Starting phenix.real_space_refine on Sun Jul 5 02:20:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7waf_32384/07_2026/7waf_32384.cif Found real_map, /net/cci-nas-00/data/ceres_data/7waf_32384/07_2026/7waf_32384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7waf_32384/07_2026/7waf_32384.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7waf_32384/07_2026/7waf_32384.cif" model { file = "/net/cci-nas-00/data/ceres_data/7waf_32384/07_2026/7waf_32384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7waf_32384/07_2026/7waf_32384.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7waf_32384/07_2026/7waf_32384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7waf_32384/07_2026/7waf_32384.map" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 12 5.21 5 S 88 5.16 5 C 15574 2.51 5 N 4356 2.21 5 O 4788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24842 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: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 3, 'ASP%COO:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 3, 'ASP%COO:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 3, 'ASP%COO:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 3, 'ASP%COO:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" 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: "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: 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: "I" 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: "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 Time building chain proxies: 5.40, per 1000 atoms: 0.22 Number of scatterers: 24842 At special positions: 0 Unit cell: (165.17, 163.51, 123.67, 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 12 11.99 O 4788 8.00 N 4356 7.00 C 15574 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 I 3 " - " ARG I 101 " " ASP I 5 " - " ARG I 102 " " 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 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.2 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: 5812 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 26 sheets defined 43.3% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 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: 3.725A pdb=" N VAL A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 140 removed outlier: 3.840A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.712A 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: 4.596A pdb=" N ASP A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.669A pdb=" N ALA A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 4.503A pdb=" N GLU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.647A 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: 3.868A 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: 3.728A pdb=" N THR A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 548 removed outlier: 4.154A pdb=" N LEU A 545 " --> pdb=" O GLN A 541 " (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: 3.797A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 627 removed outlier: 3.572A 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: 3.673A 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: 3.549A 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: 3.862A 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: 3.725A pdb=" N VAL B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 140 removed outlier: 3.843A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.715A 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: 4.606A pdb=" N ASP B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.679A pdb=" N ALA B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 345 removed outlier: 4.515A pdb=" N GLU B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.643A 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: 3.868A 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 470 through 480 Processing helix chain 'B' and resid 498 through 513 removed outlier: 3.726A pdb=" N THR B 513 " --> pdb=" O ILE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 548 removed outlier: 4.167A pdb=" N LEU B 545 " --> pdb=" O GLN B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.531A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 608 removed outlier: 3.798A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 627 removed outlier: 3.578A pdb=" N MET B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) 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: 3.667A 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: 3.552A 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: 3.861A 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: 4.051A pdb=" N VAL C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 140 removed outlier: 3.783A pdb=" N VAL C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.738A 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 219 Processing helix chain 'C' and resid 219 through 230 Processing helix chain 'C' and resid 245 through 254 removed outlier: 3.543A pdb=" N TYR C 252 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.769A 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: 4.740A pdb=" N GLU C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 374 removed outlier: 3.984A pdb=" N GLY C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 384 removed outlier: 3.899A 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: 3.862A 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: 4.040A pdb=" N THR C 513 " --> pdb=" O ILE C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 