Starting phenix.real_space_refine on Thu Mar 5 19:51:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7waf_32384/03_2026/7waf_32384.cif Found real_map, /net/cci-nas-00/data/ceres_data/7waf_32384/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7waf_32384/03_2026/7waf_32384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7waf_32384/03_2026/7waf_32384.map" model { file = "/net/cci-nas-00/data/ceres_data/7waf_32384/03_2026/7waf_32384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7waf_32384/03_2026/7waf_32384.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.08, per 1000 atoms: 0.20 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: 1.98 Conformation dependent library (CDL) restraints added in 1.0 seconds 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 1.03 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: 5.53 Time building geometry restraints manager: 2.66 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: 13893 17.73 - 35.46: 1055 35.46 - 53.19: 232 53.19 - 70.91: 45 70.91 - 88.64: 27 Dihedral angle restraints: 15252 sinusoidal: 6126 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 15249 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: 0.04 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: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.560 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 13.882 88.642 9416 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 covalent geometry : bond 0.00272 (25236) covalent geometry : angle 0.57649 (34254) hydrogen bonds : bond 0.13494 ( 1190) hydrogen bonds : angle 5.61071 ( 3351) link_ASP_CG-ANY_N : bond 0.01102 ( 8) link_ASP_CG-ANY_N : angle 0.91817 ( 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 : 0.703 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: 0.6522 time to fit residues: 160.9102 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 : 0.975 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 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 = 0.4036 r_free = 0.4036 target = 0.150664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.091152 restraints weight = 37225.626| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.62 r_work: 0.3011 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.0932 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= 0.113 Angle : 0.523 8.225 34278 Z= 0.276 Chirality : 0.045 0.151 3996 Planarity : 0.004 0.051 4396 Dihedral : 8.085 76.216 3658 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.28 % Rotamer: Outliers : 1.03 % Allowed : 8.30 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 3202 helix: 1.58 (0.15), residues: 1284 sheet: -0.04 (0.24), residues: 468 loop : -1.06 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 301 TYR 0.016 0.001 TYR A 252 PHE 0.012 0.001 PHE D 243 TRP 0.014 0.001 TRP D 278 HIS 0.004 0.001 HIS C 650 Details of bonding type rmsd covalent geometry : bond 0.00242 (25236) covalent geometry : angle 0.52318 (34254) hydrogen bonds : bond 0.03623 ( 1190) hydrogen bonds : angle 4.59002 ( 3351) link_ASP_CG-ANY_N : bond 0.00184 ( 8) link_ASP_CG-ANY_N : angle 0.77031 ( 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 195 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7985 (mm) REVERT: A 252 TYR cc_start: 0.8178 (t80) cc_final: 0.7868 (t80) REVERT: B 86 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7890 (mm) REVERT: B 252 TYR cc_start: 0.8104 (t80) cc_final: 0.7796 (t80) REVERT: C 280 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8090 (mt-10) REVERT: D 243 PHE cc_start: 0.7968 (t80) cc_final: 0.7660 (t80) REVERT: D 247 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7345 (pm20) REVERT: D 280 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8029 (mt-10) outliers start: 27 outliers final: 9 residues processed: 182 average time/residue: 0.5823 time to fit residues: 123.8163 Evaluate side-chains 153 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain B residue 32 LEU 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: 4.9990 chunk 260 optimal weight: 0.6980 chunk 313 optimal weight: 3.9990 chunk 149 optimal weight: 0.0870 chunk 307 optimal weight: 4.9990 chunk 271 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 264 optimal weight: 0.7980 chunk 170 optimal weight: 20.0000 chunk 184 optimal weight: 7.9990 overall best weight: 1.