Starting phenix.real_space_refine on Sun Jul 5 02:23:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wae_32383/07_2026/7wae_32383.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wae_32383/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7wae_32383/07_2026/7wae_32383.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wae_32383/07_2026/7wae_32383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wae_32383/07_2026/7wae_32383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wae_32383/07_2026/7wae_32383.map" model { file = "/net/cci-nas-00/data/ceres_data/7wae_32383/07_2026/7wae_32383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wae_32383/07_2026/7wae_32383.cif" } 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-6108/lib/python3.11/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: 5.40, per 1000 atoms: 0.22 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: 2.22 Conformation dependent library (CDL) restraints added in 1.0 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: 0.94 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: 5.93 Time building geometry restraints manager: 2.90 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: 13825 17.63 - 35.27: 1062 35.27 - 52.90: 212 52.90 - 70.53: 48 70.53 - 88.16: 22 Dihedral angle restraints: 15169 sinusoidal: 6041 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 15166 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: 8.160 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.420 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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:9.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 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 : 13.579 88.165 9331 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/Z covalent geometry : bond 0.00320 / 0.16 (25244) covalent geometry : angle 0.56199 / 0.30 (34264) hydrogen bonds : bond 0.15288 / 10.42 ( 1198) hydrogen bonds : angle 6.07915 / 4.26 ( 3387) link_ASP_CG-ANY_N : bond 0.01136 / 0.57 ( 8) link_ASP_CG-ANY_N : angle 0.90841 / 0.56 ( 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 : 0.956 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: 0.7183 time to fit residues: 189.7158 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 : 0.877 ------------------------------------------------------------------------------- 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... 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 = 0.4026 r_free = 0.4026 target = 0.150018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.092286 restraints weight = 38996.931| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.63 r_work: 0.2999 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25252 Z= 0.127 Angle : 0.524 6.327 34288 Z= 0.278 Chirality : 0.045 0.151 3997 Planarity : 0.004 0.054 4398 Dihedral : 7.068 73.254 3587 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 1.41 % Allowed : 7.00 % 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: 1.63 (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 0.010 0.001 PHE C 243 TRP 0.014 0.001 TRP D 278 HIS 0.006 0.001 HIS C 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (25244) covalent geometry : angle 0.52365 / 0.28 (34264) hydrogen bonds : bond 0.03826 / 2.65 ( 1198) hydrogen bonds : angle 4.80544 / 3.39 ( 3387) link_ASP_CG-ANY_N : bond 0.00242 / 0.11 ( 8) link_ASP_CG-ANY_N : angle 0.82927 / 0.48 ( 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 199 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.944 Fit side-chains REVERT: A 25 MET cc_start: 0.8496 (ptt) cc_final: 0.8272 (ptm) REVERT: A 35 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7772 (tmtt) REVERT: A 118 ASN cc_start: 0.7192 (t0) cc_final: 0.6873 (t0) REVERT: A 172 LYS cc_start: 0.9099 (mmtp) cc_final: 0.8890 (mttt) REVERT: A 269 ARG cc_start: 0.5313 (ptt-90) cc_final: 0.4933 (pmt170) REVERT: A 586 HIS cc_start: 0.6764 (OUTLIER) cc_final: 0.6035 (m90) REVERT: B 33 TYR