549 removed outlier: 4.173A pdb=" N LEU C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 568 removed outlier: 3.522A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 608 removed outlier: 3.796A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) removed outlier: 4.223A 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: 3.656A 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 Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 76 through 92 removed outlier: 4.042A 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: 3.781A pdb=" N VAL D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.732A 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: 3.527A pdb=" N TYR D 252 " --> pdb=" O ASP D 248 " (cutoff:3.500A) removed outlier: 3.768A 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: 4.724A pdb=" N GLU D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN D 344 " --> pdb=" O ILE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 374 removed outlier: 3.989A pdb=" N GLY D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 384 removed outlier: 3.873A 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: 4.037A pdb=" N THR D 513 " --> pdb=" O ILE D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 549 removed outlier: 4.147A pdb=" N LEU D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 568 removed outlier: 3.518A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 608 removed outlier: 3.795A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) removed outlier: 4.224A 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: 3.653A 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: 5.847A pdb=" N ILE A 3 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP A 28 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 3.728A 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: 5.154A pdb=" N VAL A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL A 313 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 319 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP A 307 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ILE A 427 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ALA A 453 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY A 429 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 451 " --> pdb=" O GLY A 429 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP A 431 " --> pdb=" O VAL A 449 " (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: 6.594A pdb=" N THR A 525 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 490 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE A 578 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER A 492 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLU A 575 " --> pdb=" O LYS A 612 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 618 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN A 634 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY A 613 " --> pdb=" O GLN A 634 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA A 636 " --> pdb=" O GLY A 613 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA A 615 " --> pdb=" O ALA A 636 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE A 638 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU A 617 " --> pdb=" O PHE A 638 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 660 " --> pdb=" O SER A 639 " (cutoff:3.500A) removed outlier: 6.791A 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: 6.560A 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: 5.849A pdb=" N ILE B 3 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP B 28 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 3.727A 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 Processing sheet with id=AB2, first strand: chain 'B' and resid 400 through 403 removed outlier: 5.152A pdb=" N VAL B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 313 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 319 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP B 307 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ILE B 427 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA B 453 " --> pdb=" O ILE B 427 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY B 429 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL B 451 " --> pdb=" O GLY B 429 " (cutoff:3.500A) removed outlier: 6.668A 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: 6.587A pdb=" N THR B 525 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 490 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE B 578 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER B 492 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLU B 575 " --> pdb=" O LYS B 612 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN B 618 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN B 634 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLY B 613 " --> pdb=" O GLN B 634 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA B 636 " --> pdb=" O GLY B 613 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA B 615 " --> pdb=" O ALA B 636 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE B 638 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU B 617 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR B 660 " --> pdb=" O SER B 639 " (cutoff:3.500A) removed outlier: 6.796A 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: 6.565A 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: 6.188A pdb=" N ILE C 3 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP C 28 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 3.795A 