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.148320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.089461 restraints weight = 37788.717| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.55 r_work: 0.2965 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25244 Z= 0.158 Angle : 0.526 8.207 34278 Z= 0.277 Chirality : 0.045 0.148 3996 Planarity : 0.004 0.046 4396 Dihedral : 8.034 72.556 3658 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 1.53 % Allowed : 10.18 % 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: 0.32 (0.15), residues: 3202 helix: 1.71 (0.15), residues: 1284 sheet: -0.02 (0.26), residues: 396 loop : -1.06 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 301 TYR 0.013 0.001 TYR A 252 PHE 0.010 0.001 PHE A 638 TRP 0.008 0.001 TRP A 15 HIS 0.003 0.001 HIS C 650 Details of bonding type rmsd covalent geometry : bond 0.00368 (25236) covalent geometry : angle 0.52632 (34254) hydrogen bonds : bond 0.03861 ( 1190) hydrogen bonds : angle 4.46212 ( 3351) link_ASP_CG-ANY_N : bond 0.00115 ( 8) link_ASP_CG-ANY_N : angle 0.72162 ( 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 192 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.8269 (t80) cc_final: 0.7939 (t80) REVERT: B 252 TYR cc_start: 0.8204 (t80) cc_final: 0.7878 (t80) REVERT: C 124 TYR cc_start: 0.7825 (t80) cc_final: 0.7614 (t80) REVERT: C 168 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8611 (mm-30) REVERT: C 280 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8371 (tt0) REVERT: C 710 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8545 (mtpt) REVERT: D 243 PHE cc_start: 0.7965 (t80) cc_final: 0.7711 (t80) REVERT: D 280 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8287 (tt0) outliers start: 40 outliers final: 17 residues processed: 179 average time/residue: 0.5069 time to fit residues: 107.4113 Evaluate side-chains 163 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU 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 32 LEU 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 804 THR 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 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: 1.9990 chunk 95 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 302 optimal weight: 3.9990 chunk 91 optimal weight: 0.0000 chunk 126 optimal weight: 0.0770 chunk 170 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 541 GLN D 247 GLN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.149323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.090646 restraints weight = 37338.856| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.54 r_work: 0.2999 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25244 Z= 0.106 Angle : 0.495 8.489 34278 Z= 0.259 Chirality : 0.044 0.147 3996 Planarity : 0.004 0.044 4396 Dihedral : 7.815 73.492 3656 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.31 % Rotamer: Outliers : 2.03 % Allowed : 11.59 % Favored : 86.38 % 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: 0.43 (0.15), residues: 3202 helix: 1.83 (0.15), residues: 1278 sheet: -0.05 (0.24), residues: 474 loop : -1.03 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 301 TYR 0.010 0.001 TYR A 252 PHE 0.008 0.001 PHE A 457 TRP 0.016 0.001 TRP D 278 HIS 0.003 0.000 HIS C 650 Details of bonding type rmsd covalent geometry : bond 0.00230 (25236) covalent geometry : angle 0.49478 (34254) hydrogen bonds : bond 0.03251 ( 1190) hydrogen bonds : angle 4.29214 ( 3351) link_ASP_CG-ANY_N : bond 0.00092 ( 8) link_ASP_CG-ANY_N : angle 0.64160 ( 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: 53 poor density : 152 time to evaluate : 0.918 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: 0.7958 (t80) REVERT: A 586 HIS cc_start: 0.6667 (OUTLIER) cc_final: 0.5610 (m90) REVERT: B 252 TYR cc_start: 0.8211 (t80) cc_final: 0.7859 (t80) REVERT: B 586 HIS cc_start: 0.6618 (OUTLIER) cc_final: 0.5582 (m90) REVERT: C 124 TYR cc_start: 0.7849 (t80) cc_final: 0.7648 (t80) REVERT: C 168 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8543 (mm-30) REVERT: C 243 PHE cc_start: 0.7962 (t80) cc_final: 0.7631 (t80) REVERT: C 280 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8343 (tt0) REVERT: C 710 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8478 (mtpt) REVERT: D 168 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8595 (mm-30) REVERT: D 243 PHE cc_start: 0.7964 (t80) cc_final: 0.7700 (t80) REVERT: D 280 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8232 (tt0) outliers start: 53 outliers final: 21 residues processed: 188 average time/residue: 0.5420 time to fit residues: 120.5085 Evaluate side-chains 165 