cc_start: 0.6827 (t80) cc_final: 0.6557 (t80) REVERT: C 131 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6285 (ptp-170) REVERT: C 160 GLN cc_start: 0.8835 (tt0) cc_final: 0.8305 (tm-30) REVERT: C 168 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8566 (mm-30) REVERT: C 247 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6829 (mp10) REVERT: C 278 TRP cc_start: 0.6733 (OUTLIER) cc_final: 0.5813 (m100) REVERT: C 586 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7641 (t-90) REVERT: D 586 HIS cc_start: 0.8455 (OUTLIER) cc_final: 0.8227 (t-90) outliers start: 37 outliers final: 8 residues processed: 185 average time/residue: 0.5850 time to fit residues: 126.5641 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 : 0.927 ------------------------------------------------------------------------------- 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: 9.9990 chunk 95 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 170 optimal weight: 0.0870 chunk 184 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 273 optimal weight: 7.9990 chunk 263 optimal weight: 0.9980 chunk 203 optimal weight: 7.9990 chunk 229 optimal weight: 0.9990 chunk 297 optimal weight: 2.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4003 r_free = 0.4003 target = 0.148235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.090431 restraints weight = 39116.256| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.59 r_work: 0.2927 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25252 Z= 0.176 Angle : 0.534 6.678 34288 Z= 0.282 Chirality : 0.046 0.157 3997 Planarity : 0.004 0.053 4398 Dihedral : 6.831 81.944 3569 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 1.80 % Allowed : 9.14 % Favored : 89.06 % 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 0.018 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/Z covalent geometry : bond 0.00410 / 0.18 (25244) covalent geometry : angle 0.53351 / 0.28 (34264) hydrogen bonds : bond 0.03898 / 2.67 ( 1198) hydrogen bonds : angle 4.59450 / 3.24 ( 3387) link_ASP_CG-ANY_N : bond 0.00170 / 0.08 ( 8) link_ASP_CG-ANY_N : angle 0.78326 / 0.47 ( 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 203 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 0.816 Fit side-chains REVERT: A 25 MET cc_start: 0.8516 (ptt) cc_final: 0.8098 (ptm) REVERT: A 35 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7741 (tmtt) REVERT: A 118 ASN cc_start: 0.7311 (t0) cc_final: 0.7010 (t0) REVERT: A 269 ARG cc_start: 0.5330 (ptt-90) cc_final: 0.4883 (pmt170) REVERT: A 458 ARG cc_start: 0.8871 (tpm-80) cc_final: 0.8639 (tpt170) REVERT: A 586 HIS cc_start: 0.6799 (OUTLIER) cc_final: 0.6001 (m90) REVERT: A 732 MET cc_start: 0.7183 (mmt) cc_final: 0.6629 (mpp) REVERT: B 586 HIS cc_start: 0.6887 (OUTLIER) cc_final: 0.6060 (m90) REVERT: C 131 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6320 (ptp-110) REVERT: C 160 GLN cc_start: 0.8850 (tt0) cc_final: 0.8325 (tm-30) REVERT: C 278 TRP cc_start: 0.7041 (OUTLIER) cc_final: 0.5678 (m100) REVERT: C 327 HIS cc_start: 0.7995 (p90) cc_final: 0.7747 (p90) REVERT: C 661 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7999 (pt0) REVERT: D 33 TYR cc_start: 0.7621 (t80) cc_final: 0.7396 (t80) REVERT: D 299 VAL cc_start: 0.7733 (OUTLIER) cc_final: 0.7510 (p) REVERT: D 586 HIS cc_start: 0.8550 (OUTLIER) cc_final: 0.8303 (t-90) outliers start: 47 outliers final: 11 residues processed: 192 average time/residue: 0.5797 time to fit residues: 131.1922 Evaluate side-chains 170 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 250 ILE Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 661 GLU 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: 5.9990 chunk 215 optimal weight: 0.8980 chunk 242 optimal weight: 0.0030 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 280 optimal weight: 9.9990 chunk 315 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 286 optimal weight: 4.9990 chunk 86 