Starting phenix.real_space_refine on Sun Aug 24 04:22:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3t_17394/08_2025/8p3t_17394_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3t_17394/08_2025/8p3t_17394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p3t_17394/08_2025/8p3t_17394_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3t_17394/08_2025/8p3t_17394_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p3t_17394/08_2025/8p3t_17394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3t_17394/08_2025/8p3t_17394.map" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.043 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 11054 2.51 5 N 2737 2.21 5 O 2974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16861 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2843 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 373} Chain breaks: 4 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 6, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 137 Chain: "B" Number of atoms: 2909 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 2878 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 98 Conformer: "B" Number of residues, atoms: 384, 2878 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 98 bond proxies already assigned to first conformer: 2906 Chain: "C" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2840 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 13, 'ASP:plan': 5, 'ARG:plan': 4, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "D" Number of atoms: 2847 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 379, 2816 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 367} Chain breaks: 4 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'ASP:plan': 7, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 108 Conformer: "B" Number of residues, atoms: 379, 2816 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 367} Chain breaks: 4 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'ASP:plan': 7, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 108 bond proxies already assigned to first conformer: 2842 Chain: "E" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1357 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1357 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1351 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1357 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N APHE B 570 " occ=0.54 ... (20 atoms not shown) pdb=" CZ BPHE B 570 " occ=0.46 residue: pdb=" N AGLN B 582 " occ=0.16 ... (16 atoms not shown) pdb=" NE2BGLN B 582 " occ=0.84 residue: pdb=" N APHE B 619 " occ=0.64 ... (20 atoms not shown) pdb=" CZ BPHE B 619 " occ=0.36 residue: pdb=" N APHE D 570 " occ=0.52 ... (20 atoms not shown) pdb=" CZ BPHE D 570 " occ=0.48 residue: pdb=" N AGLN D 582 " occ=0.26 ... (16 atoms not shown) pdb=" NE2BGLN D 582 " occ=0.74 residue: pdb=" N APHE D 619 " occ=0.53 ... (20 atoms not shown) pdb=" CZ BPHE D 619 " occ=0.47 Time building chain proxies: 4.97, per 1000 atoms: 0.29 Number of scatterers: 16861 At special positions: 0 Unit cell: (121.9, 112.625, 136.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2974 8.00 N 2737 7.00 C 11054 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.02 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.04 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.02 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.02 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 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 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 643.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4094 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 26 sheets defined 61.4% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.559A pdb=" N GLN A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 removed outlier: 4.086A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 625 removed outlier: 3.542A pdb=" N ARG A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 660 through 673 Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 753 through 763 Processing helix chain 'A' and resid 784 through 787 Processing helix chain 'A' and resid 788 through 814 removed outlier: 3.762A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.606A pdb=" N GLN B 410 " --> pdb=" O ASN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 419 through 433 Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 518 through 542 removed outlier: 3.703A pdb=" N PHE B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 591 through 625 removed outlier: 3.565A pdb=" N VAL B 597 " --> pdb=" O SER B 593 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 623 " --> pdb=" O APHE B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 649 through 657 Processing helix chain 'B' and resid 660 through 673 removed outlier: 3.524A pdb=" N SER B 672 " --> pdb=" O THR B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 692 Processing helix chain 'B' and resid 702 through 711 Processing helix chain 'B' and resid 738 through 752 Processing helix chain 'B' and resid 753 through 763 Processing helix chain 'B' and resid 788 through 815 removed outlier: 3.652A pdb=" N PHE B 792 " --> pdb=" O VAL B 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.549A pdb=" N GLN C 410 " --> pdb=" O ASN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 removed outlier: 4.280A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 518 through 542 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 619 Processing helix chain 'C' and resid 632 through 638 removed outlier: 3.519A pdb=" N GLN C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 788 through 814 removed outlier: 3.823A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 411 removed outlier: 3.567A pdb=" N GLN D 410 " --> pdb=" O ASN D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 415 removed outlier: 4.160A pdb=" N ASP D 415 " --> pdb=" O GLU D 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 419 through 433 Processing helix chain 'D' and resid 457 through 466 Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 518 through 542 removed outlier: 3.631A pdb=" N PHE D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 581 Processing helix chain 'D' and resid 591 through 622 removed outlier: 3.562A pdb=" N VAL D 597 " --> pdb=" O SER D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 638 Processing helix chain 'D' and resid 649 through 657 Processing helix chain 'D' and resid 660 through 673 removed outlier: 3.518A pdb=" N SER D 672 " --> pdb=" O THR D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 692 Processing helix chain 'D' and resid 702 through 711 Processing helix chain 'D' and resid 738 through 752 Processing helix chain 'D' and resid 753 through 764 Processing helix chain 'D' and resid 788 through 815 removed outlier: 3.904A pdb=" N PHE D 792 " --> pdb=" O VAL D 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 93 through 105 Processing helix chain 'E' and resid 105 through 128 removed outlier: 4.120A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 162 removed outlier: 3.723A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 209 removed outlier: 3.510A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU E 207 " --> pdb=" O LYS E 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 105 through 126 removed outlier: 3.970A pdb=" N GLU F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.862A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 209 removed outlier: 3.559A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE F 187 " --> pdb=" O ALA F 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 removed outlier: 3.529A pdb=" N ALA G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 105 removed outlier: 3.671A pdb=" N LEU G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 127 removed outlier: 3.680A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.839A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY G 162 " --> pdb=" O SER G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 209 removed outlier: 3.665A pdb=" N LEU G 207 " --> pdb=" O LYS G 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 105 through 126 removed outlier: 4.158A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.655A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 209 removed outlier: 3.587A pdb=" N ILE H 187 " --> pdb=" O ALA H 183 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU H 207 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 440 removed outlier: 6.626A pdb=" N TYR A 391 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU A 439 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 447 through 449 removed outlier: 3.671A pdb=" N ALA A 448 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 494 removed outlier: 4.063A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 643 through 644 removed outlier: 6.573A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 436 through 440 removed outlier: 6.719A pdb=" N TYR B 391 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLU B 439 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL B 393 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 470 " --> pdb=" O ILE B 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AA9, first strand: chain 'B' and resid 485 through 487 Processing sheet with id=AB1, first strand: chain 'B' and resid 492 through 494 removed outlier: 3.896A pdb=" N MET B 492 " --> pdb=" O TYR B 728 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 642 through 644 removed outlier: 6.454A pdb=" N ALA B 642 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU B 699 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY B 644 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N GLU B 701 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE B 498 " --> pdb=" O VAL B 719 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 436 through 440 removed outlier: 6.580A pdb=" N TYR C 391 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU C 439 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL C 393 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB5, first strand: chain 'C' and resid 447 through 450 removed outlier: 3.767A pdb=" N ALA C 448 " --> pdb=" O ASN C 457 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 455 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AB7, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.876A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.559A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR C 698 " --> pdb=" O MET C 499 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 436 through 440 removed outlier: 6.375A pdb=" N TYR D 391 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLU D 439 " --> pdb=" O TYR D 391 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL D 393 " --> pdb=" O GLU D 439 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D 470 " --> pdb=" O ILE D 392 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AC2, first strand: chain 'D' and resid 485 through 487 Processing sheet with id=AC3, first strand: chain 'D' and resid 492 through 494 removed outlier: 3.849A pdb=" N MET D 492 " --> pdb=" O TYR D 728 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 642 through 644 removed outlier: 6.591A pdb=" N ALA D 642 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU D 699 " --> pdb=" O ALA D 642 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY D 644 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N GLU D 701 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE D 498 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC6, first strand: chain 'F' and resid 34 through 38 Processing sheet with id=AC7, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AC8, first strand: chain 'H' and resid 77 through 79 1114 hydrogen bonds defined for protein. 