain 'C' and resid 682 through 686 Processing helix chain 'C' and resid 690 through 707 removed outlier: 3.652A pdb=" N GLN C 707 " --> pdb=" O ALA C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 721 Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'D' and resid 52 through 57 removed outlier: 3.790A pdb=" N GLU D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 76 through 92 removed outlier: 3.933A pdb=" N VAL D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 140 removed outlier: 3.780A pdb=" N VAL D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 161 Processing helix chain 'D' and resid 164 through 177 Processing helix chain 'D' and resid 194 through 198 Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'D' and resid 219 through 230 Processing helix chain 'D' and resid 245 through 254 removed outlier: 3.644A pdb=" N VAL D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY D 254 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 Processing helix chain 'D' and resid 335 through 345 removed outlier: 4.679A pdb=" N GLU D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN D 344 " --> pdb=" O ILE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 374 removed outlier: 3.982A pdb=" N GLY D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 384 removed outlier: 3.829A pdb=" N GLY D 384 " --> pdb=" O PRO D 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 381 through 384' Processing helix chain 'D' and resid 405 through 408 removed outlier: 3.860A pdb=" N ILE D 408 " --> pdb=" O THR D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 405 through 408' Processing helix chain 'D' and resid 409 through 424 Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 498 through 513 removed outlier: 4.072A pdb=" N THR D 513 " --> pdb=" O ILE D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 548 removed outlier: 4.211A pdb=" N LEU D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 568 removed outlier: 3.528A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 608 removed outlier: 3.773A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 626 Processing helix chain 'D' and resid 627 through 629 No H-bonds generated for 'chain 'D' and resid 627 through 629' Processing helix chain 'D' and resid 644 through 653 Processing helix chain 'D' and resid 682 through 686 Processing helix chain 'D' and resid 690 through 707 removed outlier: 3.655A pdb=" N GLN D 707 " --> pdb=" O ALA D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 721 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 9 removed outlier: 5.925A pdb=" N ILE A 3 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP A 28 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 5 " --> pdb=" O ARG A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 240 Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 403 removed outlier: 5.270A pdb=" N VAL A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 313 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 319 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP A 307 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 450 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A 433 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 534 removed outlier: 6.721A pdb=" N THR A 525 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE A 490 " --> pdb=" O CYS A 574 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLU A 575 " --> pdb=" O LYS A 612 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 618 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN A 634 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY A 613 " --> pdb=" O GLN A 634 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ALA A 636 " --> pdb=" O GLY A 613 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ALA A 615 " --> pdb=" O ALA A 636 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE A 638 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 617 " --> pdb=" O PHE A 638 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N ALA A 658 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR A 637 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N TYR A 660 " --> pdb=" O TYR A 637 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N SER A 639 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A 665 " --> pdb=" O ILE A 676 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 733 through 736 removed outlier: 3.514A pdb=" N ASN A 733 " --> pdb=" O VAL A 744 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 768 " --> pdb=" O VAL A 860 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2 through 9 removed outlier: 5.912A pdb=" N ILE B 3 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP B 28 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS B 5 " --> pdb=" O ARG B 26 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 237 through 240 removed outlier: 7.008A pdb=" N ILE B 258 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP B 274 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 260 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 400 through 403 removed outlier: 5.262A pdb=" N VAL B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 313 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 319 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP B 307 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ILE B 427 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA B 453 " --> pdb=" O ILE B 427 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY B 429 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL B 451 " --> pdb=" O GLY B 429 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP B 431 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AB4, first strand: chain 'B' and resid 530 through 534 removed outlier: 6.532A pdb=" N THR B 525 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 490 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE B 578 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER B 492 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLU B 575 " --> pdb=" O LYS B 612 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN B 618 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLN B 634 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY B 613 " --> pdb=" O GLN B 634 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA B 636 " --> pdb=" O GLY B 613 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ALA B 615 " --> pdb=" O ALA B 636 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N PHE B 638 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU B 617 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ALA B 658 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR B 637 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TYR B 660 " --> pdb=" O TYR B 637 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N SER B 639 " --> pdb=" O TYR B 660 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 665 " --> pdb=" O ILE B 676 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 733 through 736 removed outlier: 3.626A pdb=" N ASN B 733 " --> pdb=" O VAL B 744 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 744 " --> pdb=" O ASN B 733 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 768 " --> pdb=" O VAL B 860 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 2 through 9 removed outlier: 5.899A pdb=" N ILE C 3 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASP C 28 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 5 " --> pdb=" O ARG C 26 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'C' and resid 237 through 240 removed outlier: 3.575A pdb=" N VAL C 297 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE C 258 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP C 274 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 400 through 403 removed outlier: 5.259A pdb=" N VAL C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL C 313 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 319 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP C 307 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU C 450 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C 433 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE C 448 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AC2, first strand: chain 'C' and resid 530 through 534 removed outlier: 6.685A pdb=" N THR C 525 " --> pdb=" O ALA C 532 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 490 " --> pdb=" O CYS C 574 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLU C 575 " --> pdb=" O LYS C 612 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 618 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN C 634 " --> pdb=" O PRO C 611 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY C 613 " --> pdb=" O GLN C 634 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA C 636 " --> pdb=" O GLY C 613 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA C 615 " --> pdb=" O ALA C 636 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE C 638 " --> pdb=" O ALA C 615 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU C 617 " --> pdb=" O PHE C 638 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ALA C 658 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR C 637 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N TYR C 660 " --> pdb=" O TYR C 637 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N SER C 639 " --> pdb=" O TYR C 660 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 665 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 2 through 9 removed outlier: 6.054A pdb=" N ILE D 3 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASP D 28 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS D 5 " --> pdb=" O ARG D 26 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AC5, first strand: chain 'D' and resid 237 through 240 removed outlier: 7.002A pdb=" N ILE D 258 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP D 274 " --> pdb=" O ILE D 258 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 400 through 403 removed outlier: 5.272A pdb=" N VAL D 317 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL D 313 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP D 307 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 450 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL D 433 " --> pdb=" O ILE D 448 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE D 448 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AC8, first strand: chain 'D' and resid 530 through 534 removed outlier: 5.314A pdb=" N LEU D 531 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE D 527 " --> pdb=" O LEU D 531 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE D 490 " --> pdb=" O CYS D 574 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLU D 575 " --> pdb=" O LYS D 612 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN D 618 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR D 660 " --> pdb=" O SER D 639 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE D 665 " --> pdb=" O ILE D 676 " (cutoff:3.500A) 1198 hydrogen bonds defined for protein. 