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.149517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.091662 restraints weight = 38628.477| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.61 r_work: 0.2981 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1397 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= 0.126 Angle : 0.501 7.596 34288 Z= 0.264 Chirality : 0.045 0.192 3997 Planarity : 0.004 0.049 4398 Dihedral : 6.741 82.656 3569 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.72 % Favored : 96.25 % Rotamer: Outliers : 1.72 % Allowed : 11.32 % Favored : 86.96 % 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: 0.33 (0.15), residues: 3202 helix: 1.71 (0.15), residues: 1306 sheet: -0.02 (0.26), residues: 392 loop : -1.09 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 458 TYR 0.017 0.001 TYR C 33 PHE 0.011 0.001 PHE D 388 TRP 0.016 0.001 TRP D 278 HIS 0.003 0.001 HIS D 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (25244) covalent geometry : angle 0.50123 / 0.26 (34264) hydrogen bonds : bond 0.03357 / 2.32 ( 1198) hydrogen bonds : angle 4.42955 / 3.12 ( 3387) link_ASP_CG-ANY_N : bond 0.00136 / 0.07 ( 8) link_ASP_CG-ANY_N : angle 0.71494 / 0.44 ( 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 204 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8543 (ptt) cc_final: 0.8115 (ptm) REVERT: A 35 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7776 (tmtt) REVERT: A 58 LEU cc_start: 0.8393 (mp) cc_final: 0.8167 (mm) REVERT: A 102 ARG cc_start: 0.7739 (mmt90) cc_final: 0.7351 (mpt180) REVERT: A 103 GLU cc_start: 0.8320 (mp0) cc_final: 0.7897 (tp30) REVERT: A 118 ASN cc_start: 0.7400 (t0) cc_final: 0.7087 (t0) REVERT: A 269 ARG cc_start: 0.5236 (ptt-90) cc_final: 0.4770 (pmt170) REVERT: A 458 ARG cc_start: 0.8864 (tpm-80) cc_final: 0.8639 (tpt170) REVERT: A 586 HIS cc_start: 0.6731 (OUTLIER) cc_final: 0.5938 (m90) REVERT: B 586 HIS cc_start: 0.6788 (OUTLIER) cc_final: 0.5889 (m90) REVERT: C 131 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6320 (ptp-170) REVERT: C 160 GLN cc_start: 0.8856 (tt0) cc_final: 0.8324 (tm-30) REVERT: C 278 TRP cc_start: 0.7067 (OUTLIER) cc_final: 0.5725 (m100) REVERT: C 586 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7589 (t-90) REVERT: D 31 ASP cc_start: 0.8752 (m-30) cc_final: 0.8378 (p0) REVERT: D 33 TYR cc_start: 0.7688 (t80) cc_final: 0.7419 (t80) REVERT: D 299 VAL cc_start: 0.7684 (OUTLIER) cc_final: 0.7459 (p) REVERT: D 458 ARG cc_start: 0.9004 (ptm160) cc_final: 0.8479 (ttm-80) REVERT: D 586 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.8230 (t-90) outliers start: 45 outliers final: 13 residues processed: 190 average time/residue: 0.5842 time to fit residues: 131.0209 Evaluate side-chains 167 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 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 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 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: 4.9990 chunk 71 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 chunk 219 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 chunk 184 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3991 r_free = 0.3991 target = 0.147332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.089535 restraints weight = 39020.569| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.57 r_work: 0.2937 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 25252 Z= 0.207 Angle : 0.553 7.896 34288 Z= 0.293 Chirality : 0.047 0.161 3997 Planarity : 0.004 0.048 4398 Dihedral : 6.928 83.649 3569 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.81 % Favored : 96.16 % Rotamer: Outliers : 2.33 % Allowed : 11.74 % Favored : 85.93 % 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: 0.29 (0.15), residues: 3202 helix: 1.69 (0.15), residues: 1298 sheet: -0.10 (0.25), residues: 426 loop : -1.10 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 418 TYR 0.020 0.001 TYR C 33 PHE 0.013 0.002 PHE D 388 TRP 0.017 0.001 TRP D 278 HIS 0.008 0.001 HIS