Starting phenix.real_space_refine on Sat Jun 21 15:08:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7waf_32384/06_2025/7waf_32384.cif Found real_map, /net/cci-nas-00/data/ceres_data/7waf_32384/06_2025/7waf_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_32384/06_2025/7waf_32384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7waf_32384/06_2025/7waf_32384.map" model { file = "/net/cci-nas-00/data/ceres_data/7waf_32384/06_2025/7waf_32384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7waf_32384/06_2025/7waf_32384.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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%COO:plan': 1, 'ASP:plan': 3} 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%COO:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP%COO:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP%COO:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 8 Chain: "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: 14.64, per 1000 atoms: 0.59 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: 5.76 Conformation dependent library (CDL) restraints added in 3.2 seconds 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 3.26 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: 10.80 Time building geometry restraints manager: 6.96 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: 0.00 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 57.540 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.180 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.620 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (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 TRP 0.023 0.001 TRP D 278 HIS 0.003 0.001 HIS C 327 PHE 0.011 0.001 PHE A 638 TYR 0.010 0.001 TYR B 519 ARG 0.002 0.000 ARG A 561 Details of bonding type rmsd 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) covalent geometry : bond 0.00272 (25236) covalent geometry : angle 0.57649 (34254) *********************** 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 : 2.502 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: 1.3106 time to fit residues: 326.1139 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 : 2.739 ------------------------------------------------------------------------------- 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 268 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 249 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 288 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 247 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 HIS D 247 GLN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 713 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.148880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.087777 restraints weight = 36720.058| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.65 r_work: 0.2944 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25244 Z= 0.200 Angle : 0.574 8.174 34278 Z= 0.304 Chirality : 0.047 0.154 3996 Planarity : 0.004 0.051 4396 Dihedral : 8.276 74.611 3658 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.03 % Favored : 95.88 % Rotamer: Outliers : 1.11 % Allowed : 7.80 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 3202 helix: 1.48 (0.15), residues: 1290 sheet: -0.15 (0.25), residues: 400 loop : -1.13 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 278 HIS 0.006 0.001 HIS C 650 PHE 0.012 0.002 PHE B 480 TYR 0.015 0.001 TYR A 252 ARG 0.006 0.000 ARG C 301 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 1190) hydrogen bonds : angle 4.72702 ( 3351) link_ASP_CG-ANY_N : bond 0.00295 ( 8) link_ASP_CG-ANY_N : angle 0.81273 ( 24) covalent geometry : bond 0.00467 (25236) covalent geometry : angle 0.57368 (34254) *********************** 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 183 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.8133 (t80) cc_final: 0.7839 (t80) REVERT: B 252 TYR cc_start: 0.8119 (t80) cc_final: 0.7866 (t80) REVERT: B 586 HIS cc_start: 0.6824 (OUTLIER) cc_final: 0.5882 (m90) REVERT: C 243 PHE cc_start: 0.7955 (t80) cc_final: 0.7692 (t80) REVERT: C 247 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7330 (pm20) REVERT: C 280 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8066 (mt-10) REVERT: D 243 PHE cc_start: 0.8008 (t80) cc_final: 0.7770 (t80) REVERT: D 247 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7321 (pm20) REVERT: D 280 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8021 (mt-10) outliers start: 29 outliers final: 13 residues processed: 170 average time/residue: 1.2494 time to fit residues: 250.8016 Evaluate side-chains 157 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 2.481 ------------------------------------------------------------------------------- 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 86 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain B residue 32 LEU 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 586 HIS 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 252 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 157 optimal weight: 0.0870 chunk 225 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 200 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.6762 ------------------------------------------------------------------------------- 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 394 ASN D 89 GLN ** 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 = 0.3994 r_free = 0.3994 target = 0.147225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.087171 restraints weight = 37069.563| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.61 r_work: 0.2935 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25244 Z= 0.186 Angle : 0.544 8.007 34278 Z= 0.289 Chirality : 0.046 0.152 3996 Planarity : 0.004 0.048 4396 Dihedral : 8.210 70.495 3656 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 1.64 % Allowed : 10.18 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3202 helix: 1.57 (0.15), residues: 1290 sheet: -0.25 (0.24), residues: 442 loop : -1.08 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 15 HIS 0.004 0.001 HIS C 650 PHE 0.012 0.001 PHE A 638 TYR 0.012 0.001 TYR A 252 ARG 0.004 0.000 ARG C 301 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 1190) hydrogen bonds : angle 4.57964 ( 3351) link_ASP_CG-ANY_N : bond 0.00145 ( 8) link_ASP_CG-ANY_N : angle 0.79341 ( 24) covalent geometry : bond 0.00434 (25236) covalent geometry : angle 0.54384 (34254) *********************** 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 197 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8212 (mtp) cc_final: 0.7995 (mtp) REVERT: A 252 TYR cc_start: 0.8263 (t80) cc_final: 0.8005 (t80) REVERT: A 586 HIS cc_start: 0.6703 (OUTLIER) cc_final: 0.5664 (m90) REVERT: B 94 MET cc_start: 0.8239 (mtp) cc_final: 0.8016 (mtp) REVERT: B 252 TYR cc_start: 0.8185 (t80) cc_final: 0.7940 (t80) REVERT: B 586 HIS cc_start: 0.6792 (OUTLIER) cc_final: 0.5769 (m90) REVERT: C 168 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8610 (mm-30) REVERT: C 710 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8538 (mtpt) REVERT: D 243 PHE cc_start: 0.7983 (t80) cc_final: 0.7705 (t80) REVERT: D 280 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8328 (tt0) outliers start: 43 outliers final: 18 residues processed: 182 average time/residue: 1.1558 time to fit residues: 250.7650 Evaluate side-chains 160 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 2.880 ------------------------------------------------------------------------------- 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 151 LEU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain B residue 32 LEU 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 586 HIS Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 163 LEU 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 299 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 162 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 311 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 0.0970 chunk 296 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 394 ASN ** D 89 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.147418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.087018 restraints weight = 37222.452| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.63 r_work: 0.2866 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 25244 Z= 0.194 Angle : 0.551 8.771 34278 Z= 0.291 Chirality : 0.046 0.152 3996 Planarity : 0.004 0.046 4396 Dihedral : 8.155 73.317 3656 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 2.45 % Allowed : 11.32 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3202 helix: 1.66 (0.15), residues: 1286 sheet: -0.28 (0.23), residues: 504 loop : -1.10 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 278 HIS 0.004 0.001 HIS D 650 PHE 0.012 0.001 PHE B 638 TYR 0.012 0.001 TYR B 519 ARG 0.004 0.000 ARG D 301 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 1190) hydrogen bonds : angle 4.54265 ( 3351) link_ASP_CG-ANY_N : bond 0.00155 ( 8) link_ASP_CG-ANY_N : angle 0.71669 ( 24) covalent geometry : bond 0.00455 (25236) covalent geometry : angle 0.55098 (34254) *********************** 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 210 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 146 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8226 (mtp) cc_final: 0.8019 (mtp) REVERT: A 149 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7218 (tp40) REVERT: A 252 TYR cc_start: 0.8284 (t80) cc_final: 0.7980 (t80) REVERT: A 586 HIS cc_start: 0.6620 (OUTLIER) cc_final: 0.5514 (m90) REVERT: B 94 MET cc_start: 0.8250 (mtp) cc_final: 0.8036 (mtp) REVERT: B 252 TYR cc_start: 0.8267 (t80) cc_final: 0.7982 (t80) REVERT: B 586 HIS cc_start: 0.6715 (OUTLIER) cc_final: 0.5620 (m90) REVERT: B 732 MET cc_start: 0.8157 (mmm) cc_final: 0.7922 (mmm) REVERT: C 168 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8511 (mm-30) REVERT: C 247 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7808 (pm20) REVERT: D 168 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8530 (mm-30) REVERT: D 243 PHE cc_start: 0.8048 (t80) cc_final: 0.7809 (t80) outliers start: 64 outliers final: 28 residues processed: 188 average time/residue: 1.1030 time to fit residues: 249.3535 Evaluate side-chains 169 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 2.745 ------------------------------------------------------------------------------- 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 149 GLN Chi-restraints excluded: chain A residue 151 LEU 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 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 151 LEU Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 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 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 299 VAL Chi-restraints excluded: chain D residue 459 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 281 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 251 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 394 ASN D 89 GLN D 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.147873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.087585 restraints weight = 37201.319| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.63 r_work: 0.2941 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25244 Z= 0.159 Angle : 0.528 9.043 34278 Z= 0.279 Chirality : 0.046 0.190 3996 Planarity : 0.004 0.045 4396 Dihedral : 7.962 72.931 3656 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.25 % Rotamer: Outliers : 2.14 % Allowed : 12.24 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3202 helix: 1.75 (0.15), residues: 1280 sheet: -0.17 (0.23), residues: 474 loop : -1.06 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 278 HIS 0.003 0.001 HIS C 650 PHE 0.010 0.001 PHE B 638 TYR 0.011 0.001 TYR B 519 ARG 0.002 0.000 ARG A 418 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 1190) hydrogen bonds : angle 4.46005 ( 3351) link_ASP_CG-ANY_N : bond 0.00135 ( 8) link_ASP_CG-ANY_N : angle 0.66394 ( 24) covalent geometry : bond 0.00368 (25236) covalent geometry : angle 0.52833 (34254) *********************** 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 207 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 151 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8273 (mtp) cc_final: 0.8056 (mtp) REVERT: A 252 TYR cc_start: 0.8275 (t80) cc_final: 0.7961 (t80) REVERT: B 94 MET cc_start: 0.8287 (mtp) cc_final: 0.8060 (mtp) REVERT: B 252 TYR cc_start: 0.8271 (t80) cc_final: 0.7923 (t80) REVERT: B 732 MET cc_start: 0.8060 (mmm) cc_final: 0.7718 (mmm) REVERT: C 168 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8560 (mm-30) REVERT: C 710 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8504 (mtpt) REVERT: D 168 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8511 (mm-30) REVERT: D 243 PHE cc_start: 0.7946 (t80) cc_final: 0.7585 (t80) REVERT: D 247 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7844 (pm20) outliers start: 56 outliers final: 37 residues processed: 193 average time/residue: 1.0846 time to fit residues: 251.4630 Evaluate side-chains 177 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 2.461 ------------------------------------------------------------------------------- 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 103 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain 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 151 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 710 LYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 234 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 237 optimal weight: 0.3980 chunk 290 optimal weight: 1.9990 chunk 295 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 289 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.148340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.088104 restraints weight = 36943.880| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.62 r_work: 0.2941 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25244 Z= 0.149 Angle : 