3387 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: 5.57 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 8507 1.37 - 1.51: 7081 1.51 - 1.66: 9514 1.66 - 1.80: 123 1.80 - 1.95: 19 Bond restraints: 25244 Sorted by residual: bond pdb=" N ASN D 394 " pdb=" CA ASN D 394 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.64e+00 bond pdb=" N LYS D 220 " pdb=" CA LYS D 220 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.32e+00 bond pdb=" N LYS B 220 " pdb=" CA LYS B 220 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.20e-02 6.94e+03 6.00e+00 bond pdb=" N ARG A 458 " pdb=" CA ARG A 458 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.77e+00 bond pdb=" N ARG D 458 " pdb=" CA ARG D 458 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.30e-02 5.92e+03 5.36e+00 ... (remaining 25239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 33531 1.63 - 3.25: 614 3.25 - 4.88: 94 4.88 - 6.50: 13 6.50 - 8.13: 12 Bond angle restraints: 34264 Sorted by residual: angle pdb=" N GLU D 72 " pdb=" CA GLU D 72 " pdb=" CB GLU D 72 " ideal model delta sigma weight residual 110.12 115.79 -5.67 1.47e+00 4.63e-01 1.49e+01 angle pdb=" CA ASP K 3 " pdb=" CB ASP K 3 " pdb=" CG ASP K 3 " ideal model delta sigma weight residual 112.60 108.75 3.85 1.00e+00 1.00e+00 1.48e+01 angle pdb=" CA ASP M 3 " pdb=" CB ASP M 3 " pdb=" CG ASP M 3 " ideal model delta sigma weight residual 112.60 108.84 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CA ASP L 3 " pdb=" CB ASP L 3 " pdb=" CG ASP L 3 " ideal model delta sigma weight residual 112.60 108.95 3.65 1.00e+00 1.00e+00 1.33e+01 angle pdb=" CA ASP J 5 " pdb=" CB ASP J 5 " pdb=" CG ASP J 5 " ideal model delta sigma weight residual 112.60 109.30 3.30 1.00e+00 1.00e+00 1.09e+01 ... (remaining 34259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 13855 17.63 - 35.27: 1095 35.27 - 52.90: 227 52.90 - 70.53: 58 70.53 - 88.16: 22 Dihedral angle restraints: 15257 sinusoidal: 6129 harmonic: 9128 Sorted by residual: dihedral pdb=" CA THR C 496 " pdb=" C THR C 496 " pdb=" N ASN C 497 " pdb=" CA ASN C 497 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA THR D 496 " pdb=" C THR D 496 " pdb=" N ASN D 497 " pdb=" CA ASN D 497 " ideal model delta harmonic sigma weight residual -180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR B 660 " pdb=" C TYR B 660 " pdb=" N GLU B 661 " pdb=" CA GLU B 661 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 15254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2487 0.033 - 0.065: 927 0.065 - 0.098: 340 0.098 - 0.130: 223 0.130 - 0.163: 20 Chirality restraints: 3997 Sorted by residual: chirality pdb=" CA ASP J 2 " pdb=" N ASP J 2 " pdb=" C ASP J 2 " pdb=" CB ASP J 2 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CB ILE B 271 " pdb=" CA ILE B 271 " pdb=" CG1 ILE B 271 " pdb=" CG2 ILE B 271 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA ILE D 260 " pdb=" N ILE D 260 " pdb=" C ILE D 260 " pdb=" CB ILE D 260 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 3994 not shown) Planarity restraints: 4406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 458 " -0.231 9.50e-02 1.11e+02 1.04e-01 7.01e+00 pdb=" NE ARG B 458 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 458 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 458 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 458 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 60 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO C 61 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 60 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO D 61 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 61 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 61 " -0.030 5.00e-02 4.00e+02 ... (remaining 4403 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 198 2.57 - 3.15: 19940 3.15 - 3.73: 38665 3.73 - 4.32: 54154 4.32 - 4.90: 91118 Nonbonded interactions: 204075 Sorted by model distance: nonbonded pdb="MG MG D1003 " pdb=" O2B AGS D1005 " model vdw 1.987 2.170 nonbonded pdb="MG MG A1002 " pdb=" O2B AGS A1004 " model vdw 1.999 2.170 nonbonded pdb="MG MG B1003 " pdb=" O2B AGS B1005 " model vdw 2.009 2.170 nonbonded pdb=" OG1 THR B 522 " pdb="MG MG B1003 " model vdw 2.013 2.170 nonbonded pdb=" OG1 THR A 500 " pdb="MG MG A1002 " model vdw 2.015 2.170 ... (remaining 204070 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 1 through 1002 or resid 1004)) selection = (chain 'B' and (resid 1 through 1002 or resid 1004)) } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 1 through 1005) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.630 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.003 0.041 25252 Z= 0.161 Angle : 0.562 8.131 34288 Z= 0.303 Chirality : 0.045 0.163 3997 Planarity : 0.004 0.104 4398 Dihedral : 13.863 88.165 9419 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.60 % Rotamer: Outliers : 0.27 % Allowed : 0.42 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 0.26 (0.15), residues: 3202 helix: 1.56 (0.15), residues: 1242 sheet: 0.04 (0.24), residues: 480 loop : -0.99 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 458 TYR 0.015 0.001 TYR A 252 PHE 0.009 0.001 PHE D 480 TRP 0.027 0.001 TRP C 