C 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (25244) covalent geometry : angle 0.55329 / 0.29 (34264) hydrogen bonds : bond 0.03938 / 2.70 ( 1198) hydrogen bonds : angle 4.53819 / 3.20 ( 3387) link_ASP_CG-ANY_N : bond 0.00192 / 0.09 ( 8) link_ASP_CG-ANY_N : angle 0.74228 / 0.46 ( 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: 61 poor density : 151 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.8546 (ptt) cc_final: 0.8154 (ptm) REVERT: A 35 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7767 (tmtt) REVERT: A 102 ARG cc_start: 0.7767 (mmt90) cc_final: 0.7384 (mpt180) REVERT: A 103 GLU cc_start: 0.8348 (mp0) cc_final: 0.7984 (tp30) REVERT: A 118 ASN cc_start: 0.7457 (t0) cc_final: 0.7214 (t0) REVERT: A 269 ARG cc_start: 0.5113 (ptt-90) cc_final: 0.4740 (pmt170) REVERT: A 458 ARG cc_start: 0.8888 (tpm-80) cc_final: 0.8360 (tpt-90) REVERT: A 586 HIS cc_start: 0.6637 (OUTLIER) cc_final: 0.5815 (m90) REVERT: A 686 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8506 (mtp) REVERT: B 586 HIS cc_start: 0.6744 (OUTLIER) cc_final: 0.5850 (m90) REVERT: B 732 MET cc_start: 0.6847 (mmp) cc_final: 0.6572 (mmp) REVERT: C 131 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6535 (ptp-110) REVERT: C 160 GLN cc_start: 0.8854 (tt0) cc_final: 0.8340 (tm-30) REVERT: C 278 TRP cc_start: 0.6980 (OUTLIER) cc_final: 0.5567 (m100) REVERT: D 33 TYR cc_start: 0.7837 (t80) cc_final: 0.7501 (t80) REVERT: D 299 VAL cc_start: 0.7803 (OUTLIER) cc_final: 0.7552 (p) outliers start: 61 outliers final: 21 residues processed: 196 average time/residue: 0.5741 time to fit residues: 132.9379 Evaluate side-chains 174 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 148 GLN 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 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: 0.9980 chunk 87 optimal weight: 4.9990 chunk 245 optimal weight: 0.6980 chunk 313 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 chunk 286 optimal weight: 0.0570 chunk 187 optimal weight: 0.0970 chunk 57 optimal weight: 0.7980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 HIS ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 327 HIS ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** 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 = 0.4033 r_free = 0.4033 target = 0.151292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.093009 restraints weight = 38644.031| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.66 r_work: 0.3004 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25252 Z= 0.094 Angle : 0.485 9.992 34288 Z= 0.254 Chirality : 0.044 0.149 3997 Planarity : 0.004 0.047 4398 Dihedral : 6.656 83.399 3569 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.31 % Rotamer: Outliers : 1.76 % Allowed : 13.08 % Favored : 85.16 % 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: 0.45 (0.15), residues: 3202 helix: 1.87 (0.15), residues: 1286 sheet: -0.04 (0.24), residues: 448 loop : -1.05 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 465 TYR 0.021 0.001 TYR C 33 PHE 0.015 0.001 PHE D 388 TRP 0.020 0.001 TRP D 278 HIS 0.003 0.001 HIS D 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (25244) covalent geometry : angle 0.48528 / 0.25 (34264) hydrogen bonds : bond 0.02954 / 2.05 ( 1198) hydrogen bonds : angle 4.27362 / 3.02 ( 3387) link_ASP_CG-ANY_N : bond 0.00090 / 0.05 ( 8) link_ASP_CG-ANY_N : angle 0.67484 / 0.42 ( 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 201 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8595 (ptt) cc_final: 0.8204 (ptm) REVERT: A 35 LYS cc_start: 0.8101 (tmtt) cc_final: 0.7725 (tmtt) REVERT: A 58 LEU cc_start: 0.8355 (mp) cc_final: 0.8128 (mm) REVERT: A 118 ASN cc_start: 0.7404 (t0) cc_final: 0.7109 (t0) REVERT: A 269 ARG cc_start: 0.5060 (ptt-90) cc_final: 0.4606 (pmt170) REVERT: A 458 ARG cc_start: 0.8824 (tpm-80) cc_final: 0.8328 (tpt-90) REVERT: A 586 HIS cc_start: 0.6678 (OUTLIER) cc_final: 0.5845 (m90) REVERT: A 634 GLN cc_start: 0.9174 (mp10) cc_final: 0.8475 (mp10) REVERT: B 586 HIS cc_start: 0.6563 (OUTLIER) cc_final: 0.5593 (m90) REVERT: B 732 MET cc_start: 0.6628 (mmp) cc_final: 0.6398 (mmp) REVERT: C 131 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6381 (ptp-170) REVERT: C 160 GLN cc_start: 0.8862 (tt0) cc_final: 0.8329 (tm-30) REVERT: C 278 TRP cc_start: 0.6956 (OUTLIER) cc_final: 0.5609 (m100) REVERT: D 31 ASP cc_start: 0.8639 (m-30) cc_final: 0.8271 (p0) REVERT: D 33 TYR cc_start: 0.7781 (t80) cc_final: 0.7519 (t80) REVERT: D 458 ARG cc_start: 0.8914 (ptm160) cc_final: 0.8405 (ttm-80) REVERT: D 586 HIS cc_start: 0.8437 (OUTLIER) cc_final: 0.8131 (t-90) outliers start: 46 outliers final: 17 residues processed: 191 average time/residue: 0.5738 time to fit residues: 129.3458 Evaluate side-chains 166 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 586 HIS Chi-restraints excluded: chain A residue 591 ASP 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 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU 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 D residue 81 ILE Chi-restraints excluded: chain D residue 271 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 179 optimal weight: 8.9990 chunk 264 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 268 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 213 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS C 541 GLN D 373 GLN D 394 ASN D 713 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.150168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.091385 restraints weight = 38659.362| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.70 r_work: 0.2971 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25252 Z= 0.129 Angle : 0.500 9.674 34288 Z= 0.263 Chirality : 0.045 0.151 3997 Planarity : 0.004 0.046 4398 Dihedral : 6.652 84.079 3569 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 1.95 % Allowed : 13.50 % Favored : 84.55 % 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: 0.46 (0.15), residues: 3202 helix: 1.83 (0.15), residues: 1300 sheet: -0.06 (0.23), residues: 488 loop : -1.02 (0.16), residues: 1414 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 0.013 0.001 PHE D 388 TRP 0.019 0.001 TRP D 278 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (25244) covalent geometry : angle 0.49986 / 0.26 (34264) hydrogen bonds : bond 0.03224 / 2.23 ( 1198) hydrogen bonds : angle 4.27391 / 3.02 ( 3387) link_ASP_CG-ANY_N : bond 0.00130 / 0.06 ( 8) link_ASP_CG-ANY_N : angle 0.68952 / 0.43 ( 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 200 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8563 (ptt) cc_final: 0.8155 (ptm) REVERT: A 35 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7557 (tmtt) REVERT: A 58 LEU cc_start: 0.8340 (mp) cc_final: 0.8113 (mm) REVERT: A 103 GLU cc_start: 0.8347 (mp0) cc_final: 0.7934 (tp30) REVERT: A 118 ASN cc_start: 0.7320 (t0) cc_final: 0.7021 (t0) REVERT: A 168 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8321 (mt-10) REVERT: A 269 ARG cc_start: 0.5278 (ptt-90) cc_final: 0.4801 (pmt170) REVERT: A 458 ARG cc_start: 0.8653 (tpm-80) cc_final: 0.8188 (tpt-90) REVERT: A 586 HIS cc_start: 0.6525 (OUTLIER) cc_final: 0.5696 (m90) REVERT: B 76 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8377 (mm) REVERT: B 732 MET cc_start: 0.6516 (mmp) cc_final: 0.6263 (mmp) REVERT: C 131 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6385 (ptp-170) REVERT: C 160 GLN cc_start: 0.8732 (tt0) cc_final: 0.8237 (tm-30) REVERT: C 278 TRP cc_start: 0.6904 (OUTLIER) cc_final: 0.5523 (m100) REVERT: D 31 ASP cc_start: 0.8536 (m-30) cc_final: 0.8174 (p0) REVERT: D 33 TYR cc_start: 0.7677 (t80) cc_final: 0.7458 (t80) REVERT: D 458 ARG cc_start: 0.8856 (ptm160) cc_final: 0.8317 (ttm-80) REVERT: D 586 HIS cc_start: 0.8344 (OUTLIER) cc_final: 0.8050 (t-90) outliers start: 51 outliers final: 25 residues processed: 186 average time/residue: 0.5686 time to fit residues: 125.3447 Evaluate side-chains 173 