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: 6.954A pdb=" N ILE C 258 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 4.540A 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: 5.156A pdb=" N VAL C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL C 313 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 319 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP C 307 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ILE C 427 " --> pdb=" O ALA C 453 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALA C 453 " --> pdb=" O ILE C 427 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLY C 429 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL C 451 " --> pdb=" O GLY C 429 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP C 431 " --> pdb=" O VAL C 449 " (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 533 removed outlier: 6.578A pdb=" N THR C 525 " --> pdb=" O ALA C 532 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE C 490 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE C 578 " --> pdb=" O ILE C 490 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER C 492 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLU C 575 " --> pdb=" O LYS C 612 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN C 618 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 4.500A 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: 7.486A pdb=" N ALA C 636 " --> pdb=" O GLY C 613 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA C 615 " --> pdb=" O ALA C 636 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N PHE C 638 " --> pdb=" O ALA C 615 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU C 617 " --> pdb=" O PHE C 638 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR C 660 " --> pdb=" O SER C 639 " (cutoff:3.500A) removed outlier: 6.805A 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: 3.603A pdb=" N LYS D 2 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG D 26 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU D 6 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL D 24 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR D 8 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU D 22 " --> pdb=" O THR D 8 " (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: 3.521A pdb=" N VAL D 297 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE D 258 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 4.512A 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: 5.155A pdb=" N VAL D 317 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL D 313 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 319 " --> pdb=" O LEU D 311 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP D 307 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D 450 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL D 433 " --> pdb=" O ILE D 448 " (cutoff:3.500A) removed outlier: 5.718A 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 533 removed outlier: 6.577A pdb=" N THR D 525 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE D 490 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE D 578 " --> pdb=" O ILE D 490 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER D 492 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLU D 575 " --> pdb=" O LYS D 612 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN D 618 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN D 634 " --> pdb=" O PRO D 611 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY D 613 " --> pdb=" O GLN D 634 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ALA D 636 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ALA D 615 " --> pdb=" O ALA D 636 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N PHE D 638 " --> pdb=" O ALA D 615 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU D 617 " --> pdb=" O PHE D 638 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR D 660 " --> pdb=" O SER D 639 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 665 " --> pdb=" O ILE D 676 " (cutoff:3.500A) 1190 hydrogen bonds defined for protein. 3351 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.58 Time building geometry restraints manager: 2.79 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: 8505 1.37 - 1.51: 6855 1.51 - 1.66: 9734 1.66 - 1.80: 121 1.80 - 1.95: 21 Bond restraints: 25236 Sorted by residual: bond pdb=" N ASN C 394 " pdb=" CA ASN C 394 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.85e+00 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 6.68e+00 bond pdb=" N ARG D 323 " pdb=" CA ARG D 323 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.27e-02 6.20e+03 4.73e+00 bond pdb=" N ARG C 323 " pdb=" CA ARG C 323 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.27e-02 6.20e+03 4.73e+00 bond pdb=" CG GLU C 168 " pdb=" CD GLU C 168 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.17e+00 ... (remaining 25231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 33737 1.98 - 3.97: 441 3.97 - 5.95: 60 5.95 - 7.93: 5 7.93 - 9.92: 11 Bond angle restraints: 34254 Sorted by residual: angle pdb=" CA ASP L 3 " pdb=" CB ASP L 3 " pdb=" CG ASP L 3 " ideal model delta sigma weight residual 112.60 108.88 3.72 1.00e+00 1.00e+00 1.38e+01 angle pdb=" CA ASP I 3 " pdb=" CB ASP I 3 " pdb=" CG ASP I 3 " ideal model delta sigma weight residual 112.60 109.05 3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" CA ASP K 3 " pdb=" CB ASP K 3 " pdb=" CG ASP K 3 " ideal model delta sigma weight residual 112.60 109.15 3.45 1.00e+00 1.00e+00 1.19e+01 angle pdb=" CA ASP J 3 " pdb=" CB ASP J 3 " pdb=" CG