Starting phenix.real_space_refine on Sat Jun 21 15:33:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wae_32383/06_2025/7wae_32383.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wae_32383/06_2025/7wae_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wae_32383/06_2025/7wae_32383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wae_32383/06_2025/7wae_32383.map" model { file = "/net/cci-nas-00/data/ceres_data/7wae_32383/06_2025/7wae_32383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wae_32383/06_2025/7wae_32383.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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%COO:plan': 1, 'ASP:plan': 3} 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%COO:plan': 1, 'ASP:plan': 3} 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%COO:plan': 1, 'ASP:plan': 3} 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%COO:plan': 1, 'ASP:plan': 3} 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: 15.56, per 1000 atoms: 0.63 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: 6.08 Conformation dependent library (CDL) restraints added in 3.2 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: 3.63 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: 10.70 Time building geometry restraints manager: 7.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 8507 1.37 - 1.51: 7081 1.51 - 1.66: 9514 1.66 - 1.80: 123 1.80 - 1.95: 19 Bond restraints: 25244 Sorted by residual: bond pdb=" N ASN D 394 " pdb=" CA ASN D 394 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.64e+00 bond pdb=" N LYS D 220 " pdb=" CA LYS D 220 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.32e+00 bond pdb=" N LYS B 220 " pdb=" CA LYS B 220 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.20e-02 6.94e+03 6.00e+00 bond pdb=" N ARG A 458 " pdb=" CA ARG A 458 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.77e+00 bond pdb=" N ARG D 458 " pdb=" CA ARG D 458 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.30e-02 5.92e+03 5.36e+00 ... (remaining 25239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 33531 1.63 - 3.25: 614 3.25 - 4.88: 94 4.88 - 6.50: 13 6.50 - 8.13: 12 Bond angle restraints: 34264 Sorted by residual: angle pdb=" N GLU D 72 " pdb=" CA GLU D 72 " pdb=" CB GLU D 72 " ideal model delta sigma weight residual 110.12 115.79 -5.67 1.47e+00 4.63e-01 1.49e+01 angle pdb=" CA ASP K 3 " pdb=" CB ASP K 3 " pdb=" CG ASP K 3 " ideal model delta sigma weight residual 112.60 108.75 3.85 1.00e+00 1.00e+00 1.48e+01 angle pdb=" CA ASP M 3 " pdb=" CB ASP M 3 " pdb=" CG ASP M 3 " ideal model delta sigma weight residual 112.60 108.84 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CA ASP L 3 " pdb=" CB ASP L 3 " pdb=" CG ASP L 3 " ideal model delta sigma weight residual 112.60 108.95 3.65 1.00e+00 1.00e+00 1.33e+01 angle pdb=" CA ASP J 5 " pdb=" CB ASP J 5 " pdb=" CG ASP J 5 " ideal model delta sigma weight residual 112.60 109.30 3.30 1.00e+00 1.00e+00 1.09e+01 ... (remaining 34259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 13855 17.63 - 35.27: 1095 35.27 - 52.90: 227 52.90 - 70.53: 58 70.53 - 88.16: 22 Dihedral angle restraints: 15257 sinusoidal: 6129 harmonic: 9128 Sorted by residual: dihedral pdb=" CA THR C 496 " pdb=" C THR C 496 " pdb=" N ASN C 497 " pdb=" CA ASN C 497 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA THR D 496 " pdb=" C THR D 496 " pdb=" N ASN D 497 " pdb=" CA ASN D 497 " ideal model delta harmonic sigma weight residual -180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR B 660 " pdb=" C TYR B 660 " pdb=" N GLU B 661 " pdb=" CA GLU B 661 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 15254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2487 0.033 - 0.065: 927 0.065 - 0.098: 340 0.098 - 0.130: 223 0.130 - 0.163: 20 Chirality restraints: 3997 Sorted by residual: chirality pdb=" CA ASP J 2 " pdb=" N ASP J 2 " pdb=" C ASP J 2 " pdb=" CB ASP J 2 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CB ILE B 271 " pdb=" CA ILE B 271 " pdb=" CG1 ILE B 271 " pdb=" CG2 ILE B 271 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA ILE D 260 " pdb=" N ILE D 260 " pdb=" C ILE D 260 " pdb=" CB ILE D 260 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 3994 not shown) Planarity restraints: 4406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 458 " -0.231 9.50e-02 1.11e+02 1.04e-01 7.01e+00 pdb=" NE ARG B 458 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 458 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 458 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 458 