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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 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 76 LEU 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 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 329 VAL Chi-restraints excluded: chain D residue 586 HIS 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: 0.9990 chunk 77 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 103 optimal weight: 0.0980 chunk 265 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 247 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 269 optimal weight: 3.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS C 541 GLN D 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.150515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.092261 restraints weight = 38639.568| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.64 r_work: 0.2991 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25252 Z= 0.105 Angle : 0.489 12.158 34288 Z= 0.254 Chirality : 0.044 0.159 3997 Planarity : 0.003 0.047 4398 Dihedral : 6.575 84.055 3569 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 1.57 % Allowed : 14.19 % Favored : 84.24 % 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: 0.50 (0.15), residues: 3202 helix: 1.90 (0.15), residues: 1288 sheet: -0.01 (0.24), residues: 448 loop : -1.02 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 458 TYR 0.017 0.001 TYR A 14 PHE 0.013 0.001 PHE D 388 TRP 0.020 0.001 TRP D 278 HIS 0.002 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (25244) covalent geometry : angle 0.48890 / 0.25 (34264) hydrogen bonds : bond 0.02987 / 2.08 ( 1198) hydrogen bonds : angle 4.20681 / 2.97 ( 3387) link_ASP_CG-ANY_N : bond 0.00107 / 0.05 ( 8) link_ASP_CG-ANY_N : angle 0.66621 / 0.41 ( 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 187 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8614 (ptt) cc_final: 0.8232 (ptm) REVERT: A 35 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7666 (tmtt) REVERT: A 58 LEU cc_start: 0.8331 (mp) cc_final: 0.8109 (mm) REVERT: A 103 GLU cc_start: 0.8373 (mp0) cc_final: 0.7912 (tp30) REVERT: A 118 ASN cc_start: 0.7442 (t0) cc_final: 0.7155 (t0) REVERT: A 119 GLU cc_start: 0.8066 (tt0) cc_final: 0.7853 (tt0) REVERT: A 168 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8469 (mt-10) REVERT: A 269 ARG cc_start: 0.5129 (ptt-90) cc_final: 0.4613 (pmt170) REVERT: A 458 ARG cc_start: 0.8820 (tpm-80) cc_final: 0.8335 (tpt-90) REVERT: A 586 HIS cc_start: 0.6600 (OUTLIER) cc_final: 0.5782 (m90) REVERT: A 634 GLN cc_start: 0.9175 (mp10) cc_final: 0.8505 (mp10) REVERT: B 76 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8388 (mm) REVERT: B 586 HIS cc_start: 0.6481 (OUTLIER) cc_final: 0.5519 (m90) REVERT: C 131 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6464 (ptp-170) REVERT: C 160 GLN cc_start: 0.8859 (tt0) cc_final: 0.8329 (tm-30) REVERT: C 278 TRP cc_start: 0.7008 (OUTLIER) cc_final: 0.5633 (m100) REVERT: D 33 TYR cc_start: 0.7803 (t80) cc_final: 0.7506 (t80) REVERT: D 458 ARG cc_start: 0.8901 (ptm160) cc_final: 0.8546 (ptm160) REVERT: D 586 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.8182 (t-90) outliers start: 41 outliers final: 26 residues processed: 178 average time/residue: 0.5678 time to fit residues: 120.0034 Evaluate side-chains 172 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 744 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 76 LEU 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 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 81 ILE 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 329 VAL 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: 0.0470 chunk 199 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 190 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 256 optimal weight: 0.1980 chunk 113 optimal weight: 0.0020 chunk 301 optimal weight: 0.9990 chunk 290 optimal weight: 0.7980 overall best weight: 