0.523 9.041 34278 Z= 0.277 Chirality : 0.045 0.158 3996 Planarity : 0.004 0.044 4396 Dihedral : 7.825 74.558 3656 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.81 % Favored : 96.13 % Rotamer: Outliers : 2.49 % Allowed : 12.55 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3202 helix: 1.79 (0.15), residues: 1280 sheet: -0.26 (0.23), residues: 502 loop : -1.02 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 278 HIS 0.003 0.001 HIS C 650 PHE 0.010 0.001 PHE B 638 TYR 0.011 0.001 TYR A 519 ARG 0.003 0.000 ARG B 561 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 1190) hydrogen bonds : angle 4.40113 ( 3351) link_ASP_CG-ANY_N : bond 0.00122 ( 8) link_ASP_CG-ANY_N : angle 0.65257 ( 24) covalent geometry : bond 0.00344 (25236) covalent geometry : angle 0.52255 (34254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 142 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8261 (mtp) cc_final: 0.8037 (mtp) REVERT: A 149 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7215 (tp40) REVERT: A 252 TYR cc_start: 0.8267 (t80) cc_final: 0.7971 (t80) REVERT: A 839 ILE cc_start: 0.3882 (OUTLIER) cc_final: 0.3583 (pp) REVERT: B 94 MET cc_start: 0.8293 (mtp) cc_final: 0.8060 (mtp) REVERT: B 252 TYR cc_start: 0.8275 (t80) cc_final: 0.7974 (t80) REVERT: B 732 MET cc_start: 0.8010 (mmm) cc_final: 0.7650 (mmm) REVERT: B 839 ILE cc_start: 0.3871 (OUTLIER) cc_final: 0.3578 (pp) REVERT: C 168 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8548 (mm-30) REVERT: C 710 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8483 (mtpt) REVERT: D 168 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8512 (mm-30) REVERT: D 243 PHE cc_start: 0.7998 (t80) cc_final: 0.7735 (t80) outliers start: 65 outliers final: 41 residues processed: 191 average time/residue: 1.1095 time to fit residues: 253.7461 Evaluate side-chains 179 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 32 LEU 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 149 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 32 LEU 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 684 ILE Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 710 LYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 98 optimal weight: 1.9990 chunk 265 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 149 optimal weight: 0.3980 chunk 240 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.148463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.088809 restraints weight = 37296.704| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.74 r_work: 0.2931 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25244 Z= 0.133 Angle : 0.516 9.070 34278 Z= 0.272 Chirality : 0.045 0.150 3996 Planarity : 0.004 0.044 4396 Dihedral : 7.656 76.598 3656 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.31 % Rotamer: Outliers : 2.22 % Allowed : 13.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3202 helix: 1.79 (0.15), residues: 1294 sheet: -0.15 (0.23), residues: 472 loop : -1.03 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 278 HIS 0.003 0.001 HIS C 650 PHE 0.009 0.001 PHE A 638 TYR 0.010 0.001 TYR A 519 ARG 0.002 0.000 ARG A 561 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 1190) hydrogen bonds : angle 4.32948 ( 3351) link_ASP_CG-ANY_N : bond 0.00113 ( 8) link_ASP_CG-ANY_N : angle 0.64252 ( 24) covalent geometry : bond 0.00303 (25236) covalent geometry : angle 0.51618 (34254) *********************** 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: 58 poor density : 137 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8201 (mtp) cc_final: 0.7927 (mtp) REVERT: A 149 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7185 (tp40) REVERT: A 252 TYR cc_start: 0.8240 (t80) cc_final: 0.7966 (t80) REVERT: A 839 ILE cc_start: 0.4151 (OUTLIER) cc_final: 0.3815 (pp) REVERT: B 94 MET cc_start: 0.8219 (mtp) cc_final: 0.7941 (mtp) REVERT: B 252 TYR cc_start: 0.8215 (t80) cc_final: 0.7946 (t80) REVERT: B 541 GLN cc_start: 0.8025 (pm20) cc_final: 0.7825 (mp10) REVERT: B 732 MET cc_start: 0.7993 (mmm) cc_final: 0.7505 (mmm) REVERT: B 839 ILE cc_start: 0.4161 (OUTLIER) cc_final: 0.3831 (pp) REVERT: C 124 TYR cc_start: 0.7653 (t80) cc_final: 0.7447 (t80) REVERT: C 168 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8325 (mm-30) REVERT: C 710 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8397 (mtpt) REVERT: D 168 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8195 (mm-30) REVERT: D 243 PHE cc_start: 0.7938 (t80) cc_final: 0.7724 (t80) outliers start: 58 outliers final: 43 residues processed: 182 average time/residue: 1.1792 time to fit residues: 256.5152 Evaluate side-chains 179 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 