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 60 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO C 61 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 60 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO D 61 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 61 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 61 " -0.030 5.00e-02 4.00e+02 ... (remaining 4403 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 198 2.57 - 3.15: 19940 3.15 - 3.73: 38665 3.73 - 4.32: 54154 4.32 - 4.90: 91118 Nonbonded interactions: 204075 Sorted by model distance: nonbonded pdb="MG MG D1003 " pdb=" O2B AGS D1005 " model vdw 1.987 2.170 nonbonded pdb="MG MG A1002 " pdb=" O2B AGS A1004 " model vdw 1.999 2.170 nonbonded pdb="MG MG B1003 " pdb=" O2B AGS B1005 " model vdw 2.009 2.170 nonbonded pdb=" OG1 THR B 522 " pdb="MG MG B1003 " model vdw 2.013 2.170 nonbonded pdb=" OG1 THR A 500 " pdb="MG MG A1002 " model vdw 2.015 2.170 ... (remaining 204070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 877 or resid 1001 through 1002 or resid 1004)) selection = (chain 'B' and (resid 1 through 877 or resid 1001 through 1002 or resid 1004)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 1 through 724 or resid 1001 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: 5.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 60.130 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25252 Z= 0.161 Angle : 0.562 8.131 34288 Z= 0.303 Chirality : 0.045 0.163 3997 Planarity : 0.004 0.104 4398 Dihedral : 13.863 88.165 9419 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.60 % Rotamer: Outliers : 0.27 % Allowed : 0.42 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (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 TRP 0.027 0.001 TRP C 278 HIS 0.009 0.001 HIS B 586 PHE 0.009 0.001 PHE D 480 TYR 0.015 0.001 TYR A 252 ARG 0.011 0.000 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.15288 ( 1198) hydrogen bonds : angle 6.07915 ( 3387) link_ASP_CG-ANY_N : bond 0.01136 ( 8) link_ASP_CG-ANY_N : angle 0.90841 ( 24) covalent geometry : bond 0.00320 (25244) covalent geometry : angle 0.56199 (34264) *********************** 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 : 2.866 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: 1.4998 time to fit residues: 396.1292 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 : 2.683 ------------------------------------------------------------------------------- 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 268 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 HIS ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** D 79 HIS ** 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 = 0.3971 r_free = 0.3971 target = 0.145805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.087562 restraints weight = 38945.573| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.64 r_work: 0.2913 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 25252 Z= 0.312 Angle : 0.650 7.649 34288 Z= 0.344 Chirality : 0.050 0.200 3997 Planarity : 0.005 0.053 4398 Dihedral : 8.810 74.315 3675 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.22 % Favored : 95.75 % Rotamer: Outliers : 1.64 % Allowed : 8.03 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3202 helix: 1.34 (0.15), residues: 1296 sheet: -0.17 (0.24), residues: 456 loop : -1.13 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 278 HIS 0.007 0.001 HIS C 327 PHE 0.016 0.002 PHE C 480 TYR 0.019 0.002 TYR A 14 ARG 0.006 0.001 ARG B 418 Details of bonding type rmsd hydrogen bonds : bond 0.04725 ( 1198) hydrogen bonds : angle 4.91590 ( 3387) link_ASP_CG-ANY_N : bond 0.00397 ( 8) link_ASP_CG-ANY_N : angle 0.90772 ( 24) covalent geometry : bond 0.00741 (25244) covalent geometry : angle 0.64982 (34264) *********************** 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 202 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 2.660 Fit side-chains REVERT: A 25 MET cc_start: 0.8515 (ptt) cc_final: 0.8078 (ptm) REVERT: A 35 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7633 (tmtt) REVERT: A 118 ASN cc_start: 0.7322 (t0) cc_final: 0.6983 (t0) REVERT: A 269 ARG cc_start: 0.5132 (ptt-90) cc_final: 0.4534 (pmt170) REVERT: A 586 HIS cc_start: 0.6878 (OUTLIER) cc_final: 0.6075 (m90) REVERT: B 586 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.6168 (m90) REVERT: C 131 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6475 (ptp-170) REVERT: C 160 GLN cc_start: 0.8866 (tt0) cc_final: 0.8347 (tm-30) REVERT: C 247 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.6930 (mp10) REVERT: C 278 TRP cc_start: 0.6758 (OUTLIER) cc_final: 0.5777 (m100) REVERT: C 443 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: D 586 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.8335 (t-90) outliers start: 43 outliers final: 11 residues processed: 189 average time/residue: 1.2711 time to fit residues: 281.1443 Evaluate side-chains 161 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 3.129 ------------------------------------------------------------------------------- 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 612 LYS Chi-restraints excluded: chain A residue 656 LEU 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 247 GLN Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain D residue 33 TYR 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 94 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 237 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 chunk 309 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 306 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 537 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.148993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.091861 restraints weight = 38751.636| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.55 r_work: 0.2989 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1357 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= 0.117 Angle : 0.508 7.253 34288 Z= 0.269 Chirality : 0.045 0.193 3997 Planarity : 0.004 0.054 4398 Dihedral : 8.313 83.750 3659 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 1.68 % Allowed : 10.29 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3202 helix: 1.60 (0.15), residues: 1304 sheet: -0.10 (0.26), residues: 392 loop : -1.10 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 278 HIS 0.006 0.001 HIS C 327 PHE 0.010 0.001 PHE B 638 TYR 0.016 0.001 TYR C 33 ARG 0.004 0.000 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 1198) hydrogen bonds : angle 4.57044 ( 3387) link_ASP_CG-ANY_N : bond 0.00126 ( 8) link_ASP_CG-ANY_N : angle 0.76037 ( 24) covalent geometry : bond 0.00257 (25244) covalent geometry : angle 0.50804 (34264) *********************** 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 201 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8539 (ptt) cc_final: 0.8120 (ptm) REVERT: A 35 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7752 (tmtt) REVERT: A 102 ARG cc_start: 0.7697 (mmt90) cc_final: 0.7480 (mpt180) REVERT: A 118 ASN cc_start: 0.7376 (t0) cc_final: 0.7070 (t0) REVERT: A 269 ARG cc_start: 0.5262 (ptt-90) cc_final: 0.4713 (pmt170) REVERT: A 458 ARG cc_start: 0.8857 (tpm-80) cc_final: 0.8616 (tpt170) REVERT: A 586 HIS cc_start: 0.6742 (OUTLIER) cc_final: 0.5968 (m90) REVERT: B 586 HIS cc_start: 0.6934 (OUTLIER) cc_final: 0.6023 (m90) REVERT: C 76 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7688 (mm) REVERT: C 131 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6300 (ptp-170) REVERT: C 160 GLN cc_start: 0.8822 (tt0) cc_final: 0.8337 (tm-30) REVERT: C 278 TRP cc_start: 0.7042 (OUTLIER) cc_final: 0.5657 (m100) REVERT: C 327 HIS cc_start: 0.7999 (p90) cc_final: 0.7781 (p90) REVERT: C 586 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7653 (t-90) REVERT: C 661 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.8023 (pt0) REVERT: D 586 HIS cc_start: 0.8459 (OUTLIER) cc_final: 0.8203 (t-90) outliers start: 44 outliers final: 10 residues processed: 187 average time/residue: 1.2121 time to fit residues: 267.7857 Evaluate side-chains 168 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 2.605 ------------------------------------------------------------------------------- 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 103 GLU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 586 HIS Chi-restraints excluded: chain C residue 661 GLU 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 279 optimal weight: 10.0000 chunk 306 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 195 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 276 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 282 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4007 r_free = 0.4007 target = 0.148613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.091472 restraints weight = 39368.415| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.55 r_work: 0.2979 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25252 Z= 0.152 Angle : 0.517 7.446 34288 Z= 0.273 Chirality : 0.045 0.162 3997 Planarity : 0.004 0.048 4398 Dihedral : 8.235 84.984 3657 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.72 % Favored : 96.25 % Rotamer: Outliers : 2.03 % Allowed : 11.82 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3202 helix: 1.68 (0.15), residues: 1302 sheet: -0.15 (0.23), residues: 492 loop : -1.07 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 278 HIS 0.004 0.001 HIS C 327 PHE 0.010 0.001 PHE C 480 TYR 0.018 0.001 TYR C 33 ARG 0.003 0.000 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 1198) hydrogen bonds : angle 4.47452 ( 3387) link_ASP_CG-ANY_N : bond 0.00143 ( 8) link_ASP_CG-ANY_N : angle 0.72698 ( 24) covalent geometry : bond 0.00351 (25244) covalent geometry : angle 0.51700 (34264) *********************** 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 205 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 152 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8530 (ptt) cc_final: 0.8101 (ptm) REVERT: A 35 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7767 (tmtt) REVERT: A 118 ASN cc_start: 0.7425 (t0) cc_final: 0.7155 (t0) REVERT: A 269 ARG cc_start: 0.5246 (ptt-90) cc_final: 0.4898 (pmt170) REVERT: A 458 ARG cc_start: 0.8874 (tpm-80) cc_final: 0.8356 (tpt-90) REVERT: A 586 HIS cc_start: 0.6682 (OUTLIER) cc_final: 0.5912 (m90) REVERT: A 732 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6395 (mpp) REVERT: B 586 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.5884 (m90) REVERT: C 76 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7733 (mm) REVERT: C 131 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6412 (ptp-170) REVERT: C 160 GLN cc_start: 0.8850 (tt0) cc_final: 0.8339 (tm-30) REVERT: C 278 TRP cc_start: 0.7005 (OUTLIER) cc_final: 0.5622 (m100) REVERT: C 586 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7613 (t-90) REVERT: D 33 TYR cc_start: 0.7684 (t80) cc_final: 0.7479 (t80) REVERT: D 44 TYR cc_start: 0.7480 (t80) cc_final: 0.7174 (t80) REVERT: D 458 ARG cc_start: 0.8993 (ptm160) cc_final: 0.8754 (ptm160) outliers start: 53 outliers final: 20 residues processed: 190 average time/residue: 1.1798 time to fit residues: 265.0474 Evaluate side-chains 175 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 2.624 ------------------------------------------------------------------------------- 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 103 GLU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 586 HIS Chi-restraints excluded: chain D residue 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 298 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 70 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 234 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 275 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 255 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 HIS ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 247 GLN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 713 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.149971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.092277 restraints weight = 38969.603| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.62 r_work: 0.2996 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25252 Z= 0.104 Angle : 0.488 9.443 34288 Z= 0.256 Chirality : 0.044 0.150 3997 Planarity : 0.004 0.048 4398 Dihedral : 8.031 85.696 3657 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 1.95 % Allowed : 12.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3202 helix: 1.80 (0.15), residues: 1294 sheet: -0.05 (0.24), residues: 448 loop : -1.04 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 278 HIS 0.006 0.001 HIS C 327 PHE 0.009 0.001 PHE B 638 TYR 0.017 0.001 TYR C 33 ARG 0.002 0.000 ARG B 561 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 1198) hydrogen bonds : angle 4.31210 ( 3387) link_ASP_CG-ANY_N : bond 0.00108 ( 8) link_ASP_CG-ANY_N : angle 0.69081 ( 24) covalent geometry : bond 0.00230 (25244) covalent geometry : angle 0.48790 (34264) *********************** 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 209 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 3.