0.3486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 308 HIS ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS C 541 GLN D 89 GLN D 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.151553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.094226 restraints weight = 38807.657| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.60 r_work: 0.3039 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25252 Z= 0.089 Angle : 0.474 8.534 34288 Z= 0.247 Chirality : 0.044 0.151 3997 Planarity : 0.003 0.047 4398 Dihedral : 6.436 85.175 3569 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 1.57 % Allowed : 14.23 % Favored : 84.21 % 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: 0.56 (0.15), residues: 3202 helix: 1.95 (0.15), residues: 1288 sheet: 0.02 (0.25), residues: 448 loop : -0.97 (0.15), residues: 1466 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 0.015 0.001 PHE D 388 TRP 0.026 0.001 TRP D 278 HIS 0.003 0.000 HIS B 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (25244) covalent geometry : angle 0.47373 / 0.25 (34264) hydrogen bonds : bond 0.02723 / 1.90 ( 1198) hydrogen bonds : angle 4.12320 / 2.91 ( 3387) link_ASP_CG-ANY_N : bond 0.00091 / 0.05 ( 8) link_ASP_CG-ANY_N : angle 0.65745 / 0.41 ( 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 196 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8593 (ptt) cc_final: 0.8211 (ptm) REVERT: A 35 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7627 (tmtt) REVERT: A 118 ASN cc_start: 0.7490 (t0) cc_final: 0.7178 (t0) REVERT: A 168 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8472 (mt-10) REVERT: A 269 ARG cc_start: 0.5187 (ptt-90) cc_final: 0.4646 (pmt170) REVERT: A 458 ARG cc_start: 0.8770 (tpm-80) cc_final: 0.8310 (tpt-90) REVERT: A 586 HIS cc_start: 0.6540 (OUTLIER) cc_final: 0.5674 (m90) REVERT: A 634 GLN cc_start: 0.9174 (mp10) cc_final: 0.8500 (mp10) REVERT: B 19 ARG cc_start: 0.8793 (mmt-90) cc_final: 0.8431 (mmp80) REVERT: B 124 TYR cc_start: 0.8375 (t80) cc_final: 0.8174 (t80) REVERT: C 124 TYR cc_start: 0.7950 (t80) cc_final: 0.7693 (t80) REVERT: C 131 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6460 (ptp-170) REVERT: C 160 GLN cc_start: 0.8840 (tt0) cc_final: 0.8312 (tm-30) REVERT: C 278 TRP cc_start: 0.6985 (OUTLIER) cc_final: 0.5633 (m100) REVERT: D 33 TYR cc_start: 0.7728 (t80) cc_final: 0.7473 (t80) REVERT: D 458 ARG cc_start: 0.8859 (ptm160) cc_final: 0.8501 (ptm160) REVERT: D 586 HIS cc_start: 0.8450 (OUTLIER) cc_final: 0.8139 (t-90) outliers start: 41 outliers final: 26 residues processed: 187 average time/residue: 0.5913 time to fit residues: 130.2813 Evaluate side-chains 180 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 610 MET 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 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 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 81 ILE Chi-restraints excluded: chain D residue 271 ILE 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: 0.4980 chunk 240 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 184 optimal weight: 0.0170 chunk 85 optimal weight: 0.4980 chunk 231 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 275 optimal weight: 9.9990 chunk 257 optimal weight: 3.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS C 541 GLN D 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.151319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.093845 restraints weight = 38830.606| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.62 r_work: 0.3022 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25252 Z= 0.096 Angle : 0.489 13.859 34288 Z= 0.251 Chirality : 0.044 0.153 3997 Planarity : 0.003 0.046 4398 Dihedral : 6.406 86.284 3569 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 1.53 % Allowed : 14.65 % 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: 0.60 (0.15), residues: 3202 helix: 1.98 (0.15), residues: 1286 sheet: 0.05 (0.24), residues: 454 loop : -0.95 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 