278 HIS 0.009 0.001 HIS B 586 Details of bonding type rmsd covalent geometry : bond 0.00320 (25244) covalent geometry : angle 0.56199 (34264) hydrogen bonds : bond 0.15288 ( 1198) hydrogen bonds : angle 6.07915 ( 3387) link_ASP_CG-ANY_N : bond 0.01136 ( 8) link_ASP_CG-ANY_N : angle 0.90841 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 224 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 269 ARG cc_start: 0.5725 (ptt-90) cc_final: 0.5356 (pmt170) REVERT: C 160 GLN cc_start: 0.8274 (tt0) cc_final: 0.8070 (tm-30) REVERT: C 168 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7764 (mm-30) REVERT: D 1006 ASP cc_start: 0.5787 (OUTLIER) cc_final: 0.5507 (m-30) REVERT: J 102 ARG cc_start: 0.6361 (OUTLIER) cc_final: 0.5379 (ttt-90) REVERT: K 102 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6120 (ttt-90) REVERT: M 102 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6542 (ttm-80) outliers start: 7 outliers final: 2 residues processed: 231 average time/residue: 0.7066 time to fit residues: 185.5890 Evaluate side-chains 161 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 1006 ASP Chi-restraints excluded: chain J residue 102 ARG Chi-restraints excluded: chain K residue 102 ARG Chi-restraints excluded: chain M residue 102 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 247 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.150168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.092502 restraints weight = 39000.609| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.63 r_work: 0.2975 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25252 Z= 0.124 Angle : 0.521 6.272 34288 Z= 0.275 Chirality : 0.045 0.153 3997 Planarity : 0.004 0.053 4398 Dihedral : 8.386 72.991 3675 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.81 % Favored : 96.16 % Rotamer: Outliers : 1.34 % Allowed : 7.07 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 0.32 (0.15), residues: 3202 helix: 1.62 (0.15), residues: 1294 sheet: 0.08 (0.24), residues: 454 loop : -1.06 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 458 TYR 0.018 0.001 TYR A 14 PHE 0.009 0.001 PHE B 638 TRP 0.013 0.001 TRP D 278 HIS 0.006 0.001 HIS C 327 Details of bonding type rmsd covalent geometry : bond 0.00270 (25244) covalent geometry : angle 0.52083 (34264) hydrogen bonds : bond 0.03896 ( 1198) hydrogen bonds : angle 4.78910 ( 3387) link_ASP_CG-ANY_N : bond 0.00218 ( 8) link_ASP_CG-ANY_N : angle 0.73904 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.789 Fit side-chains REVERT: A 25 MET cc_start: 0.8498 (ptt) cc_final: 0.8272 (ptm) REVERT: A 35 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7795 (tmtt) REVERT: A 118 ASN cc_start: 0.7152 (t0) cc_final: 0.6829 (t0) REVERT: A 172 LYS cc_start: 0.9095 (mmtp) cc_final: 0.8885 (mttt) REVERT: A 269 ARG cc_start: 0.5263 (ptt-90) cc_final: 0.4880 (pmt170) REVERT: A 586 HIS cc_start: 0.6778 (OUTLIER) cc_final: 0.6038 (m90) REVERT: B 33 TYR cc_start: 0.6847 (t80) cc_final: 0.6634 (t80) REVERT: C 131 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6269 (ptp-170) REVERT: C 160 GLN cc_start: 0.8859 (tt0) cc_final: 0.8314 (tm-30) REVERT: C 168 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8562 (mm-30) REVERT: C 247 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6812 (mp10) REVERT: C 278 TRP cc_start: 0.6751 (OUTLIER) cc_final: 0.5844 (m100) REVERT: C 586 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7644 (t-90) REVERT: D 586 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.8236 (t-90) outliers start: 35 outliers final: 8 residues processed: 184 average time/residue: 0.5910 time to fit residues: 126.5516 Evaluate side-chains 162 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 586 HIS Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 586 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 198 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 184 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 273 optimal weight: 7.9990 chunk 263 optimal weight: 0.7980 chunk 203 optimal weight: 7.9990 chunk 229 optimal weight: 0.6980 chunk 297 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.148163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.090359 restraints weight = 39109.752| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.60 r_work: 0.2926 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25252 Z= 0.180 Angle : 0.537 7.016 34288 Z= 0.283 Chirality : 0.046 0.198 3997 Planarity : 0.004 0.049 4398 Dihedral : 8.208 81.126 3657 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 1.64 % Allowed : 9.25 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 0.31 (0.15), residues: 3202 helix: 1.64 (0.15), residues: 1306 sheet: -0.04 (0.25), residues: 440 loop : -1.06 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 418 TYR 0.017 0.001 TYR D 33 PHE 0.012 0.002 PHE D 388 TRP 0.016 0.001 TRP D 278 HIS 0.007 0.001 HIS C 327 Details of bonding type rmsd covalent geometry : bond 0.00418 (25244) covalent geometry : angle 0.53632 (34264) hydrogen bonds : bond 0.03922 ( 1198) hydrogen bonds : angle 4.60952 ( 3387) link_ASP_CG-ANY_N : bond 0.00167 ( 8) link_ASP_CG-ANY_N : angle 0.77076 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8526 (ptt) cc_final: 0.8120 (ptm) REVERT: A 35 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7744 (tmtt) REVERT: A 118 ASN cc_start: 0.7309 (t0) cc_final: 0.7012 (t0) REVERT: A 269 ARG cc_start: 0.5203 (ptt-90) cc_final: 