3251 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: 3.20 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2614 1.32 - 1.44: 4986 1.44 - 1.57: 9496 1.57 - 1.70: 0 1.70 - 1.83: 156 Bond restraints: 17252 Sorted by residual: bond pdb=" C SER A 631 " pdb=" O SER A 631 " ideal model delta sigma weight residual 1.235 1.311 -0.076 1.03e-02 9.43e+03 5.42e+01 bond pdb=" CA SER A 631 " pdb=" CB SER A 631 " ideal model delta sigma weight residual 1.532 1.475 0.058 1.28e-02 6.10e+03 2.03e+01 bond pdb=" N VAL C 484 " pdb=" CA VAL C 484 " ideal model delta sigma weight residual 1.456 1.497 -0.041 9.50e-03 1.11e+04 1.86e+01 bond pdb=" C MET B 499 " pdb=" O MET B 499 " ideal model delta sigma weight residual 1.235 1.283 -0.048 1.12e-02 7.97e+03 1.82e+01 bond pdb=" C TYR D 391 " pdb=" O TYR D 391 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.34e-02 5.57e+03 1.76e+01 ... (remaining 17247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 23281 4.72 - 9.44: 125 9.44 - 14.15: 8 14.15 - 18.87: 4 18.87 - 23.59: 1 Bond angle restraints: 23419 Sorted by residual: angle pdb=" N LEU A 635 " pdb=" CA LEU A 635 " pdb=" C LEU A 635 " ideal model delta sigma weight residual 112.54 97.84 14.70 1.22e+00 6.72e-01 1.45e+02 angle pdb=" C LYS A 637 " pdb=" CA LYS A 637 " pdb=" CB LYS A 637 " ideal model delta sigma weight residual 110.42 86.83 23.59 1.99e+00 2.53e-01 1.41e+02 angle pdb=" C THR A 639 " pdb=" CA THR A 639 " pdb=" CB THR A 639 " ideal model delta sigma weight residual 110.36 95.36 15.00 1.78e+00 3.16e-01 7.10e+01 angle pdb=" C GLU C 630 " pdb=" CA GLU C 630 " pdb=" CB GLU C 630 " ideal model delta sigma weight residual 110.10 94.16 15.94 1.90e+00 2.77e-01 7.04e+01 angle pdb=" N ILE A 641 " pdb=" CA ILE A 641 " pdb=" C ILE A 641 " ideal model delta sigma weight residual 109.34 94.11 15.23 2.08e+00 2.31e-01 5.36e+01 ... (remaining 23414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8741 17.96 - 35.93: 877 35.93 - 53.89: 217 53.89 - 71.86: 45 71.86 - 89.82: 9 Dihedral angle restraints: 9889 sinusoidal: 3475 harmonic: 6414 Sorted by residual: dihedral pdb=" C LYS A 637 " pdb=" N LYS A 637 " pdb=" CA LYS A 637 " pdb=" CB LYS A 637 " ideal model delta harmonic sigma weight residual -122.60 -94.65 -27.95 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" CD ARG A 624 " pdb=" NE ARG A 624 " pdb=" CZ ARG A 624 " pdb=" NH1 ARG A 624 " ideal model delta sinusoidal sigma weight residual 0.00 -65.68 65.68 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" C GLU C 630 " pdb=" N GLU C 630 " pdb=" CA GLU C 630 " pdb=" CB GLU C 630 " ideal model delta harmonic sigma weight residual -122.60 -105.89 -16.71 0 2.50e+00 1.60e-01 4.47e+01 ... (remaining 9886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1722 0.099 - 0.199: 907 0.199 - 0.298: 58 0.298 - 0.398: 14 0.398 - 0.497: 3 Chirality restraints: 2704 Sorted by residual: chirality pdb=" CA ILE B 500 " pdb=" N ILE B 500 " pdb=" C ILE B 500 " pdb=" CB ILE B 500 " both_signs ideal model delta sigma weight residual False 2.43 2.93 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CA LYS A 637 " pdb=" N LYS A 637 " pdb=" C LYS A 637 " pdb=" CB LYS A 637 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA ILE D 500 " pdb=" N ILE D 500 " pdb=" C ILE D 500 " pdb=" CB ILE D 500 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 2701 not shown) Planarity restraints: 2877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 624 " 0.947 9.50e-02 1.11e+02 4.25e-01 1.10e+02 pdb=" NE ARG A 624 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 624 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 624 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 624 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 630 " -0.033 2.00e-02 2.50e+03 7.05e-02 4.97e+01 pdb=" C GLU A 630 " 0.122 2.00e-02 2.50e+03 pdb=" O GLU A 630 " -0.047 2.00e-02 2.50e+03 pdb=" N SER A 631 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 632 " -0.026 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C ALA A 632 " 0.094 2.00e-02 2.50e+03 pdb=" O ALA A 632 " -0.036 2.00e-02 2.50e+03 pdb=" N GLU A 633 " -0.032 2.00e-02 2.50e+03 ... (remaining 2874 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2830 2.76 - 3.30: 17309 3.30 - 3.83: 27708 3.83 - 4.37: 33539 4.37 - 4.90: 56817 Nonbonded interactions: 138203 Sorted by model distance: nonbonded pdb=" O ALA A 636 " pdb=" N GLN A 638 " model vdw 2.226 3.120 nonbonded pdb=" OG SER A 631 " pdb=" N ALA A 632 " model vdw 2.237 3.120 nonbonded pdb=" OG1 THR G 30 " pdb=" OG SER G 178 " model vdw 2.238 3.040 nonbonded pdb=" N GLU G 95 " pdb=" OE1 GLU G 95 " model vdw 2.260 3.120 nonbonded pdb=" O LYS B 501 " pdb=" O LYS B 502 " model vdw 2.263 3.040 ... (remaining 138198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 390 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 414 or (resid 415 through 416 and (name N o \ r name CA or name C or name O or name CB )) or resid 417 through 429 or (resid 4 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 431 through \ 444 or (resid 445 and (name N or name CA or name C or name O or name CB )) or r \ esid 446 through 502 or resid 509 through 546 or resid 567 through 569 or resid \ 571 through 581 or resid 583 through 618 or resid 620 through 622 or resid 631 t \ hrough 664 or (resid 665 and (name N or name CA or name C or name O or name CB ) \ ) or resid 666 through 767 or resid 782 through 815)) selection = (chain 'B' and ((resid 390 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 398 or (resid 399 and (name N or name CA or \ name C or name O or name CB )) or resid 400 through 403 or (resid 404 and (name \ N or name CA or name C or name O or name CB )) or resid 405 through 415 or (res \ id 416 and (name N or name CA or name C or name O or name CB )) or resid 417 thr \ ough 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) \ or resid 431 through 444 or (resid 445 and (name N or name CA or name C or name \ O or name CB )) or resid 446 through 461 or (resid 462 and (name N or name CA or \ name C or name O or name CB )) or resid 463 through 500 or (resid 501 through 5 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 509 through \ 545 or (resid 566 and (name N or name CA or name C or name O or name CB )) or r \ esid 567 through 569 or resid 571 through 581 or resid 583 through 618 or resid \ 620 through 622 or resid 631 through 632 or (resid 633 through 634 and (name N o \ r name CA or name C or name O or name CB )) or resid 635 through 658 or (resid 6 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 660 through \ 664 or (resid 665 and (name N or name CA or name C or name O or name CB )) or r \ esid 666 through 683 or (resid 684 and (name N or name CA or name C or name O or \ name CB )) or resid 685 through 687 or (resid 688 and (name N or name CA or nam \ e C or name O or name CB )) or resid 689 through 690 or (resid 691 through 693 a \ nd (name N or name CA or name C or name O or name CB )) or resid 694 through 705 \ or (resid 706 and (name N or name CA or name C or name O or name CB )) or resid \ 707 through 767 or resid 782 