ASP J 3 " ideal model delta sigma weight residual 112.60 109.23 3.37 1.00e+00 1.00e+00 1.13e+01 angle pdb=" CA ASP K 5 " pdb=" CB ASP K 5 " pdb=" CG ASP K 5 " ideal model delta sigma weight residual 112.60 109.34 3.26 1.00e+00 1.00e+00 1.06e+01 ... (remaining 34249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 13863 17.73 - 35.46: 1023 35.46 - 53.19: 216 53.19 - 70.91: 35 70.91 - 88.64: 27 Dihedral angle restraints: 15164 sinusoidal: 6038 harmonic: 9126 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 -160.60 -19.40 0 5.00e+00 4.00e-02 1.51e+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 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+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 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 15161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2570 0.035 - 0.071: 917 0.071 - 0.106: 307 0.106 - 0.141: 189 0.141 - 0.177: 13 Chirality restraints: 3996 Sorted by residual: 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 2.61 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE C 260 " pdb=" N ILE C 260 " pdb=" C ILE C 260 " pdb=" CB ILE C 260 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA ILE B 114 " pdb=" N ILE B 114 " pdb=" C ILE B 114 " pdb=" CB ILE B 114 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 3993 not shown) Planarity restraints: 4404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 60 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 61 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 60 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO D 61 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 61 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 61 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 60 " -0.031 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO A 61 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " -0.026 5.00e-02 4.00e+02 ... (remaining 4401 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 187 2.56 - 3.15: 19697 3.15 - 3.73: 38845 3.73 - 4.32: 54366 4.32 - 4.90: 91202 Nonbonded interactions: 204297 Sorted by model distance: nonbonded pdb=" OD1 ASP A 745 " pdb=" O3' AGS A1005 " model vdw 1.979 3.040 nonbonded pdb=" OG1 THR A 500 " pdb="MG MG A1003 " model vdw 1.984 2.170 nonbonded pdb="MG MG A1003 " pdb=" O2B AGS A1005 " model vdw 1.984 2.170 nonbonded pdb="MG MG C1003 " pdb=" O2B AGS C1005 " model vdw 1.987 2.170 nonbonded pdb=" OG1 THR C 522 " pdb="MG MG C1003 " model vdw 1.990 2.170 ... (remaining 204292 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 5.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.970 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 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 0.037 25244 Z= 0.138 Angle : 0.577 9.917 34278 Z= 0.309 Chirality : 0.046 0.177 3996 Planarity : 0.004 0.054 4396 Dihedral : 13.605 88.642 9328 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.25 % Rotamer: Outliers : 0.11 % Allowed : 0.38 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 3202 helix: 1.54 (0.15), residues: 1238 sheet: -0.12 (0.24), residues: 440 loop : -1.06 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 561 TYR 0.010 0.001 TYR B 519 PHE 0.011 0.001 PHE A 638 TRP 0.023 0.001 TRP D 278 HIS 0.003 0.001 HIS C 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (25236) covalent geometry : angle 0.57649 / 0.31 (34254) hydrogen bonds : bond 0.13494 / 9.00 ( 1190) hydrogen bonds : angle 5.61071 / 3.97 ( 3351) link_ASP_CG-ANY_N : bond 0.01102 / 0.57 ( 8) link_ASP_CG-ANY_N : angle 0.91817 / 0.56 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 211 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: B 476 MET cc_start: 0.9317 (mmm) cc_final: 0.9027 (tpt) REVERT: C 280 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7962 (mt-10) REVERT: D 280 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7949 (mt-10) outliers start: 3 outliers final: 1 residues processed: 214 average time/residue: 0.6572 time to fit residues: 162.3766 Evaluate side-chains 144 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.0020 chunk 298 optimal weight: 3.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 GLN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 HIS ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 713 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.150760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.090974 restraints weight = 37191.519| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.64 r_work: 0.3009 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25244 Z= 0.114 Angle : 0.523 8.311 34278 Z= 0.276 Chirality : 0.045 0.152 3996 Planarity : 0.004 0.051 4396 Dihedral : 6.828 76.159 3570 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 1.03 % Allowed : 8.00 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 3202 helix: 1.59 (0.15), residues: 1284 sheet: -0.04 (0.24), residues: 468 loop : -1.07 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 301 TYR 0.015 0.001 TYR A 252 PHE 0.011 0.001 PHE D 243 TRP 0.014 0.001 TRP D 278 HIS 0.004 0.001 HIS D 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (25236) covalent geometry : angle 0.52299 / 0.28 (34254) hydrogen bonds : bond 0.03734 / 2.51 ( 1190) hydrogen bonds : angle 4.61112 / 3.28 ( 3351) link_ASP_CG-ANY_N : bond 0.00216 / 0.11 ( 8) link_ASP_CG-ANY_N : angle 0.73799 / 0.43 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7995 (mm) REVERT: A 252 TYR cc_start: 0.8199 (t80) cc_final: 0.7892 (t80) REVERT: B 86 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7894 (mm) REVERT: B 252 TYR cc_start: 0.8097 (t80) cc_final: 0.7822 (t80) REVERT: C 243 PHE cc_start: 0.8009 (t80) cc_final: 0.7718 (t80) REVERT: C 247 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7377 (pm20) REVERT: C 280 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8093 (mt-10) REVERT: D 243 PHE cc_start: 0.7983 (t80) cc_final: 0.7689 (t80) REVERT: D 247 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7369 (pm20) REVERT: D 280 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8037 (mt-10) outliers start: 27 outliers final: 7 residues processed: 184 average time/residue: 0.6144 time to fit residues: 132.5420 Evaluate side-chains 152 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain L residue 5 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 2 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 149 optimal weight: 0.0670 chunk 307 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 170 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN D 89 GLN ** D 247 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.148050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.088000 restraints weight = 37508.551| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.62 r_work: 0.2944 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25244 Z= 0.180 Angle : 0.548 8.082 34278 Z= 0.288 Chirality : 0.046 0.152 3996 Planarity : 0.004 0.045 4396 Dihedral : 6.903 70.800 3570 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.87 % Favored : 96.06 % Rotamer: Outliers : 1.57 % Allowed : 10.14 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.15), residues: 3202 helix: 1.61 (0.15), residues: 1288 sheet: -0.06 (0.26), residues: 396 loop : -1.11 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 301 TYR 0.014 0.001 TYR A 252 PHE 0.011 0.001 PHE B 638 TRP 0.008 0.001 TRP A 15 HIS 0.004 0.001 HIS D 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (25236) covalent geometry : angle 0.54747 / 0.29 (34254) hydrogen bonds : bond 0.04070 / 2.75 ( 1190) hydrogen bonds : angle 4.52471 / 3.24 ( 3351) link_ASP_CG-ANY_N : bond 0.00151 / 0.07 ( 8) link_ASP_CG-ANY_N : angle 0.75180 / 0.45 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.8266 (t80) cc_final: 0.7904 (t80) REVERT: B 252 TYR cc_start: 0.8223 (t80) cc_final: 0.7947 (t80) REVERT: B 586 HIS cc_start: 0.6755 (OUTLIER) cc_final: 0.5744 (m90) REVERT: C 124 TYR cc_start: 0.7842 (t80) cc_final: 0.7628 (t80) REVERT: C 168 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8624 (mm-30) REVERT: C 280 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8385 (tt0) REVERT: C 710 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8543 (mtpt) REVERT: D 243 PHE cc_start: 0.7982 (t80) cc_final: 0.7712 (t80) REVERT: D 280 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8323 (tt0) outliers start: 41 outliers final: 15 residues processed: 179 average time/residue: 0.5541 time to fit residues: 118.2021 Evaluate side-chains 162 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 710 LYS Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 99 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 170 optimal weight: 30.0000 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 GLN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.147025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.087705 restraints weight = 37576.863| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.55 r_work: 0.2908 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 25244 Z= 0.261 Angle : 0.602 8.363 34278 Z= 0.317 Chirality : 0.049 0.164 3996 Planarity : 0.004 0.042 4396 Dihedral : 7.036 69.468 3568 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.15 % Favored : 95.78 % Rotamer: Outliers : 2.18 % Allowed : 11.67 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3202 helix: 1.54 (0.15), residues: 1292 sheet: -0.26 (0.24), residues: 442 loop : -1.10 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 418 TYR 0.013 0.002 TYR A 116 PHE 0.015 0.002 PHE B 638 TRP 0.017 0.002 TRP C 278 HIS 0.005 0.001 HIS C 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.26 (25236) covalent geometry : angle 0.60183 / 0.32 (34254) hydrogen bonds : bond 0.04416 / 2.99 ( 1190) hydrogen bonds : angle 4.63622 / 3.34 ( 3351) link_ASP_CG-ANY_N : bond 0.00210 / 0.11 ( 8) link_ASP_CG-ANY_N : angle 0.74104 / 0.46 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 148 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.8295 (t80) cc_final: 0.7975 (t80) REVERT: A 586 HIS cc_start: 0.6597 (OUTLIER) cc_final: 0.5517 (m90) REVERT: B 252 TYR cc_start: 0.8220 (t80) cc_final: 0.7882 (t80) REVERT: B 586 HIS cc_start: 0.6630 (OUTLIER) cc_final: 0.5549 (m90) REVERT: B 732 MET cc_start: 0.8221 (mmm) cc_final: 0.7966 (mmm) REVERT: C 124 TYR cc_start: 0.7912 (t80) cc_final: 0.7681 (t80) REVERT: C 168 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8475 (mm-30) REVERT: C 247 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7793 (pm20) REVERT: D 243 PHE cc_start: 0.7911 (t80) cc_final: 0.7658 (t80) REVERT: D 280 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8346 (mt-10) outliers start: 57 outliers final: 25 residues processed: 189 average time/residue: 0.5062 time to fit residues: 114.5673 Evaluate side-chains 166 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 586 HIS 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 80 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 289 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** D 247 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 = 0.3990 r_free = 0.3990 target = 