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8564 (ptt) cc_final: 0.8166 (ptm) REVERT: A 35 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7709 (tmtt) REVERT: A 58 LEU cc_start: 0.8378 (mp) cc_final: 0.8159 (mm) REVERT: A 118 ASN cc_start: 0.7426 (t0) cc_final: 0.7192 (t0) REVERT: A 269 ARG cc_start: 0.5195 (ptt-90) cc_final: 0.4740 (pmt170) REVERT: A 458 ARG cc_start: 0.8849 (tpm-80) cc_final: 0.8345 (tpt-90) REVERT: A 586 HIS cc_start: 0.6592 (OUTLIER) cc_final: 0.5808 (m90) REVERT: A 634 GLN cc_start: 0.9180 (mp10) cc_final: 0.8461 (mp10) REVERT: B 732 MET cc_start: 0.6615 (mmp) cc_final: 0.6340 (mmp) REVERT: C 76 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7643 (mm) REVERT: C 131 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6390 (ptp-170) REVERT: C 160 GLN cc_start: 0.8853 (tt0) cc_final: 0.8324 (tm-30) REVERT: C 247 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.6993 (pm20) REVERT: C 278 TRP cc_start: 0.6971 (OUTLIER) cc_final: 0.6021 (m100) REVERT: C 586 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.7639 (t-90) REVERT: D 33 TYR cc_start: 0.7660 (t80) cc_final: 0.7426 (t80) REVERT: D 44 TYR cc_start: 0.7607 (t80) cc_final: 0.7331 (t80) REVERT: D 586 HIS cc_start: 0.8435 (OUTLIER) cc_final: 0.8126 (t-90) outliers start: 51 outliers final: 23 residues processed: 195 average time/residue: 1.2541 time to fit residues: 289.9550 Evaluate side-chains 178 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 3.190 ------------------------------------------------------------------------------- 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 103 GLU 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 82 GLU Chi-restraints excluded: chain B residue 86 ILE 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 76 LEU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 586 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 266 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 273 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 281 optimal weight: 20.0000 chunk 218 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 327 HIS C 541 GLN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.146440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.087566 restraints weight = 38658.981| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.61 r_work: 0.2859 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 25252 Z= 0.249 Angle : 0.570 8.374 34288 Z= 0.301 Chirality : 0.048 0.169 3997 Planarity : 0.004 0.047 4398 Dihedral : 8.213 86.386 3657 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 2.37 % Allowed : 13.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3202 helix: 1.65 (0.15), residues: 1304 sheet: -0.10 (0.25), residues: 426 loop : -1.08 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 278 HIS 0.006 0.001 HIS A 327 PHE 0.014 0.002 PHE C 480 TYR 0.017 0.002 TYR A 14 ARG 0.004 0.000 ARG B 418 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 1198) hydrogen bonds : angle 4.52472 ( 3387) link_ASP_CG-ANY_N : bond 0.00217 ( 8) link_ASP_CG-ANY_N : angle 0.74948 ( 24) covalent geometry : bond 0.00597 (25244) covalent geometry : angle 0.57027 (34264) *********************** 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 209 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 147 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8524 (ptt) cc_final: 0.8124 (ptm) REVERT: A 35 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7627 (tmtt) REVERT: A 118 ASN cc_start: 0.7500 (t0) cc_final: 0.7196 (t0) REVERT: A 269 ARG cc_start: 0.5094 (ptt-90) cc_final: 0.4615 (pmt170) REVERT: A 458 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8315 (tpt-90) REVERT: A 586 HIS cc_start: 0.6644 (OUTLIER) cc_final: 0.5778 (m90) REVERT: B 586 HIS cc_start: 0.6601 (OUTLIER) cc_final: 0.5714 (m90) REVERT: B 732 MET cc_start: 0.6730 (mmp) cc_final: 0.6489 (mmp) REVERT: C 76 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7858 (mm) REVERT: C 131 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6601 (ptp-170) REVERT: C 160 GLN cc_start: 0.8857 (tt0) cc_final: 0.8338 (tm-30) REVERT: C 278 TRP cc_start: 0.7077 (OUTLIER) cc_final: 0.5667 (m100) REVERT: D 33 TYR cc_start: 0.7785 (t80) cc_final: 0.7554 (t80) REVERT: D 44 TYR cc_start: 0.7815 (t80) cc_final: 0.7376 (t80) REVERT: D 458 ARG cc_start: 0.8926 (ptm160) cc_final: 0.8602 (ptm160) outliers start: 62 outliers final: 31 residues processed: 195 average time/residue: 1.1803 time to fit residues: 273.0679 Evaluate side-chains 181 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 2.680 ------------------------------------------------------------------------------- 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 107 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 1 MET 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 631 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 134 optimal weight: 0.7980 chunk 171 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 278 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 308 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 209 optimal