0.4779 (pmt170) REVERT: A 458 ARG cc_start: 0.8889 (tpm-80) cc_final: 0.8650 (tpt170) REVERT: A 586 HIS cc_start: 0.6796 (OUTLIER) cc_final: 0.6008 (m90) REVERT: B 586 HIS cc_start: 0.6911 (OUTLIER) cc_final: 0.6097 (m90) REVERT: C 131 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6317 (ptp-170) REVERT: C 160 GLN cc_start: 0.8844 (tt0) cc_final: 0.8319 (tm-30) REVERT: C 278 TRP cc_start: 0.7071 (OUTLIER) cc_final: 0.5728 (m100) REVERT: C 327 HIS cc_start: 0.8003 (p90) cc_final: 0.7759 (p90) REVERT: D 33 TYR cc_start: 0.7610 (t80) cc_final: 0.7365 (t80) REVERT: D 299 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.7472 (p) REVERT: D 586 HIS cc_start: 0.8566 (OUTLIER) cc_final: 0.8317 (t-90) outliers start: 43 outliers final: 13 residues processed: 188 average time/residue: 0.5634 time to fit residues: 124.1229 Evaluate side-chains 169 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 586 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 242 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 chunk 315 optimal weight: 2.9990 chunk 88 optimal weight: 0.0270 chunk 286 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 713 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.149967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.092174 restraints weight = 38602.534| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.61 r_work: 0.2998 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25252 Z= 0.116 Angle : 0.491 7.669 34288 Z= 0.258 Chirality : 0.044 0.157 3997 Planarity : 0.004 0.049 4398 Dihedral : 8.031 82.302 3657 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.31 % Rotamer: Outliers : 1.76 % Allowed : 11.09 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 0.35 (0.15), residues: 3202 helix: 1.74 (0.15), residues: 1306 sheet: 0.01 (0.26), residues: 392 loop : -1.08 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 458 TYR 0.018 0.001 TYR C 33 PHE 0.013 0.001 PHE D 388 TRP 0.017 0.001 TRP D 278 HIS 0.004 0.001 HIS C 327 Details of bonding type rmsd covalent geometry : bond 0.00258 (25244) covalent geometry : angle 0.49040 (34264) hydrogen bonds : bond 0.03226 ( 1198) hydrogen bonds : angle 4.37854 ( 3387) link_ASP_CG-ANY_N : bond 0.00120 ( 8) link_ASP_CG-ANY_N : angle 0.70562 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8547 (ptt) cc_final: 0.8129 (ptm) REVERT: A 35 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7740 (tmtt) REVERT: A 58 LEU cc_start: 0.8384 (mp) cc_final: 0.8158 (mm) REVERT: A 102 ARG cc_start: 0.7718 (mmt90) cc_final: 0.7318 (mpt180) REVERT: A 103 GLU cc_start: 0.8302 (mp0) cc_final: 0.7916 (tp30) REVERT: A 118 ASN cc_start: 0.7435 (t0) cc_final: 0.7108 (t0) REVERT: A 269 ARG cc_start: 0.5262 (ptt-90) cc_final: 0.4793 (pmt170) REVERT: A 458 ARG cc_start: 0.8851 (tpm-80) cc_final: 0.8637 (tpt170) REVERT: A 586 HIS cc_start: 0.6710 (OUTLIER) cc_final: 0.5924 (m90) REVERT: B 586 HIS cc_start: 0.6764 (OUTLIER) cc_final: 0.5848 (m90) REVERT: C 131 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6299 (ptp-170) REVERT: C 160 GLN cc_start: 0.8855 (tt0) cc_final: 0.8321 (tm-30) REVERT: C 278 TRP cc_start: 0.7054 (OUTLIER) cc_final: 0.5724 (m100) REVERT: C 586 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7577 (t-90) REVERT: D 31 ASP cc_start: 0.8732 (m-30) cc_final: 0.8363 (p0) REVERT: D 33 TYR cc_start: 0.7627 (t80) cc_final: 0.7378 (t80) REVERT: D 299 VAL cc_start: 0.7647 (OUTLIER) cc_final: 0.7423 (p) REVERT: D 458 ARG cc_start: 0.9013 (ptm160) cc_final: 0.8501 (ttm-80) REVERT: D 586 HIS cc_start: 0.8461 (OUTLIER) cc_final: 0.8223 (t-90) outliers start: 46 outliers final: 16 residues processed: 193 average time/residue: 0.5635 time to fit residues: 127.4279 Evaluate side-chains 173 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 586 HIS Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 586 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 258 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 295 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 219 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 chunk 184 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 HIS C 89 GLN C 247 GLN ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.145092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.086710 restraints weight = 38688.306| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.56 r_work: 0.2840 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 25252 Z= 0.319 Angle : 0.632 8.785 34288 Z= 0.333 Chirality : 0.050 0.188 3997 Planarity : 0.005 0.046 4398 Dihedral : 8.355 83.070 3657 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.18 % Favored : 95.78 % Rotamer: Outliers : 2.49 % Allowed : 11.93 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 0.15 (0.15), residues: 3202 helix: 1.51 (0.15), residues: 1304 sheet: -0.31 (0.24), residues: 464 loop : -1.09 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 418 TYR 0.019 0.002 TYR C 33 PHE 0.015 0.002 PHE C 480 TRP 0.016 0.002 TRP D 278 HIS 0.008 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00757 (25244) covalent geometry : angle 0.63212 (34264) hydrogen bonds : bond 0.04559 ( 1198) hydrogen bonds : angle 4.69550 ( 3387) link_ASP_CG-ANY_N : bond 0.00267 ( 8) link_ASP_CG-ANY_N : angle 0.80016 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 147 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8535 (ptt) cc_final: 0.8118 (ptm) REVERT: A 35 