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 107 THR 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 32 LEU Chi-restraints excluded: chain B residue 33 TYR 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 B residue 814 GLU 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 710 LYS 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: 6.9990 chunk 23 optimal weight: 0.3980 chunk 289 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 238 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 541 GLN D 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.147893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.087506 restraints weight = 37080.446| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.61 r_work: 0.2921 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25244 Z= 0.186 Angle : 0.544 8.738 34278 Z= 0.286 Chirality : 0.046 0.192 3996 Planarity : 0.004 0.042 4396 Dihedral : 7.847 74.743 3656 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.84 % Favored : 96.10 % Rotamer: Outliers : 1.91 % Allowed : 12.32 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.15), residues: 3202 helix: 1.75 (0.15), residues: 1286 sheet: -0.17 (0.25), residues: 440 loop : -1.02 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 301 TYR 0.012 0.001 TYR A 519 PHE 0.013 0.001 PHE A 638 TRP 0.020 0.001 TRP D 278 HIS 0.004 0.001 HIS D 544 Details of bonding type rmsd covalent geometry : bond 0.00438 (25236) covalent geometry : angle 0.54377 (34254) hydrogen bonds : bond 0.03897 ( 1190) hydrogen bonds : angle 4.41960 ( 3351) link_ASP_CG-ANY_N : bond 0.00149 ( 8) link_ASP_CG-ANY_N : angle 0.66786 ( 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 198 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.8316 (t80) cc_final: 0.7992 (t80) REVERT: B 252 TYR cc_start: 0.8282 (t80) cc_final: 0.7943 (t80) REVERT: B 541 GLN cc_start: 0.8054 (pm20) cc_final: 0.7818 (mp10) REVERT: B 586 HIS cc_start: 0.6652 (OUTLIER) cc_final: 0.5565 (m90) REVERT: B 839 ILE cc_start: 0.3729 (OUTLIER) cc_final: 0.3449 (pp) REVERT: C 124 TYR cc_start: 0.7862 (t80) cc_final: 0.7639 (t80) REVERT: C 243 PHE cc_start: 0.7941 (t80) cc_final: 0.7678 (t80) REVERT: D 168 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8536 (mm-30) REVERT: D 243 PHE cc_start: 0.7914 (t80) cc_final: 0.7686 (t80) REVERT: D 280 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8361 (tt0) outliers start: 50 outliers final: 29 residues processed: 187 average time/residue: 0.5140 time to fit residues: 114.2428 Evaluate side-chains 171 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 107 THR 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 33 TYR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 86 ILE 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 362 VAL Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain 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 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET 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: 0.8980 chunk 34 optimal weight: 20.0000 chunk 289 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 233 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 chunk 194 optimal weight: 0.1980 chunk 139 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 541 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 541 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.150074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.089908 restraints weight = 36793.455| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.61 r_work: 0.2977 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25244 Z= 0.111 Angle : 0.498 8.766 34278 Z= 0.261 Chirality : 0.044 0.152 3996 Planarity : 0.004 0.043 4396 Dihedral : 7.610 77.458 3656 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.38 % Rotamer: Outliers : 2.03 % Allowed : 13.12 % Favored : 84.85 % 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: 0.44 (0.15), residues: 3202 helix: 1.89 (0.15), residues: 1278 sheet: -0.11 (0.24), residues: 472 loop : -1.05 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 301 TYR 0.010 0.001 TYR B 33 PHE 0.007 0.001 PHE C 638 TRP 0.021 0.001 TRP D 278 HIS 0.003 0.000 HIS C 650 Details of bonding type rmsd covalent geometry : bond 0.00251 (25236) covalent geometry : angle 0.49750 (34254) hydrogen bonds : bond 0.03209 ( 1190) hydrogen bonds : angle 4.25116 ( 3351) link_ASP_CG-ANY_N : bond 0.00089 ( 8) link_ASP_CG-ANY_N : angle 0.61865 ( 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 