weight: 3.9990 chunk 126 optimal weight: 0.4980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.146752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.087901 restraints weight = 38664.605| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.62 r_work: 0.2867 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25252 Z= 0.205 Angle : 0.553 11.001 34288 Z= 0.291 Chirality : 0.046 0.169 3997 Planarity : 0.004 0.046 4398 Dihedral : 8.153 86.225 3657 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 2.10 % Allowed : 14.00 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3202 helix: 1.62 (0.15), residues: 1300 sheet: -0.25 (0.25), residues: 432 loop : -1.07 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 278 HIS 0.004 0.001 HIS A 327 PHE 0.011 0.002 PHE C 480 TYR 0.016 0.001 TYR C 33 ARG 0.004 0.000 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 1198) hydrogen bonds : angle 4.49871 ( 3387) link_ASP_CG-ANY_N : bond 0.00179 ( 8) link_ASP_CG-ANY_N : angle 0.72328 ( 24) covalent geometry : bond 0.00483 (25244) covalent geometry : angle 0.55272 (34264) *********************** 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 202 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 147 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8576 (ptt) cc_final: 0.8162 (ptm) REVERT: A 35 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7680 (tmtt) REVERT: A 103 GLU cc_start: 0.8354 (mp0) cc_final: 0.7997 (tp30) REVERT: A 118 ASN cc_start: 0.7546 (t0) cc_final: 0.7319 (t0) REVERT: A 269 ARG cc_start: 0.4929 (ptt-90) cc_final: 0.4423 (pmt170) REVERT: A 458 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8334 (tpt-90) REVERT: A 586 HIS cc_start: 0.6619 (OUTLIER) cc_final: 0.5741 (m90) REVERT: B 586 HIS cc_start: 0.6677 (OUTLIER) cc_final: 0.5796 (m90) REVERT: B 732 MET cc_start: 0.6780 (mmp) cc_final: 0.6480 (mmp) REVERT: C 76 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7916 (mm) REVERT: C 131 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6590 (ptp-170) REVERT: C 160 GLN cc_start: 0.8848 (tt0) cc_final: 0.8336 (tm-30) REVERT: C 278 TRP cc_start: 0.7079 (OUTLIER) cc_final: 0.5621 (m100) REVERT: D 33 TYR cc_start: 0.7838 (t80) cc_final: 0.7633 (t80) REVERT: D 44 TYR cc_start: 0.7872 (t80) cc_final: 0.7561 (t80) REVERT: D 458 ARG cc_start: 0.8944 (ptm160) cc_final: 0.8622 (ptm160) REVERT: D 586 HIS cc_start: 0.8608 (OUTLIER) cc_final: 0.8239 (t-90) REVERT: J 101 ARG cc_start: 0.2533 (OUTLIER) cc_final: 0.1628 (ttm-80) outliers start: 55 outliers final: 25 residues processed: 186 average time/residue: 1.2673 time to fit residues: 281.5835 Evaluate side-chains 176 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 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 76 LEU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 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 1 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 586 HIS Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain J residue 101 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 73 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 292 optimal weight: 0.9990 chunk 306 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS D 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.148630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.091253 restraints weight = 39070.626| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.58 r_work: 0.2990 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1929 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= 0.127 Angle : 0.501 7.627 34288 Z= 0.264 Chirality : 0.045 0.146 3997 Planarity : 0.004 0.046 4398 Dihedral : 7.852 86.333 3657 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 1.95 % Allowed : 14.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3202 helix: 1.79 (0.15), residues: 1288 sheet: -0.21 (0.23), residues: 490 loop : -1.03 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 278 HIS 0.003 0.001 HIS D 650 PHE 0.011 0.001 PHE D 638 TYR 0.017 0.001 TYR A 14 ARG 0.003 0.000 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 1198) hydrogen bonds : angle 4.33432 ( 3387) link_ASP_CG-ANY_N : bond 0.00117 ( 8) link_ASP_CG-ANY_N : angle 0.68825 ( 24) covalent geometry : bond 0.00290 (25244) covalent geometry : angle 0.50112 (34264) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8588 (ptt) cc_final: 0.8194 (ptm) REVERT: A 35 LYS cc_start: 0.8024 (tmtt) cc_final: 0.7684 (tmtt) REVERT: A 103 GLU cc_start: 0.8369 (mp0) cc_final: 0.8012 (tp30) REVERT: A 118 ASN cc_start: 0.7552 (t0) cc_final: 0.7322 (t0) REVERT: A 269 ARG cc_start: 0.5033 (ptt-90) cc_final: 0.4499 (pmt170) REVERT: A 458 ARG cc_start: 0.8774 (tpm-80) cc_final: 0.8290 (tpt-90) REVERT: A 586 HIS cc_start: 0.6589 (OUTLIER) cc_final: 0.5721 (m90) REVERT: B 76 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8439 (mm) REVERT: B 586 HIS cc_start: 0.6600 (OUTLIER) cc_final: 0.5723 (m90) REVERT: B 732 MET cc_start: 0.6548 (mmp) cc_final: 0.6274 (mmp) REVERT: C 76 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7862 (mm) REVERT: C 131 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6475 (ptp-170) REVERT: C 160 GLN cc_start: 0.8858 (tt0) cc_final: 0.8351 (tm-30) REVERT: C 278 TRP cc_start: 0.7006 (OUTLIER) cc_final: 0.5581 (m100) REVERT: D 301 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8103 (ttt90) REVERT: D 458 ARG cc_start: 0.8931 (ptm160) cc_final: 0.8594 (ptm160) REVERT: D 586 HIS cc_start: 0.8476 (OUTLIER) cc_final: 0.8135 (t-90) REVERT: J 101 ARG cc_start: 0.2526 (OUTLIER) cc_final: 0.1636 (ttm-80) outliers start: 51 outliers final: 29 residues processed: 184 average time/residue: 1.2751 time to fit residues: 276.5149 Evaluate side-chains 178 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 2.789 ------------------------------------------------------------------------------- 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 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 82 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 328 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 76 LEU 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 251 GLU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 586 HIS Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain J residue 101 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 1.9990 chunk 247 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 225 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 278 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 260 optimal weight: 0.3980 chunk 130 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS D 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.147766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.090317 restraints weight = 39377.445| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.57 r_work: 0.2959 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25252 Z= 0.177 Angle : 0.538 11.787 34288 Z= 0.282 Chirality : 0.046 0.152 3997 Planarity : 0.004 0.045 4398 Dihedral : 7.795 87.040 3657 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.10 % Allowed : 14.11 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3202 helix: 1.74 (0.15), residues: 1296 sheet: -0.16 (0.23), residues: 482 loop : -1.10 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 278 HIS 0.003 0.001 HIS A 327 PHE 0.011 0.001 PHE C 480 TYR 0.021 0.001 TYR D 44 ARG 0.003 0.000 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 1198) hydrogen bonds : angle 4.40262 ( 3387) link_ASP_CG-ANY_N : bond 0.00165 ( 8) link_ASP_CG-ANY_N : angle 0.71872 ( 24) covalent geometry : bond 0.00416 (25244) covalent geometry : angle 0.53774 (34264) *********************** 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 195 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 140 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8572 (ptt) cc_final: 0.8182 (ptm) REVERT: A 35 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7623 (tmtt) REVERT: A 103 GLU cc_start: 0.8425 (mp0) cc_final: 0.8016 (tp30) REVERT: A 118 ASN cc_start: 0.7568 (t0) cc_final: 0.7347 (t0) REVERT: A 269 ARG cc_start: 0.4974 (ptt-90) cc_final: 0.4447 (pmt170) REVERT: A 458 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8304 (tpt-90) REVERT: A 586 HIS cc_start: 0.6647 (OUTLIER) cc_final: 0.5757 (m90) REVERT: B 76 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8443 (mm) REVERT: B 586 HIS cc_start: 0.6677 (OUTLIER) cc_final: 0.5836 (m90) REVERT: B 732 MET cc_start: 0.6592 (mmp) cc_final: 0.6375 (mmp) REVERT: C 76 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.7921 (mm) REVERT: C 131 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6582 (ptp-170) REVERT: C 160 GLN cc_start: 0.8857 (tt0) cc_final: 0.8341 (tm-30) REVERT: C 278 TRP cc_start: 0.7047 (OUTLIER) cc_final: 0.5612 (m100) REVERT: C 677 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8510 (mm-30) REVERT: D 458 ARG cc_start: 0.8905 (ptm160) cc_final: 0.8573 (ptm160) REVERT: D 586 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.8115 (t-90) REVERT: J 101 ARG cc_start: 0.2512 (OUTLIER) cc_final: 0.1628 (ttm-80) outliers start: 55 outliers final: 30 residues processed: 