through 813 or (resid 814 through 815 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'C' and ((resid 390 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 398 or (resid 399 and (name N or name CA or \ name C or name O or name CB )) or resid 400 through 415 or (resid 416 and (name \ N or name CA or name C or name O or name CB )) or resid 417 through 466 or (res \ id 467 through 469 and (name N or name CA or name C or name O or name CB )) or r \ esid 470 through 502 or resid 509 through 546 or resid 567 through 569 or resid \ 571 through 581 or resid 583 through 618 or resid 620 through 622 or resid 631 t \ hrough 633 or (resid 634 and (name N or name CA or name C or name O or name CB ) \ ) or resid 635 through 687 or (resid 688 and (name N or name CA or name C or nam \ e O or name CB )) or resid 689 through 691 or (resid 692 through 693 and (name N \ or name CA or name C or name O or name CB )) or resid 694 through 708 or (resid \ 709 and (name N or name CA or name C or name O or name CB )) or resid 710 throu \ gh 815)) selection = (chain 'D' and (resid 390 through 444 or (resid 445 and (name N or name CA or na \ me C or name O or name CB )) or resid 446 through 466 or (resid 467 through 469 \ and (name N or name CA or name C or name O or name CB )) or resid 470 through 54 \ 5 or (resid 566 and (name N or name CA or name C or name O or name CB )) or resi \ d 567 through 569 or resid 571 through 581 or resid 583 through 618 or resid 620 \ through 658 or (resid 659 and (name N or name CA or name C or name O or name CB \ )) or resid 660 through 664 or (resid 665 and (name N or name CA or name C or n \ ame O or name CB )) or resid 666 through 687 or (resid 688 and (name N or name C \ A or name C or name O or name CB )) or resid 689 through 691 or (resid 692 throu \ gh 693 and (name N or name CA or name C or name O or name CB )) or resid 694 thr \ ough 705 or (resid 706 and (name N or name CA or name C or name O or name CB )) \ or resid 707 through 708 or (resid 709 and (name N or name CA or name C or name \ O or name CB )) or resid 710 through 767 or resid 782 through 813 or (resid 814 \ through 815 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'E' and (resid 5 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 209)) selection = (chain 'F' and (resid 5 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 209)) selection = chain 'G' selection = (chain 'H' and (resid 5 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 209)) } 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=0.16 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.220 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 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 : 0.012 0.076 17260 Z= 0.856 Angle : 1.401 23.589 23435 Z= 1.028 Chirality : 0.102 0.497 2704 Planarity : 0.014 0.425 2877 Dihedral : 15.562 89.821 5771 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.54 % Favored : 97.09 % Rotamer: Outliers : 4.78 % Allowed : 17.33 % Favored : 77.88 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.16), residues: 2183 helix: 0.76 (0.13), residues: 1313 sheet: -2.80 (0.34), residues: 154 loop : -1.05 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 624 TYR 0.026 0.004 TYR C 391 PHE 0.028 0.003 PHE D 542 TRP 0.016 0.003 TRP D 456 HIS 0.006 0.001 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.01163 (17252) covalent geometry : angle 1.40175 (23419) SS BOND : bond 0.00494 ( 8) SS BOND : angle 0.82187 ( 16) hydrogen bonds : bond 0.19843 ( 1114) hydrogen bonds : angle 5.98405 ( 3251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 203 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 666 MET cc_start: 0.7899 (mtp) cc_final: 0.7465 (mtt) REVERT: D 581 MET cc_start: 0.9295 (mmm) cc_final: 0.9062 (mtm) REVERT: D 666 MET cc_start: 0.6785 (mtt) cc_final: 0.6245 (mmt) REVERT: E 6 ARG cc_start: 0.7082 (ttt-90) cc_final: 0.5954 (tmm160) REVERT: E 56 GLU cc_start: 0.9008 (tp30) cc_final: 0.8727 (tp30) REVERT: E 70 GLU cc_start: 0.9104 (pt0) cc_final: 0.8670 (pm20) REVERT: E 81 ASP cc_start: 0.8926 (t0) cc_final: 0.8648 (t70) REVERT: E 128 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.7068 (t-90) REVERT: F 81 ASP cc_start: 0.9142 (OUTLIER) cc_final: 0.8755 (t0) REVERT: F 206 GLN cc_start: 0.8634 (tt0) cc_final: 0.8106 (tm-30) REVERT: G 58 MET cc_start: 0.8878 (tpp) cc_final: 0.8601 (tpp) REVERT: H 10 MET cc_start: 0.9064 (tmm) cc_final: 0.8315 (tmm) REVERT: H 13 THR cc_start: 0.9280 (m) cc_final: 0.8987 (t) REVERT: H 81 ASP cc_start: 0.8478 (t0) cc_final: 0.8209 (t70) REVERT: H 202 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8427 (mp0) outliers start: 79 outliers final: 44 residues processed: 274 average time/residue: 0.1519 time to fit residues: 59.6662 Evaluate side-chains 189 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 501 LYS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 128 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 202 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 9.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN B 582 GLN A B 710 GLN ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN E 160 ASN F 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 HIS H 9 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.125834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.077837 restraints weight = 173499.436| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 7.90 r_work: 0.2844 rms_B_bonded: 6.42 restraints_weight: 2.0000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17260 Z= 0.141 Angle : 0.549 7.603 23435 Z= 0.294 Chirality : 0.040 0.213 2704 Planarity : 0.004 0.053 2877 Dihedral : 6.012 59.603 2488 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.06 % Favored : 98.85 % Rotamer: Outliers : 2.93 % Allowed : 18.71 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.18), residues: 2183 helix: 2.40 (0.14), residues: 1333 sheet: -1.78 (0.37), residues: 153 loop : -0.73 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 657 TYR 0.016 0.001 TYR D 669 PHE 0.012 0.001 PHE A 619 TRP 0.016 0.001 TRP A 667 HIS 0.007 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00307 (17252) covalent geometry : angle 0.54890 (23419) SS BOND : bond 0.00319 ( 8) SS BOND : angle 0.80164 ( 16) hydrogen bonds : bond 0.04463 ( 1114) hydrogen bonds : angle 4.02081 ( 3251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 GLU cc_start: 0.9186 (mp0) cc_final: 0.8885 (mp0) REVERT: A 637 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7412 (ptmt) REVERT: A 656 ARG cc_start: 0.8976 (mtt90) cc_final: 0.7986 (mtt180) REVERT: B 666 MET cc_start: 0.8400 (mtp) cc_final: 0.7854 (mtt) REVERT: C 403 MET cc_start: 0.4920 (OUTLIER) cc_final: 0.3016 (pmm) REVERT: C 499 MET cc_start: 0.7492 (ttp) cc_final: 0.7119 (ppp) REVERT: C 635 LEU cc_start: 0.8086 (tp) cc_final: 0.7836 (tt) REVERT: C 637 LYS cc_start: 0.7383 (mmtt) cc_final: 0.6999 (ptmm) REVERT: C 717 MET cc_start: 0.9310 (mtt) cc_final: 0.8943 (mmm) REVERT: E 6 ARG cc_start: 0.6731 (ttt-90) cc_final: 0.5830 (tmm160) REVERT: E 56 GLU cc_start: 0.9278 (tp30) cc_final: 0.8676 (tp30) REVERT: E 70 GLU cc_start: 0.9203 (pt0) cc_final: 0.8983 (pm20) REVERT: E 81 ASP cc_start: 0.9119 (t0) cc_final: 0.8785 (t0) REVERT: F 78 LYS cc_start: 0.8619 (ptmm) cc_final: 0.8363 (pttt) REVERT: F 81 ASP cc_start: 0.9413 (t0) cc_final: 0.8957 (t0) REVERT: F 95 GLU cc_start: 0.9076 (tp30) cc_final: 0.8838 (tp30) REVERT: F 206 GLN cc_start: 0.8755 (tt0) cc_final: 0.8352 (tm-30) REVERT: G 58 MET cc_start: 0.8898 (tpp) cc_final: 0.8648 (tpp) REVERT: H 10 MET cc_start: 0.8795 (tmm) cc_final: 0.8440 (tmm) REVERT: H 81 ASP cc_start: 0.8764 (t0) cc_final: 0.8482 (t70) REVERT: H 149 ASN cc_start: 0.9528 (t0) cc_final: 0.9269 (t0) REVERT: H 190 GLU cc_start: 0.9278 (mm-30) cc_final: 0.9077 (mm-30) REVERT: H 202 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8607 (mp0) REVERT: H 204 HIS cc_start: 0.6690 (OUTLIER) cc_final: 0.6196 (m-70) outliers start: 47 outliers final: 27 residues processed: 213 average time/residue: 0.1468 time to fit residues: 46.3529 Evaluate side-chains 172 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 171 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 116 optimal weight: 40.0000 chunk 10 optimal weight: 30.0000 chunk 214 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 129 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.121009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.073756 restraints weight = 154185.796| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 8.05 r_work: 0.2751 rms_B_bonded: 6.78 restraints_weight: 2.0000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 17260 Z= 0.304 Angle : 0.635 12.242 23435 Z= 0.341 Chirality : 0.042 0.182 2704 Planarity : 0.004 0.058 2877 Dihedral : 4.761 57.902 2426 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.66 % Favored : 98.24 % Rotamer: Outliers : 4.18 % Allowed : 19.49 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.18), residues: 2183 helix: 2.48 (0.14), residues: 1340 sheet: -1.89 (0.33), residues: 204 loop : -0.54 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 657 TYR 0.014 0.002 TYR H 32 PHE 0.016 0.002 PHE B 810 TRP 0.012 0.002 TRP A 667 HIS 0.005 0.001 HIS C 431 Details of bonding type rmsd covalent geometry : bond 0.00694 (17252) covalent geometry : angle 0.63481 (23419) SS BOND : bond 0.00425 ( 8) SS BOND : angle 0.74652 ( 16) hydrogen bonds : bond 0.05011 ( 1114) hydrogen bonds : angle 4.26767 ( 3251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 133 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 GLU cc_start: 0.9245 (mp0) cc_final: 0.8958 (mp0) REVERT: A 657 ARG cc_start: 0.8678 (mmt180) cc_final: 0.7618 (mtm180) REVERT: B 459 MET cc_start: 0.7122 (mmm) cc_final: 0.6892 (mmm) REVERT: B 499 MET cc_start: 0.7183 (ttt) cc_final: 0.6825 (tpp) REVERT: B 666 MET cc_start: 0.8374 (mtp) cc_final: 0.7837 (mtt) REVERT: B 686 MET cc_start: 0.8873 (tmm) cc_final: 0.8293 (ppp) REVERT: C 403 MET cc_start: 0.5323 (OUTLIER) cc_final: 0.5045 (mtm) REVERT: C 416 ARG cc_start: 0.6932 (tpt90) cc_final: 0.5555 (ttp-170) REVERT: C 492 MET cc_start: 0.8701 (tpp) cc_final: 0.8448 (tpp) REVERT: C 637 LYS cc_start: 0.7373 (mmtt) cc_final: 0.7091 (ptmm) REVERT: C 717 MET cc_start: 0.9394 (mtt) cc_final: 0.9061 (mmt) REVERT: D 714 CYS cc_start: 0.6607 (p) cc_final: 0.6350 (t) REVERT: E 70 GLU cc_start: 0.9238 (pt0) cc_final: 0.8943 (pm20) REVERT: E 81 ASP cc_start: 0.9187 (t0) cc_final: 0.8819 (t70) REVERT: E 99 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8523 (mtp-110) REVERT: E 128 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7278 (t-90) REVERT: F 37 ARG cc_start: 0.8276 (ttm-80) cc_final: 0.8063 (ttm-80) REVERT: F 81 ASP cc_start: 0.9346 (t0) cc_final: 0.8999 (t0) REVERT: F 95 GLU cc_start: 0.9066 (tp30) cc_final: 0.8595 (tp30) REVERT: F 206 GLN cc_start: 0.8823 (tt0) cc_final: 0.8436 (tm-30) REVERT: G 81 ASP cc_start: 0.8949 (t0) cc_final: 0.8740 (t0) REVERT: H 81 ASP cc_start: 0.8815 (t0) cc_final: 0.8487 (t70) REVERT: H 202 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8431 (mp0) outliers start: 68 outliers final: 47 residues processed: 193 average time/residue: 0.1160 time to fit residues: 34.0736 Evaluate side-chains 179 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 128 HIS Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 202 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 147 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 chunk 205 optimal weight: 10.0000 chunk 38 optimal weight: 40.0000 chunk 103 optimal weight: 8.9990 chunk 186 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 743 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.120287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.073432 restraints weight = 154022.180| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 9.13 r_work: 0.2771 rms_B_bonded: 6.45 restraints_weight: 2.0000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 17260 Z= 0.294 Angle : 0.609 10.551 23435 Z= 0.327 Chirality : 0.042 0.189 2704 Planarity : 0.004 0.045 2877 Dihedral : 4.618 59.323 2422 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.48 % Favored : 98.43 % Rotamer: Outliers : 5.44 % Allowed : 19.19 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.18), residues: 2183 helix: 2.50 (0.14), residues: 1334 sheet: -1.77 (0.37), residues: 184 loop : -0.59 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 102 TYR 0.017 0.002 TYR C 391 PHE 0.013 0.002 PHE B 810 TRP 0.014 0.002 TRP A 456 HIS 0.005 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00670 (17252) covalent geometry : angle 0.60905 (23419) SS BOND : bond 0.00341 ( 8) SS BOND : angle 0.72321 ( 16) hydrogen bonds : bond 0.04692 ( 1114) hydrogen bonds : angle 4.23564 ( 3251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 131 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 MET cc_start: 0.6956 (tmm) cc_final: 0.6652 (ppp) REVERT: A 520 GLU cc_start: 0.9078 (mp0) cc_final: 0.8778 (mp0) REVERT: B 666 MET cc_start: 0.8248 (mtp) cc_final: 0.7816 (mtp) REVERT: B 686 MET cc_start: 0.8803 (tmm) cc_final: 0.8357 (ppp) REVERT: C 403 MET cc_start: 0.5374 (OUTLIER) cc_final: 0.4544 (mtm) REVERT: C 717 MET cc_start: 0.9360 (mtt) cc_final: 0.9029 (mmt) REVERT: D 714 CYS cc_start: 0.6513 (p) cc_final: 0.6210 (t) REVERT: D 809 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: E 56 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8872 (tp30) REVERT: E 70 GLU cc_start: 0.9131 (pt0) cc_final: 0.8871 (pm20) REVERT: E 81 ASP cc_start: 0.9056 (t0) cc_final: 0.8443 (p0) REVERT: E 99 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8667 (mtp-110) REVERT: F 81 ASP cc_start: 0.9338 (t0) cc_final: 0.9029 (t0) REVERT: F 95 GLU cc_start: 0.9123 (tp30) cc_final: 0.8617 (tp30) REVERT: F 102 ARG cc_start: 0.9442 (OUTLIER) cc_final: 0.8387 (tpt-90) REVERT: F 206 GLN cc_start: 0.8822 (tt0) cc_final: 0.8444 (tm-30) REVERT: G 58 MET cc_start: 0.9124 (tpp) cc_final: 0.8886 (tpp) REVERT: G 81 ASP cc_start: 0.9068 (t0) cc_final: 0.8819 (t0) REVERT: H 81 ASP cc_start: 0.8827 (t0) cc_final: 0.8481 (t70) REVERT: H 102 ARG cc_start: 0.9431 (OUTLIER) cc_final: 0.9181 (tpt-90) REVERT: H 149 ASN cc_start: 0.9689 (t0) cc_final: 0.9378 (t0) REVERT: H 202 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8527 (mp0) outliers start: 89 outliers final: 58 residues processed: 207 average time/residue: 0.1209 time to fit residues: 37.8519 Evaluate side-chains 189 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 124 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 669 TYR Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain D residue 809 GLU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 128 HIS Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 202 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 44 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 217 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 137 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 743 ASN G 149 ASN H 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.122834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.076672 restraints weight = 141817.907| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 7.21 r_work: 0.2869 rms_B_bonded: 5.73 restraints_weight: 2.0000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17260 Z= 0.150 Angle : 0.517 9.832 23435 Z= 0.274 Chirality : 0.039 0.189 2704 Planarity : 0.003 0.049 2877 Dihedral : 4.341 59.995 2422 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.15 % Favored : 98.80 % Rotamer: Outliers : 4.12 % Allowed : 20.14 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.19), residues: 2183 helix: 2.76 (0.14), residues: 1342 sheet: -1.73 (0.43), residues: 133 loop : -0.51 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 102 TYR 0.017 0.001 TYR A 728 PHE 0.011 0.001 PHE D 604 TRP 0.011 0.001 TRP H 177 HIS 0.004 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00344 (17252) covalent geometry : angle 0.51717 (23419) SS BOND : bond 0.00241 ( 8) SS BOND : angle 0.60053 ( 16) hydrogen bonds : bond 0.04034 ( 1114) hydrogen bonds : angle 3.84323 ( 3251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 141 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.5325 (mpp) cc_final: 0.5080 (mpp) REVERT: A 472 VAL cc_start: 0.6976 (OUTLIER) cc_final: 0.6671 (t) REVERT: A 520 GLU cc_start: 0.8955 (mp0) cc_final: 0.8669 (mp0) REVERT: B 666 MET cc_start: 0.8185 (mtp) cc_final: 0.7764 (mtp) REVERT: B 686 MET cc_start: 0.8780 (tmm) cc_final: 0.8390 (ppp) REVERT: B 751 GLU cc_start: 0.8922 (pt0) cc_final: 0.8694 (pp20) REVERT: C 403 MET cc_start: 0.5422 (OUTLIER) cc_final: 0.4414 (mtm) REVERT: C 717 MET cc_start: 0.9405 (mtt) cc_final: 0.9125 (mmt) REVERT: D 714 CYS cc_start: 0.6439 (p) cc_final: 0.6065 (t) REVERT: E 56 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8743 (tp30) REVERT: E 70 GLU cc_start: 0.9121 (pt0) cc_final: 0.8860 (pm20) REVERT: E 81 ASP cc_start: 0.9002 (t0) cc_final: 0.8416 (p0) REVERT: E 99 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8649 (mtp-110) REVERT: E 149 ASN cc_start: 0.9392 (t0) cc_final: 0.9158 (t0) REVERT: F 78 LYS cc_start: 0.8699 (ptmm) cc_final: 0.8474 (ptpt) REVERT: F 81 ASP cc_start: 0.9369 (t0) cc_final: 0.9031 (t0) REVERT: F 95 GLU cc_start: 0.9069 (tp30) cc_final: 0.8602 (tp30) REVERT: F 206 GLN cc_start: 0.8855 (tt0) cc_final: 0.8446 (tm-30) REVERT: G 81 ASP cc_start: 0.8980 (t0) cc_final: 0.8777 (t0) REVERT: H 81 ASP cc_start: 0.8690 (t0) cc_final: 0.8425 (t70) REVERT: H 102 ARG cc_start: 0.9382 (OUTLIER) cc_final: 0.9084 (tpt-90) REVERT: H 149 ASN cc_start: 0.9653 (t0) cc_final: 0.9304 (t0) REVERT: H 204 HIS cc_start: 0.7044 (OUTLIER) cc_final: 0.6720 (m-70) outliers start: 67 outliers final: 47 residues processed: 196 average time/residue: 0.1179 time to fit residues: 35.8427 Evaluate side-chains 187 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 134 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 50.0000 chunk 198 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN H 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.122751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.076237 restraints weight = 131542.838| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 7.16 r_work: 0.2845 rms_B_bonded: 5.54 restraints_weight: 2.0000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17260 Z= 0.135 Angle : 0.505 10.289 23435 Z= 0.264 Chirality : 0.038 0.214 2704 Planarity : 0.003 0.049 2877 Dihedral : 3.984 59.493 2417 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.11 % Favored : 98.85 % Rotamer: Outliers : 4.36 % Allowed : 19.84 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.18), residues: 2183 helix: 2.86 (0.14), residues: 1342 sheet: -1.50 (0.41), residues: 150 loop : -0.40 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 102 TYR 0.013 0.001 TYR A 728 PHE 0.011 0.001 PHE D 604 TRP 0.010 0.001 TRP C 456 HIS 0.019 