0.147445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.087090 restraints weight = 36893.804| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.62 r_work: 0.2934 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25244 Z= 0.174 Angle : 0.543 9.230 34278 Z= 0.286 Chirality : 0.046 0.190 3996 Planarity : 0.004 0.044 4396 Dihedral : 6.882 70.809 3568 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 1.87 % Allowed : 12.82 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3202 helix: 1.66 (0.15), residues: 1286 sheet: -0.20 (0.23), residues: 474 loop : -1.11 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 301 TYR 0.012 0.001 TYR B 519 PHE 0.011 0.001 PHE A 638 TRP 0.019 0.002 TRP D 278 HIS 0.004 0.001 HIS D 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (25236) covalent geometry : angle 0.54333 / 0.29 (34254) hydrogen bonds : bond 0.03786 / 2.56 ( 1190) hydrogen bonds : angle 4.49729 / 3.24 ( 3351) link_ASP_CG-ANY_N : bond 0.00141 / 0.08 ( 8) link_ASP_CG-ANY_N : angle 0.67356 / 0.41 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7296 (tp40) REVERT: A 252 TYR cc_start: 0.8297 (t80) cc_final: 0.7971 (t80) REVERT: B 252 TYR cc_start: 0.8270 (t80) cc_final: 0.7928 (t80) REVERT: B 732 MET cc_start: 0.8067 (mmm) cc_final: 0.7726 (mmm) REVERT: C 168 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8535 (mm-30) REVERT: D 168 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8504 (mm-30) REVERT: D 243 PHE cc_start: 0.7938 (t80) cc_final: 0.7651 (t80) REVERT: D 247 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7791 (pm20) REVERT: D 280 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8319 (mt-10) outliers start: 49 outliers final: 28 residues processed: 188 average time/residue: 0.5443 time to fit residues: 121.8614 Evaluate side-chains 167 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 362 VAL 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 163 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 459 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 193 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 289 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN D 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.146743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.086455 restraints weight = 37124.391| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.62 r_work: 0.2917 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25244 Z= 0.191 Angle : 0.554 9.159 34278 Z= 0.293 Chirality : 0.046 0.165 3996 Planarity : 0.004 0.043 4396 Dihedral : 6.848 70.714 3568 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 2.41 % Allowed : 12.85 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3202 helix: 1.61 (0.15), residues: 1298 sheet: -0.30 (0.23), residues: 504 loop : -1.06 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 561 TYR 0.012 0.001 TYR A 519 PHE 0.012 0.001 PHE B 638 TRP 0.020 0.002 TRP B 278 HIS 0.004 0.001 HIS C 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (25236) covalent geometry : angle 0.55349 / 0.29 (34254) hydrogen bonds : bond 0.03881 / 2.63 ( 1190) hydrogen bonds : angle 4.48809 / 3.23 ( 3351) link_ASP_CG-ANY_N : bond 0.00162 / 0.09 ( 8) link_ASP_CG-ANY_N : angle 0.68346 / 0.42 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 135 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.8311 (t80) cc_final: 0.7975 (t80) REVERT: A 586 HIS cc_start: 0.6625 (OUTLIER) cc_final: 0.5542 (m90) REVERT: A 839 ILE cc_start: 0.3972 (OUTLIER) cc_final: 0.3639 (pp) REVERT: B 252 TYR cc_start: 0.8300 (t80) cc_final: 0.7961 (t80) REVERT: B 586 HIS cc_start: 0.6615 (OUTLIER) cc_final: 0.5535 (m90) REVERT: B 732 MET cc_start: 0.7991 (mmm) cc_final: 0.7672 (mmm) REVERT: B 839 ILE cc_start: 0.3938 (OUTLIER) cc_final: 0.3611 (pp) REVERT: C 168 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8519 (mm-30) REVERT: C 710 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8508 (mtpt) REVERT: D 168 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8509 (mm-30) REVERT: D 243 PHE cc_start: 0.8016 (t80) cc_final: 0.7804 (t80) REVERT: D 280 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7950 (mt-10) outliers start: 63 outliers final: 38 residues processed: 184 average time/residue: 0.5161 time to fit residues: 112.8354 Evaluate side-chains 173 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 151 LEU 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 804 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 362 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 B residue 839 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 710 LYS Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 591 ASP 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 44 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 125 optimal weight: 0.0170 chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.148576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.088570 restraints weight = 37189.579| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.63 r_work: 0.2962 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25244 Z= 0.118 Angle : 0.513 9.133 34278 Z= 0.269 Chirality : 0.045 0.151 3996 Planarity : 0.004 0.044 4396 Dihedral : 6.665 72.713 3568 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.50 % Favored : 96.44 % Rotamer: Outliers : 2.10 % Allowed : 13.70 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 3202 helix: 1.79 (0.15), residues: 1292 sheet: -0.12 (0.23), residues: 470 loop : -1.04 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 561 TYR 0.010 0.001 TYR A 519 PHE 0.008 0.001 