184 average time/residue: 1.1998 time to fit residues: 262.6154 Evaluate side-chains 178 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 2.713 ------------------------------------------------------------------------------- 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 94 MET Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 631 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 329 VAL Chi-restraints excluded: chain D residue 586 HIS Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain J residue 101 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 55 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 240 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.144651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085868 restraints weight = 38564.026| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.63 r_work: 0.2849 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 25252 Z= 0.265 Angle : 0.598 8.715 34288 Z= 0.317 Chirality : 0.049 0.187 3997 Planarity : 0.004 0.045 4398 Dihedral : 7.977 87.238 3657 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.87 % Allowed : 14.38 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3202 helix: 1.55 (0.15), residues: 1306 sheet: -0.39 (0.24), residues: 436 loop : -1.14 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 278 HIS 0.005 0.001 HIS A 327 PHE 0.014 0.002 PHE C 480 TYR 0.020 0.002 TYR A 14 ARG 0.004 0.000 ARG B 418 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 1198) hydrogen bonds : angle 4.60637 ( 3387) link_ASP_CG-ANY_N : bond 0.00220 ( 8) link_ASP_CG-ANY_N : angle 0.78841 ( 24) covalent geometry : bond 0.00628 (25244) covalent geometry : angle 0.59826 (34264) ********************** 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 187 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 138 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8559 (ptt) cc_final: 0.8164 (ptm) REVERT: A 35 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7658 (tmtt) REVERT: A 118 ASN cc_start: 0.7589 (t0) cc_final: 0.7323 (t0) REVERT: A 269 ARG cc_start: 0.4857 (ptt-90) cc_final: 0.4297 (pmt170) REVERT: A 458 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8312 (tpt-90) REVERT: A 586 HIS cc_start: 0.6647 (OUTLIER) cc_final: 0.5735 (m90) REVERT: B 586 HIS cc_start: 0.6648 (OUTLIER) cc_final: 0.5766 (m90) REVERT: B 732 MET cc_start: 0.6773 (mmp) cc_final: 0.6520 (mmp) REVERT: C 76 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.7926 (mm) REVERT: C 131 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6680 (ptp-170) REVERT: C 278 TRP cc_start: 0.7112 (OUTLIER) cc_final: 0.5630 (m100) REVERT: C 677 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8556 (mm-30) REVERT: D 458 ARG cc_start: 0.8915 (ptm160) cc_final: 0.8587 (ptm160) REVERT: J 101 ARG cc_start: 0.2581 (OUTLIER) cc_final: 0.1697 (ttm-80) outliers start: 49 outliers final: 29 residues processed: 176 average time/residue: 1.3685 time to fit residues: 284.7374 Evaluate side-chains 170 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain D residue 145 THR 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 631 VAL Chi-restraints excluded: chain J residue 101 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 144 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 220 optimal weight: 0.0060 chunk 143 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS D 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.148877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.091947 restraints weight = 39218.337| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.55 r_work: 0.2989 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25252 Z= 0.116 Angle : 0.518 13.399 34288 Z= 0.272 Chirality : 0.045 0.174 3997 Planarity : 0.004 0.046 4398 Dihedral : 7.576 87.211 3657 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.53 % Allowed : 14.84 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3202 helix: 1.77 (0.15), residues: 1288 sheet: -0.28 (0.24), residues: 448 loop : -1.09 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 278 HIS 0.003 0.000 HIS D 650 PHE 0.012 0.001 PHE D 43 TYR 0.017 0.001 TYR D 44 ARG 0.004 0.000 ARG D 301 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 1198) hydrogen bonds : angle 4.35497 ( 3387) link_ASP_CG-ANY_N : bond 0.00114 ( 8) link_ASP_CG-ANY_N : angle 0.68808 ( 24) covalent geometry : bond 0.00258 (25244) covalent geometry : angle 0.51811 (34264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26559.44 seconds wall clock time: 457 minutes 16.92 seconds (27436.92 seconds total)