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7756 (tmtt) REVERT: A 103 GLU cc_start: 0.8355 (mp0) cc_final: 0.7978 (tp30) REVERT: A 118 ASN cc_start: 0.7464 (t0) cc_final: 0.7220 (t0) REVERT: A 269 ARG cc_start: 0.5053 (ptt-90) cc_final: 0.4679 (pmt170) REVERT: A 458 ARG cc_start: 0.8922 (tpm-80) cc_final: 0.8394 (tpt-90) REVERT: A 586 HIS cc_start: 0.6741 (OUTLIER) cc_final: 0.5842 (m90) REVERT: A 686 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8499 (mtp) REVERT: B 586 HIS cc_start: 0.6778 (OUTLIER) cc_final: 0.5875 (m90) REVERT: B 732 MET cc_start: 0.6871 (mmp) cc_final: 0.6550 (mmp) REVERT: C 131 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6592 (ptp-170) REVERT: C 160 GLN cc_start: 0.8829 (tt0) cc_final: 0.8307 (tm-30) REVERT: C 247 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7049 (pm20) REVERT: C 278 TRP cc_start: 0.7035 (OUTLIER) cc_final: 0.6017 (m100) REVERT: C 443 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: D 33 TYR cc_start: 0.7876 (t80) cc_final: 0.7485 (t80) REVERT: D 299 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7638 (p) outliers start: 65 outliers final: 26 residues processed: 196 average time/residue: 0.5701 time to fit residues: 130.6370 Evaluate side-chains 176 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 329 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 287 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 245 optimal weight: 0.5980 chunk 313 optimal weight: 0.7980 chunk 208 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 286 optimal weight: 0.5980 chunk 187 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.149114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092056 restraints weight = 39144.318| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.56 r_work: 0.2990 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25252 Z= 0.111 Angle : 0.502 6.817 34288 Z= 0.264 Chirality : 0.044 0.148 3997 Planarity : 0.004 0.047 4398 Dihedral : 8.012 82.886 3657 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 2.07 % Allowed : 13.04 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 0.37 (0.15), residues: 3202 helix: 1.78 (0.15), residues: 1290 sheet: -0.19 (0.25), residues: 434 loop : -1.02 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 458 TYR 0.016 0.001 TYR C 33 PHE 0.012 0.001 PHE D 388 TRP 0.019 0.001 TRP D 278 HIS 0.003 0.001 HIS D 650 Details of bonding type rmsd covalent geometry : bond 0.00240 (25244) covalent geometry : angle 0.50158 (34264) hydrogen bonds : bond 0.03259 ( 1198) hydrogen bonds : angle 4.39976 ( 3387) link_ASP_CG-ANY_N : bond 0.00104 ( 8) link_ASP_CG-ANY_N : angle 0.68376 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 153 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.8562 (ptt) cc_final: 0.8148 (ptm) REVERT: A 35 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7738 (tmtt) REVERT: A 118 ASN cc_start: 0.7497 (t0) cc_final: 0.7187 (t0) REVERT: A 269 ARG cc_start: 0.5083 (ptt-90) cc_final: 0.4600 (pmt170) REVERT: A 458 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8313 (tpt-90) REVERT: A 586 HIS cc_start: 0.6616 (OUTLIER) cc_final: 0.5803 (m90) REVERT: B 586 HIS cc_start: 0.6607 (OUTLIER) cc_final: 0.5640 (m90) REVERT: B 732 MET cc_start: 0.6713 (mmp) cc_final: 0.6492 (mmp) REVERT: C 131 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6479 (ptp-170) REVERT: C 160 GLN cc_start: 0.8867 (tt0) cc_final: 0.8352 (tm-30) REVERT: C 278 TRP cc_start: 0.6972 (OUTLIER) cc_final: 0.5573 (m100) REVERT: C 661 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7941 (pt0) REVERT: D 33 TYR cc_start: 0.7827 (t80) cc_final: 0.7509 (t80) REVERT: D 458 ARG cc_start: 0.8962 (ptm160) cc_final: 0.8425 (ttm-80) REVERT: D 586 HIS cc_start: 0.8459 (OUTLIER) cc_final: 0.8147 (t-90) outliers start: 54 outliers final: 24 residues processed: 193 average time/residue: 0.5553 time to fit residues: 125.8848 Evaluate side-chains 177 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 586 HIS Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 179 optimal weight: 7.9990 chunk 264 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 91 optimal weight: 0.0070 chunk 99 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 213 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 327 HIS ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.147577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.090078 restraints weight = 39270.323| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.55 r_work: 0.2951 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25252 Z= 0.188 Angle : 0.544 10.626 34288 Z= 0.285 Chirality : 0.046 0.156 3997 Planarity : 0.004 0.045 4398 Dihedral : 7.945 83.875 3657 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 2.03 % Allowed : 13.61 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 0.30 (0.15), residues: 3202 helix: 1.69 (0.15), residues: 1300 sheet: -0.14 (0.25), residues: 428 loop : -1.08 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 458 TYR 0.015 0.001 TYR C 33 PHE 0.012 0.002 PHE D 388 TRP 0.019 0.001 TRP A 278 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00441 (25244) covalent geometry : angle 0.54411 (34264) hydrogen bonds : bond 0.03697 ( 1198) hydrogen bonds : angle 4.44649 ( 3387) link_ASP_CG-ANY_N : bond 0.00172 ( 8) link_ASP_CG-ANY_N : angle 0.72750 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.8580 (ptt) cc_final: 0.8165 (ptm) REVERT: A 35 