197 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.8313 (t80) cc_final: 0.8011 (t80) REVERT: A 541 GLN cc_start: 0.8008 (pm20) cc_final: 0.7796 (mp10) REVERT: A 586 HIS cc_start: 0.6584 (OUTLIER) cc_final: 0.5501 (m90) REVERT: A 839 ILE cc_start: 0.3899 (OUTLIER) cc_final: 0.3607 (pp) REVERT: B 252 TYR cc_start: 0.8286 (t80) cc_final: 0.7949 (t80) REVERT: B 586 HIS cc_start: 0.6564 (OUTLIER) cc_final: 0.5506 (m90) REVERT: C 124 TYR cc_start: 0.7847 (t80) cc_final: 0.7615 (t80) REVERT: C 168 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8586 (mm-30) REVERT: C 243 PHE cc_start: 0.7942 (t80) cc_final: 0.7683 (t80) REVERT: C 710 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8460 (mtpt) REVERT: D 168 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8501 (mm-30) REVERT: D 243 PHE cc_start: 0.7960 (t80) cc_final: 0.7754 (t80) REVERT: D 280 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8309 (tt0) REVERT: D 476 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.8983 (mmt) outliers start: 53 outliers final: 29 residues processed: 185 average time/residue: 0.5330 time to fit residues: 117.0226 Evaluate side-chains 170 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 63 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 163 LEU 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 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 631 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 44 optimal weight: 0.0370 chunk 106 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 541 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.147788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.087750 restraints weight = 37209.843| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.61 r_work: 0.2950 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1613 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= 0.158 Angle : 0.527 8.980 34278 Z= 0.276 Chirality : 0.045 0.151 3996 Planarity : 0.004 0.041 4396 Dihedral : 7.599 78.264 3656 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.81 % Favored : 96.13 % Rotamer: Outliers : 1.95 % Allowed : 13.62 % Favored : 84.43 % 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: 1.88 (0.15), residues: 1280 sheet: -0.13 (0.23), residues: 498 loop : -1.01 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 418 TYR 0.011 0.001 TYR A 519 PHE 0.011 0.001 PHE A 638 TRP 0.021 0.001 TRP B 278 HIS 0.003 0.001 HIS C 544 Details of bonding type rmsd covalent geometry : bond 0.00370 (25236) covalent geometry : angle 0.52672 (34254) hydrogen bonds : bond 0.03590 ( 1190) hydrogen bonds : angle 4.29104 ( 3351) link_ASP_CG-ANY_N : bond 0.00122 ( 8) link_ASP_CG-ANY_N : angle 0.65952 ( 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: 51 poor density : 144 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 VAL cc_start: 0.8548 (m) cc_final: 0.8282 (p) REVERT: A 252 TYR cc_start: 0.8256 (t80) cc_final: 0.8003 (t80) REVERT: A 541 GLN cc_start: 0.8026 (pm20) cc_final: 0.7816 (mp10) REVERT: A 839 ILE cc_start: 0.3997 (OUTLIER) cc_final: 0.3683 (pp) REVERT: B 252 TYR cc_start: 0.8268 (t80) cc_final: 0.7928 (t80) REVERT: B 839 ILE cc_start: 0.3979 (OUTLIER) cc_final: 0.3674 (pp) REVERT: C 124 TYR cc_start: 0.7849 (t80) cc_final: 0.7601 (t80) REVERT: C 168 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8577 (mm-30) REVERT: D 124 TYR cc_start: 0.7823 (t80) cc_final: 0.7616 (t80) REVERT: D 168 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8471 (mm-30) REVERT: D 280 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8336 (tt0) outliers start: 51 outliers final: 30 residues processed: 185 average time/residue: 0.5162 time to fit residues: 113.6579 Evaluate side-chains 168 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 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 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: 0.5980 chunk 36 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 267 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 285 optimal weight: 0.0670 chunk 82 optimal weight: 5.9990 chunk 231 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 GLN C 541 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN D 373 GLN D 541 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.158806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099525 restraints weight = 37435.764| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.60 r_work: 0.2983 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1668 