744 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 251 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 710 LYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 54 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 chunk 283 optimal weight: 0.0170 chunk 251 optimal weight: 9.9990 chunk 317 optimal weight: 1.9990 chunk 312 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 overall best weight: 0.8020 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 GLN C 541 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.149050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.089494 restraints weight = 37068.602| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.77 r_work: 0.2965 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 25244 Z= 0.117 Angle : 0.500 8.981 34278 Z= 0.262 Chirality : 0.044 0.145 3996 Planarity : 0.004 0.044 4396 Dihedral : 7.448 78.942 3656 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.28 % Rotamer: Outliers : 2.18 % Allowed : 13.81 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.15), residues: 3202 helix: 1.86 (0.15), residues: 1294 sheet: -0.08 (0.23), residues: 498 loop : -1.02 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 278 HIS 0.002 0.001 HIS D 79 PHE 0.008 0.001 PHE D 638 TYR 0.010 0.001 TYR A 519 ARG 0.002 0.000 ARG C 301 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 1190) hydrogen bonds : angle 4.22786 ( 3351) link_ASP_CG-ANY_N : bond 0.00100 ( 8) link_ASP_CG-ANY_N : angle 0.63883 ( 24) covalent geometry : bond 0.00263 (25236) covalent geometry : angle 0.50024 (34254) *********************** 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 198 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 141 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8248 (mtp) cc_final: 0.7958 (mtp) REVERT: A 149 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7177 (tp40) REVERT: A 252 TYR cc_start: 0.8222 (t80) cc_final: 0.7980 (t80) REVERT: A 839 ILE cc_start: 0.4231 (OUTLIER) cc_final: 0.3900 (pp) REVERT: B 94 MET cc_start: 0.8242 (mtp) cc_final: 0.7952 (mtp) REVERT: B 252 TYR cc_start: 0.8206 (t80) cc_final: 0.7944 (t80) REVERT: B 629 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7551 (p0) REVERT: B 732 MET cc_start: 0.7963 (mmm) cc_final: 0.7456 (mmm) REVERT: B 839 ILE cc_start: 0.4173 (OUTLIER) cc_final: 0.3839 (pp) REVERT: C 124 TYR cc_start: 0.7698 (t80) cc_final: 0.7484 (t80) REVERT: C 168 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8293 (mm-30) REVERT: C 710 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8372 (mtpt) REVERT: D 124 TYR cc_start: 0.7681 (t80) cc_final: 0.7479 (t80) REVERT: D 168 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8224 (mm-30) outliers start: 57 outliers final: 35 residues processed: 187 average time/residue: 1.2350 time to fit residues: 274.3791 Evaluate side-chains 171 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 710 LYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 171 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 295 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 274 optimal weight: 9.9990 chunk 111 optimal weight: 0.0870 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 GLN C 541 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.148039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.088764 restraints weight = 37537.346| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.75 r_work: 0.2933 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25244 Z= 0.139 Angle : 0.518 8.942 34278 Z= 0.272 Chirality : 0.045 0.171 3996 Planarity : 0.004 0.043 4396 Dihedral : 7.414 79.621 3656 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Rotamer: Outliers : 1.76 % Allowed : 14.38 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.15), residues: 3202 helix: 1.85 (0.15), residues: 1294 sheet: -0.14 (0.23), residues: 500 loop : -0.99 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 278 HIS 0.005 0.001 HIS C 18 PHE 0.010 0.001 PHE B 638 TYR 0.010 0.001 TYR A 519 ARG 0.002 0.000 ARG B 123 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 1190) hydrogen bonds : angle 4.26333 ( 3351) link_ASP_CG-ANY_N : bond 0.00126 ( 8) link_ASP_CG-ANY_N : angle 0.65443 ( 24) covalent geometry : bond 0.00320 (25236) covalent geometry : angle 0.51768 (34254) *********************** 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 183 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8240 (mtp) cc_final: 0.7938 (mtp) REVERT: A 149 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7185 (tp40) REVERT: A 252 TYR cc_start: 0.8275 (t80) cc_final: 0.8000 (t80) REVERT: A 839 ILE cc_start: 0.4201 (OUTLIER) cc_final: 