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7625 (tmtt) REVERT: A 103 GLU cc_start: 0.8425 (mp0) cc_final: 0.7981 (tp30) REVERT: A 118 ASN cc_start: 0.7533 (t0) cc_final: 0.7328 (t0) REVERT: A 269 ARG cc_start: 0.5032 (ptt-90) cc_final: 0.4530 (pmt170) REVERT: A 458 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8314 (tpt-90) REVERT: A 586 HIS cc_start: 0.6612 (OUTLIER) cc_final: 0.5752 (m90) REVERT: B 76 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8443 (mm) REVERT: B 586 HIS cc_start: 0.6737 (OUTLIER) cc_final: 0.5867 (m90) REVERT: B 732 MET cc_start: 0.6740 (mmp) cc_final: 0.6528 (mmp) REVERT: C 131 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6554 (ptp-170) REVERT: C 160 GLN cc_start: 0.8865 (tt0) cc_final: 0.8352 (tm-30) REVERT: C 278 TRP cc_start: 0.7054 (OUTLIER) cc_final: 0.5689 (m100) REVERT: C 661 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8023 (pt0) REVERT: D 33 TYR cc_start: 0.7884 (t80) cc_final: 0.7596 (t80) outliers start: 53 outliers final: 29 residues processed: 184 average time/residue: 0.5230 time to fit residues: 114.1655 Evaluate side-chains 177 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 297 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 291 optimal weight: 3.9990 chunk 103 optimal weight: 0.0770 chunk 265 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 247 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS D 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.148864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.091045 restraints weight = 38816.003| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.77 r_work: 0.2969 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25252 Z= 0.125 Angle : 0.502 7.667 34288 Z= 0.264 Chirality : 0.045 0.154 3997 Planarity : 0.004 0.045 4398 Dihedral : 7.700 83.319 3657 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.31 % Rotamer: Outliers : 1.95 % Allowed : 13.92 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 0.39 (0.15), residues: 3202 helix: 1.79 (0.15), residues: 1294 sheet: -0.17 (0.23), residues: 490 loop : -1.03 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 458 TYR 0.016 0.001 TYR A 14 PHE 0.014 0.001 PHE D 388 TRP 0.023 0.001 TRP D 278 HIS 0.003 0.001 HIS D 650 Details of bonding type rmsd covalent geometry : bond 0.00283 (25244) covalent geometry : angle 0.50232 (34264) hydrogen bonds : bond 0.03242 ( 1198) hydrogen bonds : angle 4.32246 ( 3387) link_ASP_CG-ANY_N : bond 0.00117 ( 8) link_ASP_CG-ANY_N : angle 0.68269 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8564 (ptt) cc_final: 0.8160 (ptm) REVERT: A 35 LYS cc_start: 0.8073 (tmtt) cc_final: 0.7729 (tmtt) REVERT: A 103 GLU cc_start: 0.8317 (mp0) cc_final: 0.7950 (tp30) REVERT: A 118 ASN cc_start: 0.7357 (t0) cc_final: 0.7053 (t0) REVERT: A 168 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8315 (mt-10) REVERT: A 269 ARG cc_start: 0.5189 (ptt-90) cc_final: 0.4654 (pmt170) REVERT: A 458 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8157 (tpt-90) REVERT: A 586 HIS cc_start: 0.6606 (OUTLIER) cc_final: 0.5752 (m90) REVERT: B 586 HIS cc_start: 0.6431 (OUTLIER) cc_final: 0.5517 (m90) REVERT: C 131 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6431 (ptp-170) REVERT: C 160 GLN cc_start: 0.8739 (tt0) cc_final: 0.8251 (tm-30) REVERT: C 278 TRP cc_start: 0.6974 (OUTLIER) cc_final: 0.5637 (m100) REVERT: D 33 TYR cc_start: 0.7763 (t80) cc_final: 0.7516 (t80) REVERT: D 301 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7900 (ttt90) REVERT: D 586 HIS cc_start: 0.8384 (OUTLIER) cc_final: 0.8066 (t-90) outliers start: 51 outliers final: 28 residues processed: 184 average time/residue: 0.5515 time to fit residues: 119.6806 Evaluate side-chains 175 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 586 HIS Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 236 optimal weight: 0.1980 chunk 199 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 269 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 chunk 190 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 256 optimal weight: 7.9990 chunk 113 optimal weight: 0.0030 chunk 301 optimal weight: 2.9990 chunk 290 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 HIS B 89 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 327 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.150170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.093028 restraints weight = 38872.065| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.71 r_work: 0.3011 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 25252 Z= 0.098 Angle : 0.489 14.344 34288 Z= 0.254 Chirality : 0.044 0.154 3997 Planarity : 0.003 0.046 4398 Dihedral : 7.319 81.852 3657 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 1.64 % Allowed : 14.53 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 0.49 (0.15), residues: 3202 helix: 1.91 (0.15), residues: 1284 sheet: -0.03 (0.24), residues: 448 loop : -1.02 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 458 TYR 0.018 0.001 TYR C 33 PHE 0.014 0.001 PHE D 388 TRP 0.028 0.001 TRP D 278 HIS 0.003 0.001 HIS C 308 Details of bonding type rmsd covalent geometry : bond 0.00216 (25244) covalent geometry : angle 0.48866 (34264) hydrogen bonds : bond 0.02883 ( 1198) hydrogen bonds : angle 4.19084 ( 3387) link_ASP_CG-ANY_N : bond 0.00096 ( 8) link_ASP_CG-ANY_N : angle 0.67181 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8572 (ptt) cc_final: 