561 TYR 0.018 0.001 TYR C 33 PHE 0.008 0.001 PHE D 638 TRP 0.025 0.001 TRP D 278 HIS 0.002 0.000 HIS D 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (25244) covalent geometry : angle 0.48858 / 0.25 (34264) hydrogen bonds : bond 0.02772 / 1.93 ( 1198) hydrogen bonds : angle 4.10929 / 2.90 ( 3387) link_ASP_CG-ANY_N : bond 0.00097 / 0.05 ( 8) link_ASP_CG-ANY_N : angle 0.65935 / 0.41 ( 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 193 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8603 (ptt) cc_final: 0.8217 (ptm) REVERT: A 35 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7503 (tmtt) REVERT: A 103 GLU cc_start: 0.8354 (mp0) cc_final: 0.7906 (tp30) REVERT: A 118 ASN cc_start: 0.7520 (t0) cc_final: 0.7209 (t0) REVERT: A 168 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8395 (mt-10) REVERT: A 269 ARG cc_start: 0.5202 (ptt-90) cc_final: 0.4655 (pmt170) REVERT: A 458 ARG cc_start: 0.8777 (tpm-80) cc_final: 0.8318 (tpt-90) REVERT: A 586 HIS cc_start: 0.6593 (OUTLIER) cc_final: 0.5763 (m90) REVERT: A 634 GLN cc_start: 0.9183 (mp10) cc_final: 0.8535 (mp10) REVERT: B 19 ARG cc_start: 0.8801 (mmt-90) cc_final: 0.8426 (mmp80) REVERT: B 76 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8433 (mm) REVERT: B 124 TYR cc_start: 0.8388 (t80) cc_final: 0.8184 (t80) REVERT: C 124 TYR cc_start: 0.7970 (t80) cc_final: 0.7685 (t80) REVERT: C 131 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6505 (ptp-170) REVERT: C 160 GLN cc_start: 0.8845 (tt0) cc_final: 0.8309 (tm-30) REVERT: C 278 TRP cc_start: 0.6996 (OUTLIER) cc_final: 0.5650 (m100) REVERT: D 33 TYR cc_start: 0.7720 (t80) cc_final: 0.7503 (t80) REVERT: D 124 TYR cc_start: 0.7905 (t80) cc_final: 0.7404 (t80) REVERT: D 394 ASN cc_start: 0.7820 (t0) cc_final: 0.7310 (m-40) REVERT: D 458 ARG cc_start: 0.8861 (ptm160) cc_final: 0.8499 (ptm160) REVERT: D 586 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.8130 (t-90) outliers start: 40 outliers final: 28 residues processed: 183 average time/residue: 0.5346 time to fit residues: 115.7731 Evaluate side-chains 177 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 610 MET 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 76 LEU 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 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 541 GLN Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 275 VAL 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 90 optimal weight: 9.9990 chunk 3 optimal weight: 0.3980 chunk 199 optimal weight: 4.9990 chunk 287 optimal weight: 0.9980 chunk 260 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 190 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 304 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.152012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.095536 restraints weight = 39104.443| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.56 r_work: 0.3047 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.235 25252 Z= 0.149 Angle : 0.658 59.190 34288 Z= 0.367 Chirality : 0.044 0.150 3997 Planarity : 0.003 0.046 4398 Dihedral : 6.409 86.293 3569 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 1.38 % Allowed : 14.99 % Favored : 83.63 % Cbeta Deviations : 0.03 % 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: 0.58 (0.15), residues: 3202 helix: 1.97 (0.15), residues: 1288 sheet: 0.05 (0.24), residues: 454 loop : -0.97 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 561 TYR 0.015 0.001 TYR C 33 PHE 0.008 0.001 PHE D 638 TRP 0.022 0.001 TRP D 278 HIS 0.002 0.000 HIS D 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (25244) covalent geometry : angle 0.65779 / 0.37 (34264) hydrogen bonds : bond 0.02789 / 1.94 ( 1198) hydrogen bonds : angle 4.10860 / 2.90 ( 3387) link_ASP_CG-ANY_N : bond 0.00103 / 0.05 ( 8) link_ASP_CG-ANY_N : angle 0.65989 / 0.41 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11741.88 seconds wall clock time: 200 minutes 17.33 seconds (12017.33 seconds total)