0.001 HIS H 204 Details of bonding type rmsd covalent geometry : bond 0.00310 (17252) covalent geometry : angle 0.50418 (23419) SS BOND : bond 0.00309 ( 8) SS BOND : angle 0.93323 ( 16) hydrogen bonds : bond 0.03856 ( 1114) hydrogen bonds : angle 3.76711 ( 3251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 151 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.5862 (mpp) cc_final: 0.5643 (mpp) REVERT: A 472 VAL cc_start: 0.6716 (OUTLIER) cc_final: 0.6411 (t) REVERT: A 520 GLU cc_start: 0.8919 (mp0) cc_final: 0.8613 (mp0) REVERT: A 657 ARG cc_start: 0.8749 (mmt180) cc_final: 0.7901 (mtp180) REVERT: A 666 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8544 (ptp) REVERT: A 669 TYR cc_start: 0.9189 (t80) cc_final: 0.8986 (t80) REVERT: A 670 MET cc_start: 0.7183 (ptp) cc_final: 0.6890 (ptp) REVERT: B 395 THR cc_start: 0.0522 (OUTLIER) cc_final: 0.0237 (p) REVERT: B 666 MET cc_start: 0.8192 (mtp) cc_final: 0.7788 (mtp) REVERT: B 686 MET cc_start: 0.8836 (tmm) cc_final: 0.8296 (ppp) REVERT: B 751 GLU cc_start: 0.8960 (pt0) cc_final: 0.8729 (pp20) REVERT: C 403 MET cc_start: 0.5242 (OUTLIER) cc_final: 0.4501 (mtm) REVERT: C 717 MET cc_start: 0.9385 (mtt) cc_final: 0.9080 (mmt) REVERT: D 492 MET cc_start: 0.1843 (ptt) cc_final: -0.0714 (ttp) REVERT: D 714 CYS cc_start: 0.6398 (p) cc_final: 0.6020 (t) REVERT: E 56 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8779 (tp30) REVERT: E 70 GLU cc_start: 0.9152 (pt0) cc_final: 0.8858 (pm20) REVERT: E 81 ASP cc_start: 0.9088 (t0) cc_final: 0.8693 (t70) REVERT: E 97 LEU cc_start: 0.9080 (mt) cc_final: 0.8877 (mt) REVERT: E 99 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8505 (mtp-110) REVERT: E 149 ASN cc_start: 0.9356 (t0) cc_final: 0.9120 (t0) REVERT: F 56 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8444 (tm-30) REVERT: F 78 LYS cc_start: 0.8627 (ptmm) cc_final: 0.8294 (ptpp) REVERT: F 81 ASP cc_start: 0.9323 (t0) cc_final: 0.8996 (t0) REVERT: F 95 GLU cc_start: 0.9035 (tp30) cc_final: 0.8454 (tp30) REVERT: F 102 ARG cc_start: 0.9374 (OUTLIER) cc_final: 0.8673 (tpt90) REVERT: F 206 GLN cc_start: 0.8872 (tt0) cc_final: 0.8445 (tm-30) REVERT: G 58 MET cc_start: 0.9098 (tpp) cc_final: 0.8671 (tpp) REVERT: G 81 ASP cc_start: 0.8938 (t0) cc_final: 0.8631 (t0) REVERT: H 6 ARG cc_start: 0.8212 (tmm-80) cc_final: 0.7959 (tmm160) REVERT: H 81 ASP cc_start: 0.8701 (t0) cc_final: 0.8370 (t70) REVERT: H 149 ASN cc_start: 0.9650 (t0) cc_final: 0.9357 (t0) REVERT: H 202 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8595 (mp0) outliers start: 71 outliers final: 51 residues processed: 206 average time/residue: 0.1246 time to fit residues: 39.0209 Evaluate side-chains 203 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 144 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 669 TYR Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 128 HIS Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 202 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 88 optimal weight: 0.7980 chunk 195 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 38 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 84 optimal weight: 40.0000 chunk 101 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN G 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.123034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.076169 restraints weight = 150623.422| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 8.27 r_work: 0.2832 rms_B_bonded: 6.13 restraints_weight: 2.0000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17260 Z= 0.129 Angle : 0.499 8.125 23435 Z= 0.262 Chirality : 0.039 0.241 2704 Planarity : 0.003 0.049 2877 Dihedral : 3.898 58.756 2417 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.11 % Favored : 98.85 % Rotamer: Outliers : 3.77 % Allowed : 21.04 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.19), residues: 2183 helix: 2.91 (0.14), residues: 1342 sheet: -1.32 (0.43), residues: 141 loop : -0.32 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 74 TYR 0.012 0.001 TYR A 728 PHE 0.010 0.001 PHE D 604 TRP 0.009 0.001 TRP C 456 HIS 0.003 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00295 (17252) covalent geometry : angle 0.49901 (23419) SS BOND : bond 0.00222 ( 8) SS BOND : angle 0.84465 ( 16) hydrogen bonds : bond 0.03775 ( 1114) hydrogen bonds : angle 3.70658 ( 3251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 152 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.5952 (mpp) cc_final: 0.5752 (mpp) REVERT: A 472 VAL cc_start: 0.6704 (OUTLIER) cc_final: 0.6390 (t) REVERT: A 492 MET cc_start: 0.6571 (ppp) cc_final: 0.5464 (ppp) REVERT: A 520 GLU cc_start: 0.9001 (mp0) cc_final: 0.8655 (mp0) REVERT: A 657 ARG cc_start: 0.8815 (mmt180) cc_final: 0.7771 (ttm170) REVERT: A 666 MET cc_start: 0.8943 (ptp) cc_final: 0.8455 (ptp) REVERT: A 669 TYR cc_start: 0.9235 (t80) cc_final: 0.9010 (t80) REVERT: A 670 MET cc_start: 0.7422 (ptp) cc_final: 0.7106 (ptp) REVERT: B 666 MET cc_start: 0.8136 (mtp) cc_final: 0.7768 (mtp) REVERT: B 686 MET cc_start: 0.8841 (tmm) cc_final: 0.8318 (ppp) REVERT: B 751 GLU cc_start: 0.9005 (pt0) cc_final: 0.8758 (pp20) REVERT: C 403 MET cc_start: 0.4968 (OUTLIER) cc_final: 0.4467 (mtm) REVERT: C 459 MET cc_start: 0.5793 (mpp) cc_final: 0.5100 (tpp) REVERT: D 492 MET cc_start: 0.1386 (ptt) cc_final: -0.1407 (ttp) REVERT: D 714 CYS cc_start: 0.6373 (p) cc_final: 0.6038 (t) REVERT: E 56 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8777 (tp30) REVERT: E 70 GLU cc_start: 0.9122 (pt0) cc_final: 0.8847 (pm20) REVERT: E 81 ASP cc_start: 0.9164 (t0) cc_final: 0.8753 (t70) REVERT: E 99 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8574 (mtp-110) REVERT: E 149 ASN cc_start: 0.9344 (t0) cc_final: 0.9114 (t0) REVERT: F 56 GLU cc_start: 0.8643 (tm-30) cc_final: 0.7930 (mp0) REVERT: F 78 LYS cc_start: 0.8579 (ptmm) cc_final: 0.8285 (ptpp) REVERT: F 81 ASP cc_start: 0.9372 (t0) cc_final: 0.9034 (t0) REVERT: F 95 GLU cc_start: 0.9061 (tp30) cc_final: 0.8482 (tp30) REVERT: F 102 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.8698 (tpt90) REVERT: F 206 GLN cc_start: 0.8948 (tt0) cc_final: 0.8522 (tm-30) REVERT: G 58 MET cc_start: 0.9079 (tpp) cc_final: 0.8878 (tpp) REVERT: G 81 ASP cc_start: 0.9012 (t0) cc_final: 0.8687 (t0) REVERT: H 6 ARG cc_start: 0.8209 (tmm-80) cc_final: 0.7969 (tmm160) REVERT: H 70 GLU cc_start: 0.9087 (tp30) cc_final: 0.8414 (tp30) REVERT: H 74 ARG cc_start: 0.8834 (ttp80) cc_final: 0.8623 (ttm110) REVERT: H 81 ASP cc_start: 0.8728 (t0) cc_final: 0.8390 (t70) REVERT: H 149 ASN cc_start: 0.9680 (t0) cc_final: 0.9374 (t0) outliers start: 61 outliers final: 49 residues processed: 198 average time/residue: 0.1323 time to fit residues: 39.3968 Evaluate side-chains 199 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 669 TYR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 128 HIS Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 132 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 163 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 136 optimal weight: 30.0000 chunk 92 optimal weight: 0.7980 chunk 105 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 153 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 81 optimal weight: 30.