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= 0.118 Angle : 0.511 9.027 34278 Z= 0.267 Chirality : 0.044 0.174 3996 Planarity : 0.004 0.041 4396 Dihedral : 7.470 78.979 3656 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 1.80 % Allowed : 14.23 % Favored : 83.97 % 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: 0.48 (0.15), residues: 3202 helix: 1.92 (0.15), residues: 1280 sheet: -0.06 (0.24), residues: 472 loop : -1.03 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 465 TYR 0.010 0.001 TYR A 519 PHE 0.008 0.001 PHE A 638 TRP 0.022 0.001 TRP B 278 HIS 0.003 0.001 HIS D 650 Details of bonding type rmsd covalent geometry : bond 0.00267 (25236) covalent geometry : angle 0.51101 (34254) hydrogen bonds : bond 0.03238 ( 1190) hydrogen bonds : angle 4.21349 ( 3351) link_ASP_CG-ANY_N : bond 0.00095 ( 8) link_ASP_CG-ANY_N : angle 0.63198 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.8251 (t80) cc_final: 0.8019 (t80) REVERT: A 629 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7693 (p0) REVERT: A 839 ILE cc_start: 0.3968 (OUTLIER) cc_final: 0.3676 (pp) REVERT: B 252 TYR cc_start: 0.8219 (t80) cc_final: 0.7934 (t80) REVERT: B 839 ILE cc_start: 0.3940 (OUTLIER) cc_final: 0.3648 (pp) REVERT: C 124 TYR cc_start: 0.7882 (t80) cc_final: 0.7634 (t80) REVERT: C 168 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8584 (mm-30) REVERT: D 168 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8476 (mm-30) REVERT: D 280 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8289 (tt0) outliers start: 47 outliers final: 29 residues processed: 179 average time/residue: 0.5325 time to fit residues: 112.9919 Evaluate side-chains 164 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 151 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 629 ASP 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 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 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 1 MET Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 163 LEU 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 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 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: 0.3980 chunk 132 optimal weight: 0.5980 chunk 280 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 chunk 287 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 247 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN D 541 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.149606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.089780 restraints weight = 37145.009| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.63 r_work: 0.2980 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25244 Z= 0.110 Angle : 0.505 8.943 34278 Z= 0.263 Chirality : 0.044 0.154 3996 Planarity : 0.003 0.041 4396 Dihedral : 7.347 79.600 3656 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.44 % Favored : 96.50 % Rotamer: Outliers : 1.61 % Allowed : 14.80 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.15), residues: 3202 helix: 1.98 (0.15), residues: 1280 sheet: -0.05 (0.24), residues: 474 loop : -1.00 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 731 TYR 0.012 0.001 TYR A 33 PHE 0.009 0.001 PHE C 243 TRP 0.026 0.001 TRP D 278 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00247 (25236) covalent geometry : angle 0.50526 (34254) hydrogen bonds : bond 0.03105 ( 1190) hydrogen bonds : angle 4.15920 ( 3351) link_ASP_CG-ANY_N : bond 0.00091 ( 8) link_ASP_CG-ANY_N : angle 0.63516 ( 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 178 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 839 ILE cc_start: 0.3838 (OUTLIER) cc_final: 0.3561 (pp) REVERT: B 252 TYR cc_start: 0.8205 (t80) cc_final: 0.7958 (t80) REVERT: B 839 ILE cc_start: 0.3826 (OUTLIER) cc_final: 0.3542 (pp) REVERT: C 124 TYR cc_start: 0.7864 (t80) cc_final: 0.7611 (t80) REVERT: C 168 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8631 (mm-30) REVERT: D 168 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8469 (mm-30) REVERT: D 280 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8286 (tt0) outliers start: 42 outliers final: 29 residues processed: 170 average time/residue: 0.5604 time to fit residues: 111.3580 Evaluate side-chains 159 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 151 LEU 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 80 VAL 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 297 VAL 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 80 