PHE C 638 TRP 0.022 0.001 TRP B 278 HIS 0.003 0.001 HIS C 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (25236) covalent geometry : angle 0.51284 / 0.27 (34254) hydrogen bonds : bond 0.03308 / 2.24 ( 1190) hydrogen bonds : angle 4.32285 / 3.11 ( 3351) link_ASP_CG-ANY_N : bond 0.00103 / 0.06 ( 8) link_ASP_CG-ANY_N : angle 0.63656 / 0.39 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 140 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.8301 (t80) cc_final: 0.7999 (t80) REVERT: A 839 ILE cc_start: 0.3990 (OUTLIER) cc_final: 0.3677 (pp) REVERT: B 76 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8458 (mm) REVERT: B 252 TYR cc_start: 0.8265 (t80) cc_final: 0.7944 (t80) REVERT: B 732 MET cc_start: 0.7905 (mmm) cc_final: 0.7367 (mmm) REVERT: B 839 ILE cc_start: 0.3962 (OUTLIER) cc_final: 0.3657 (pp) REVERT: C 168 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8557 (mm-30) REVERT: C 710 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8453 (mtpt) REVERT: D 168 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8459 (mm-30) REVERT: D 243 PHE cc_start: 0.7984 (t80) cc_final: 0.7740 (t80) REVERT: D 280 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7879 (mt-10) outliers start: 55 outliers final: 38 residues processed: 185 average time/residue: 0.5251 time to fit residues: 114.8395 Evaluate side-chains 173 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain B residue 8 THR 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 103 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 710 LYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 49 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 267 optimal weight: 2.9990 chunk 203 optimal weight: 0.0770 chunk 285 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 231 optimal weight: 0.4980 chunk 151 optimal weight: 3.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 GLN D 541 GLN 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 = 0.149217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.089089 restraints weight = 36818.150| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.63 r_work: 0.2959 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 25244 Z= 0.126 Angle : 0.516 9.040 34278 Z= 0.269 Chirality : 0.045 0.152 3996 Planarity : 0.004 0.043 4396 Dihedral : 6.580 73.498 3568 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.84 % Favored : 96.10 % Rotamer: Outliers : 2.41 % Allowed : 14.04 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 3202 helix: 1.85 (0.15), residues: 1294 sheet: -0.08 (0.24), residues: 470 loop : -1.02 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 731 TYR 0.010 0.001 TYR B 519 PHE 0.008 0.001 PHE B 638 TRP 0.022 0.001 TRP B 278 HIS 0.003 0.001 HIS C 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (25236) covalent geometry : angle 0.51589 / 0.27 (34254) hydrogen bonds : bond 0.03312 / 2.24 ( 1190) hydrogen bonds : angle 4.26440 / 3.07 ( 3351) link_ASP_CG-ANY_N : bond 0.00108 / 0.06 ( 8) link_ASP_CG-ANY_N : angle 0.64758 / 0.40 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 136 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8233 (mtp) cc_final: 0.8021 (mtp) REVERT: A 149 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7228 (tp40) REVERT: A 252 TYR cc_start: 0.8248 (t80) cc_final: 0.8009 (t80) REVERT: A 541 GLN cc_start: 0.8015 (pm20) cc_final: 0.7794 (mp10) REVERT: A 839 ILE cc_start: 0.3921 (OUTLIER) cc_final: 0.3618 (pp) REVERT: B 76 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8514 (mm) REVERT: B 252 TYR cc_start: 0.8228 (t80) cc_final: 0.7936 (t80) REVERT: B 541 GLN cc_start: 0.7996 (pm20) cc_final: 0.7795 (mp10) REVERT: B 732 MET cc_start: 0.7855 (mmm) cc_final: 0.7334 (mmm) REVERT: B 839 ILE cc_start: 0.3894 (OUTLIER) cc_final: 0.3598 (pp) REVERT: C 168 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8480 (mm-30) REVERT: C 710 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8477 (mtpt) REVERT: D 168 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8472 (mm-30) REVERT: D 280 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7911 (mt-10) REVERT: D 476 MET cc_start: 0.9432 (OUTLIER) cc_final: 0.8996 (mmt) outliers start: 63 outliers final: 40 residues processed: 185 average time/residue: 0.5330 time to fit residues: 116.5484 Evaluate side-chains 176 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain B residue 8 THR 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 103 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 710 LYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 476 MET Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 294 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 280 optimal weight: 7.9990 chunk 59 optimal weight: 0.0370 chunk 287 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 186 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.0170 chunk 247 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 GLN C 541 GLN D 541 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.150253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.090506 restraints weight = 37070.853| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.63 r_work: 0.2993 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25244 Z= 0.100 Angle : 0.503 9.011 34278 Z= 0.262 Chirality : 0.044 0.145 3996 Planarity : 0.004 0.044 4396 Dihedral : 6.431 75.545 3568 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.44 % Favored : 96.50 % Rotamer: Outliers : 1.91 % Allowed : 14.54 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.15), residues: 3202 helix: 1.92 (0.15), residues: 1292 sheet: -0.06 (0.23), residues: 500 loop : -0.96 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 465 TYR 0.010 0.001 TYR D 285 PHE 0.008 0.001 PHE C 638 TRP 0.021 0.001 TRP B 278 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (25236) covalent geometry : angle 0.50243 / 0.26 (34254) hydrogen bonds : bond 0.02989 / 2.02 ( 1190) hydrogen bonds : angle 4.15935 / 2.99 ( 3351) link_ASP_CG-ANY_N : bond 0.00081 / 0.05 ( 8) link_ASP_CG-ANY_N : angle 0.62386 / 0.38 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 138 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8281 (mtp) cc_final: 0.8038 (mtp) REVERT: A 149 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7157 (tp40) REVERT: A 839 ILE cc_start: 0.3976 (OUTLIER) cc_final: 0.3678 (pp) REVERT: B 76 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8400 (mm) REVERT: B 732 MET cc_start: 0.7846 (mmm) cc_final: 0.7320 (mmm) REVERT: B 839 ILE cc_start: 0.3959 (OUTLIER) cc_final: 0.3660 (pp) REVERT: C 124 TYR cc_start: 0.7864 (t80) cc_final: 0.7647 (t80) REVERT: C 168 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8540 (mm-30) REVERT: C 710 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8413 (mtpt) REVERT: D 168 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8473 (mm-30) REVERT: D 280 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8199 (tt0) outliers start: 50 outliers final: 29 residues processed: 179 average time/residue: 0.5279 time to fit residues: 111.1000 Evaluate side-chains 163 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 710 LYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 237 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 316 optimal weight: 0.5980 chunk 296 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 310 optimal weight: 0.5980 chunk 179 optimal weight: 0.0770 chunk 87 optimal weight: 5.9990 chunk 317 optimal weight: 0.5980 chunk 190 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 267 HIS C 373 GLN C 541 GLN D 89 GLN D 541 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.150468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.090632 restraints weight = 36964.518| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.63 r_work: 0.3000 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25244 Z= 0.101 Angle : 0.492 8.974 34278 Z= 0.256 Chirality : 0.044 0.152 3996 Planarity : 0.003 0.043 4396 Dihedral : 6.357 76.735 3568 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.50 % Favored : 96.44 % Rotamer: Outliers : 1.64 % Allowed : 15.00 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.15), residues: 3202 helix: 1.99 (0.15), residues: 1292 sheet: 0.02 (0.22), residues: 554 loop : -0.94 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 301 TYR 0.009 0.001 TYR A 519 PHE 0.008 0.001 PHE C 638 TRP 0.020 0.001 TRP B 278 HIS 0.002 0.000 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (25236) covalent geometry : angle 0.49234 / 0.26 (34254) hydrogen bonds : bond 0.03004 / 2.04 ( 1190) hydrogen bonds : angle 4.12642 / 2.97 ( 3351) link_ASP_CG-ANY_N : bond 0.00087 / 0.05 ( 8) link_ASP_CG-ANY_N : angle 0.63015 / 0.39 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8293 (mtp) cc_final: 0.8032 (mtp) REVERT: A 839 ILE cc_start: 0.3974 (OUTLIER) cc_final: 0.3673 (pp) REVERT: B 732 MET cc_start: 0.7836 (mmm) cc_final: 0.7322 (mmm) REVERT: B 839 ILE cc_start: 0.3946 (OUTLIER) cc_final: 0.3646 (pp) REVERT: C 124 TYR cc_start: 0.7878 (t80) cc_final: 0.7657 (t80) REVERT: C 168 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8505 (mm-30) REVERT: C 710 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8408 (mtpt) REVERT: D 168 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8488 (mm-30) REVERT: D 280 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8208 (tt0) outliers start: 43 outliers final: 33 residues processed: 170 average time/residue: 0.6018 time to fit residues: 120.1689 Evaluate side-chains 166 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 710 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 111 optimal weight: 9.9990 chunk 311 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 25 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 HIS A 541 GLN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS B 541 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 373 GLN C 541 GLN D 89 GLN D 541 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.148710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.088365 restraints weight = 37315.874| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.63 r_work: 0.2956 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25244 Z= 0.145 Angle : 0.518 8.856 34278 Z= 0.271 Chirality : 0.045 0.158 3996 Planarity : 0.004 0.043 4396 Dihedral : 6.448 76.206 3568 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 2.03 % Allowed : 14.77 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3202 helix: 1.97 (0.15), residues: 1294 sheet: -0.10 (0.23), residues: 502 loop : -0.93 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 123 TYR 0.011 0.001 TYR A 519 PHE 0.010 0.001 PHE A 638 TRP 0.021 0.001 TRP B 278 HIS 0.003 0.001 HIS D 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (25236) covalent geometry : angle 0.51748 / 0.27 (34254) hydrogen bonds : bond 0.03376 / 2.29 ( 1190) hydrogen bonds : angle 4.20658 / 3.03 ( 3351) link_ASP_CG-ANY_N : bond 0.00127 / 0.07 ( 8) link_ASP_CG-ANY_N : angle 0.66408 / 0.41 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11503.47 seconds wall clock time: 195 minutes 56.84 seconds (11756.84 seconds total)