0.8199 (ptm) REVERT: A 35 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7691 (tmtt) REVERT: A 118 ASN cc_start: 0.7344 (t0) cc_final: 0.7064 (t0) REVERT: A 168 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8232 (mt-10) REVERT: A 269 ARG cc_start: 0.5278 (ptt-90) cc_final: 0.4756 (pmt170) REVERT: A 458 ARG cc_start: 0.8605 (tpm-80) cc_final: 0.8147 (tpt-90) REVERT: A 586 HIS cc_start: 0.6590 (OUTLIER) cc_final: 0.5791 (m90) REVERT: A 634 GLN cc_start: 0.9044 (mp10) cc_final: 0.8320 (mp10) REVERT: B 124 TYR cc_start: 0.8320 (t80) cc_final: 0.8113 (t80) REVERT: C 124 TYR cc_start: 0.7902 (t80) cc_final: 0.7650 (t80) REVERT: C 131 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6441 (ptp-170) REVERT: C 160 GLN cc_start: 0.8722 (tt0) cc_final: 0.8234 (tm-30) REVERT: C 278 TRP cc_start: 0.6933 (OUTLIER) cc_final: 0.5625 (m100) REVERT: D 33 TYR cc_start: 0.7704 (t80) cc_final: 0.7486 (t80) REVERT: D 301 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7882 (ttt90) REVERT: D 458 ARG cc_start: 0.8809 (ptm160) cc_final: 0.8481 (ttm-80) REVERT: D 586 HIS cc_start: 0.8367 (OUTLIER) cc_final: 0.8052 (t-90) outliers start: 43 outliers final: 26 residues processed: 183 average time/residue: 0.5509 time to fit residues: 118.9513 Evaluate side-chains 174 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 586 HIS Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 314 optimal weight: 1.9990 chunk 240 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 184 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 231 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 275 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.148771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.090778 restraints weight = 38880.136| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.61 r_work: 0.2982 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25252 Z= 0.145 Angle : 0.512 7.594 34288 Z= 0.268 Chirality : 0.045 0.151 3997 Planarity : 0.004 0.045 4398 Dihedral : 7.297 81.038 3657 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 1.68 % Allowed : 14.65 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 0.47 (0.15), residues: 3202 helix: 1.84 (0.15), residues: 1294 sheet: -0.11 (0.23), residues: 488 loop : -0.99 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 561 TYR 0.018 0.001 TYR A 14 PHE 0.015 0.001 PHE D 388 TRP 0.026 0.001 TRP D 278 HIS 0.003 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00338 (25244) covalent geometry : angle 0.51188 (34264) hydrogen bonds : bond 0.03296 ( 1198) hydrogen bonds : angle 4.28064 ( 3387) link_ASP_CG-ANY_N : bond 0.00139 ( 8) link_ASP_CG-ANY_N : angle 0.69745 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.8611 (ptt) cc_final: 0.8230 (ptm) REVERT: A 35 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7654 (tmtt) REVERT: A 58 LEU cc_start: 0.8340 (mp) cc_final: 0.8098 (mm) REVERT: A 103 GLU cc_start: 0.8385 (mp0) cc_final: 0.7957 (tp30) REVERT: A 118 ASN cc_start: 0.7511 (t0) cc_final: 0.7217 (t0) REVERT: A 269 ARG cc_start: 0.5095 (ptt-90) cc_final: 0.4575 (pmt170) REVERT: A 458 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8314 (tpt-90) REVERT: A 586 HIS cc_start: 0.6552 (OUTLIER) cc_final: 0.5700 (m90) REVERT: A 634 GLN cc_start: 0.9174 (mp10) cc_final: 0.8483 (mp10) REVERT: C 131 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6577 (ptp-170) REVERT: C 160 GLN cc_start: 0.8848 (tt0) cc_final: 0.8332 (tm-30) REVERT: C 278 TRP cc_start: 0.7019 (OUTLIER) cc_final: 0.5711 (m100) REVERT: D 33 TYR cc_start: 0.7866 (t80) cc_final: 0.7616 (t80) REVERT: D 301 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8115 (ttt90) REVERT: D 458 ARG cc_start: 0.8938 (ptm160) cc_final: 0.8552 (ttm-80) REVERT: D 586 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.8144 (t-90) outliers start: 44 outliers final: 25 residues processed: 173 average time/residue: 0.5490 time to fit residues: 112.3485 Evaluate side-chains 173 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 586 HIS Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 90 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 190 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 304 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 327 HIS ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.146957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.089462 restraints weight = 39251.921| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.54 r_work: 0.2940 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25252 Z= 0.229 Angle : 0.572 7.963 34288 Z= 0.300 Chirality : 0.047 0.165 3997 Planarity : 0.004 0.045 4398 Dihedral : 7.503 80.256 3657 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.76 % Allowed : 14.57 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 0.30 (0.15), residues: 3202 helix: 1.69 (0.15), residues: 1300 sheet: -0.15 (0.23), residues: 484 loop : -1.09 (0.15), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 418 TYR 0.018 0.001 TYR C 33 PHE 0.015 0.002 PHE D 388 TRP 0.028 0.002 TRP D 278 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00540 (25244) covalent geometry : angle 0.57166 (34264) hydrogen bonds : bond 0.03913 ( 1198) hydrogen bonds : angle 4.46993 ( 3387) link_ASP_CG-ANY_N : bond 0.00192 ( 8) link_ASP_CG-ANY_N : angle 0.75679 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10932.37 seconds wall clock time: 185 minutes 53.30 seconds (11153.30 seconds total)