VAL Chi-restraints excluded: chain C residue 163 LEU 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 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 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: 0.9980 chunk 62 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 296 optimal weight: 0.8980 chunk 162 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 310 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 317 optimal weight: 0.9990 chunk 190 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 541 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.149784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.089820 restraints weight = 37093.586| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.64 r_work: 0.2989 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1808 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= 0.114 Angle : 0.501 8.919 34278 Z= 0.260 Chirality : 0.044 0.148 3996 Planarity : 0.003 0.041 4396 Dihedral : 7.273 83.573 3656 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.38 % Rotamer: Outliers : 1.53 % Allowed : 14.80 % Favored : 83.66 % 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: 0.61 (0.15), residues: 3202 helix: 2.02 (0.15), residues: 1278 sheet: -0.04 (0.24), residues: 474 loop : -0.94 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 301 TYR 0.010 0.001 TYR A 519 PHE 0.010 0.001 PHE B 43 TRP 0.021 0.001 TRP B 278 HIS 0.003 0.000 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00257 (25236) covalent geometry : angle 0.50120 (34254) hydrogen bonds : bond 0.03117 ( 1190) hydrogen bonds : angle 4.14238 ( 3351) link_ASP_CG-ANY_N : bond 0.00096 ( 8) link_ASP_CG-ANY_N : angle 0.63814 ( 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: 40 poor density : 135 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8293 (mtp) cc_final: 0.8088 (mtp) REVERT: A 476 MET cc_start: 0.9584 (tpt) cc_final: 0.9369 (tpt) REVERT: A 839 ILE cc_start: 0.4032 (OUTLIER) cc_final: 0.3720 (pp) REVERT: B 94 MET cc_start: 0.8292 (mtp) cc_final: 0.8087 (mtp) REVERT: B 476 MET cc_start: 0.9585 (tpt) cc_final: 0.9366 (tpt) REVERT: B 839 ILE cc_start: 0.4018 (OUTLIER) cc_final: 0.3707 (pp) REVERT: C 124 TYR cc_start: 0.7860 (t80) cc_final: 0.7605 (t80) REVERT: C 168 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8608 (mm-30) REVERT: D 168 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8497 (mm-30) outliers start: 40 outliers final: 30 residues processed: 171 average time/residue: 0.5605 time to fit residues: 112.1730 Evaluate side-chains 160 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 151 LEU Chi-restraints excluded: chain A residue 297 VAL 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 63 VAL 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 297 VAL 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 272 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 631 VAL 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 Chi-restraints excluded: chain D residue 459 MET 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: 0.9990 chunk 311 optimal weight: 0.4980 chunk 244 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 274 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 267 HIS C 541 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.150190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.090265 restraints weight = 36873.236| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.64 r_work: 0.2996 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25244 Z= 0.106 Angle : 0.494 8.763 34278 Z= 0.257 Chirality : 0.044 0.153 3996 Planarity : 0.003 0.042 4396 Dihedral : 7.201 89.592 3656 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.37 % Favored : 96.56 % Rotamer: Outliers : 1.61 % Allowed : 14.92 % Favored : 83.47 % 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: 0.64 (0.15), residues: 3202 helix: 2.06 (0.15), residues: 1280 sheet: -0.01 (0.24), residues: 474 loop : -0.94 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 465 TYR 0.009 0.001 TYR A 519 PHE 0.009 0.001 PHE B 43 TRP 0.027 0.001 TRP D 278 HIS 0.004 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00236 (25236) covalent geometry : angle 0.49376 (34254) hydrogen bonds : bond 0.03012 ( 1190) hydrogen bonds : angle 4.10776 ( 3351) link_ASP_CG-ANY_N : bond 0.00088 ( 8) link_ASP_CG-ANY_N : angle 0.63557 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11753.37 seconds wall clock time: 199 minutes 52.73 seconds (11992.73 seconds total)