0.3865 (pp) REVERT: B 94 MET cc_start: 0.8266 (mtp) cc_final: 0.7954 (mtp) REVERT: B 252 TYR cc_start: 0.8296 (t80) cc_final: 0.8007 (t80) REVERT: B 732 MET cc_start: 0.7874 (mmm) cc_final: 0.7385 (mmm) REVERT: B 839 ILE cc_start: 0.4133 (OUTLIER) cc_final: 0.3802 (pp) REVERT: C 124 TYR cc_start: 0.7805 (t80) cc_final: 0.7583 (t80) REVERT: C 168 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8536 (mm-30) REVERT: D 124 TYR cc_start: 0.7792 (t80) cc_final: 0.7585 (t80) REVERT: D 168 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8524 (mm-30) outliers start: 46 outliers final: 37 residues processed: 175 average time/residue: 1.2129 time to fit residues: 250.4371 Evaluate side-chains 173 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 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 80 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 252 optimal weight: 0.6980 chunk 225 optimal weight: 0.0370 chunk 8 optimal weight: 0.6980 chunk 208 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 233 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 373 GLN C 541 GLN D 89 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 = 0.149665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.090989 restraints weight = 37564.352| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.54 r_work: 0.2975 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25244 Z= 0.103 Angle : 0.498 8.878 34278 Z= 0.259 Chirality : 0.044 0.153 3996 Planarity : 0.004 0.044 4396 Dihedral : 7.195 82.280 3656 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 1.84 % Allowed : 14.54 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3202 helix: 1.91 (0.15), residues: 1292 sheet: 0.02 (0.22), residues: 552 loop : -0.97 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 278 HIS 0.003 0.000 HIS C 79 PHE 0.010 0.001 PHE B 43 TYR 0.009 0.001 TYR B 519 ARG 0.002 0.000 ARG A 731 Details of bonding type rmsd hydrogen bonds : bond 0.02972 ( 1190) hydrogen bonds : angle 4.15017 ( 3351) link_ASP_CG-ANY_N : bond 0.00084 ( 8) link_ASP_CG-ANY_N : angle 0.62605 ( 24) covalent geometry : bond 0.00229 (25236) covalent geometry : angle 0.49818 (34254) ********************** 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 194 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8260 (mtp) cc_final: 0.8023 (mtp) REVERT: A 149 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7142 (tp40) REVERT: A 252 TYR cc_start: 0.8236 (t80) cc_final: 0.7967 (t80) REVERT: A 839 ILE cc_start: 0.4071 (OUTLIER) cc_final: 0.3759 (pp) REVERT: B 94 MET cc_start: 0.8278 (mtp) cc_final: 0.7966 (mtp) REVERT: B 252 TYR cc_start: 0.8288 (t80) cc_final: 0.8014 (t80) REVERT: B 732 MET cc_start: 0.7832 (mmm) cc_final: 0.7308 (mmm) REVERT: B 839 ILE cc_start: 0.4036 (OUTLIER) cc_final: 0.3724 (pp) REVERT: C 124 TYR cc_start: 0.7830 (t80) cc_final: 0.7611 (t80) REVERT: C 168 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8509 (mm-30) REVERT: D 124 TYR cc_start: 0.7826 (t80) cc_final: 0.7621 (t80) REVERT: D 168 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8472 (mm-30) outliers start: 48 outliers final: 35 residues processed: 185 average time/residue: 1.2423 time to fit residues: 273.6275 Evaluate side-chains 172 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 225 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 306 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 275 optimal weight: 10.0000 chunk 303 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 541 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.148696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.088369 restraints weight = 37518.409| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.63 r_work: 0.2955 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25244 Z= 0.138 Angle : 0.515 8.804 34278 Z= 0.270 Chirality : 0.045 0.158 3996 Planarity : 0.004 0.042 4396 Dihedral : 7.202 81.273 3656 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 1.80 % Allowed : 14.80 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.15), residues: 3202 helix: 1.92 (0.15), residues: 1292 sheet: -0.08 (0.23), residues: 502 loop : -0.93 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 278 HIS 0.004 0.001 HIS D 18 PHE 0.012 0.001 PHE B 43 TYR 0.022 0.001 TYR B 44 ARG 0.002 0.000 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 1190) hydrogen bonds : angle 4.22132 ( 3351) link_ASP_CG-ANY_N : bond 0.00122 ( 8) link_ASP_CG-ANY_N : angle 0.66246 ( 24) covalent geometry : bond 0.00320 (25236) covalent geometry : angle 0.51535 (34254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23635.86 seconds wall clock time: 402 minutes 14.60 seconds (24134.60 seconds total)