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS F 160 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.121308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.076154 restraints weight = 159014.494| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 9.31 r_work: 0.2791 rms_B_bonded: 6.63 restraints_weight: 2.0000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17260 Z= 0.234 Angle : 0.578 9.551 23435 Z= 0.306 Chirality : 0.040 0.258 2704 Planarity : 0.004 0.049 2877 Dihedral : 4.098 59.973 2417 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.57 % Favored : 98.38 % Rotamer: Outliers : 4.06 % Allowed : 21.64 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.18), residues: 2183 helix: 2.71 (0.14), residues: 1342 sheet: -1.16 (0.43), residues: 143 loop : -0.36 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 449 TYR 0.017 0.001 TYR H 32 PHE 0.013 0.001 PHE A 491 TRP 0.014 0.001 TRP D 667 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00538 (17252) covalent geometry : angle 0.57722 (23419) SS BOND : bond 0.00316 ( 8) SS BOND : angle 0.92323 ( 16) hydrogen bonds : bond 0.04486 ( 1114) hydrogen bonds : angle 4.05271 ( 3251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 136 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 MET cc_start: 0.6038 (ppp) cc_final: 0.5400 (ppp) REVERT: A 498 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9094 (tp) REVERT: A 520 GLU cc_start: 0.9060 (mp0) cc_final: 0.8768 (mp0) REVERT: A 657 ARG cc_start: 0.8921 (mmt180) cc_final: 0.8153 (mtp180) REVERT: A 666 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8689 (ptp) REVERT: A 669 TYR cc_start: 0.9226 (t80) cc_final: 0.8996 (t80) REVERT: B 666 MET cc_start: 0.8036 (mtp) cc_final: 0.7574 (mtp) REVERT: B 686 MET cc_start: 0.8846 (tmm) cc_final: 0.8254 (ptm) REVERT: C 403 MET cc_start: 0.4989 (OUTLIER) cc_final: 0.4545 (mtm) REVERT: C 459 MET cc_start: 0.5985 (mpp) cc_final: 0.5210 (tpp) REVERT: C 499 MET cc_start: 0.6721 (ppp) cc_final: 0.5414 (ppp) REVERT: C 717 MET cc_start: 0.8479 (mmt) cc_final: 0.8243 (mmp) REVERT: D 492 MET cc_start: 0.1700 (ptt) cc_final: -0.0997 (ttp) REVERT: E 56 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8815 (tp30) REVERT: E 70 GLU cc_start: 0.9142 (pt0) cc_final: 0.8893 (pm20) REVERT: E 81 ASP cc_start: 0.8993 (t0) cc_final: 0.8436 (p0) REVERT: E 99 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8553 (mtp-110) REVERT: F 56 GLU cc_start: 0.8665 (tm-30) cc_final: 0.7991 (mp0) REVERT: F 81 ASP cc_start: 0.9340 (t0) cc_final: 0.9051 (t0) REVERT: F 95 GLU cc_start: 0.9131 (tp30) cc_final: 0.8639 (tp30) REVERT: F 102 ARG cc_start: 0.9458 (OUTLIER) cc_final: 0.8634 (tpt-90) REVERT: F 206 GLN cc_start: 0.8933 (tt0) cc_final: 0.8507 (tm-30) REVERT: G 81 ASP cc_start: 0.9050 (t0) cc_final: 0.8732 (t0) REVERT: H 81 ASP cc_start: 0.8745 (t0) cc_final: 0.8425 (t70) REVERT: H 149 ASN cc_start: 0.9691 (t0) cc_final: 0.9402 (t0) REVERT: H 206 GLN cc_start: 0.8613 (pp30) cc_final: 0.8394 (pp30) outliers start: 65 outliers final: 51 residues processed: 189 average time/residue: 0.1426 time to fit residues: 40.5713 Evaluate side-chains 189 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 132 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 132 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 115 optimal weight: 50.0000 chunk 204 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 182 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.122831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.076529 restraints weight = 175345.801| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 8.81 r_work: 0.2797 rms_B_bonded: 7.21 restraints_weight: 2.0000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17260 Z= 0.151 Angle : 0.536 10.395 23435 Z= 0.279 Chirality : 0.039 0.232 2704 Planarity : 0.003 0.050 2877 Dihedral : 4.004 59.075 2417 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.11 % Favored : 98.85 % Rotamer: Outliers : 3.89 % Allowed : 21.82 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.19), residues: 2183 helix: 2.82 (0.14), residues: 1342 sheet: -1.12 (0.45), residues: 133 loop : -0.32 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 74 TYR 0.011 0.001 TYR C 519 PHE 0.015 0.001 PHE D 663 TRP 0.015 0.001 TRP D 667 HIS 0.003 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00349 (17252) covalent geometry : angle 0.53532 (23419) SS BOND : bond 0.00238 ( 8) SS BOND : angle 0.85675 ( 16) hydrogen bonds : bond 0.03950 ( 1114) hydrogen bonds : angle 3.84113 ( 3251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 142 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 MET cc_start: 0.6306 (ppp) cc_final: 0.5620 (ppp) REVERT: A 498 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9126 (tp) REVERT: A 520 GLU cc_start: 0.9085 (mp0) cc_final: 0.8758 (mp0) REVERT: A 657 ARG cc_start: 0.8873 (mmt180) cc_final: 0.8196 (mtt-85) REVERT: B 395 THR cc_start: 0.0281 (OUTLIER) cc_final: 0.0013 (p) REVERT: B 666 MET cc_start: 0.7803 (mtp) cc_final: 0.7339 (mtp) REVERT: B 686 MET cc_start: 0.8824 (tmm) cc_final: 0.8340 (ppp) REVERT: B 751 GLU cc_start: 0.9024 (pt0) cc_final: 0.8742 (pp20) REVERT: C 403 MET cc_start: 0.5188 (OUTLIER) cc_final: 0.4781 (mtm) REVERT: C 459 MET cc_start: 0.5929 (mpp) cc_final: 0.4966 (tpp) REVERT: C 499 MET cc_start: 0.7077 (ppp) cc_final: 0.5839 (ppp) REVERT: D 492 MET cc_start: 0.1398 (ptt) cc_final: -0.1136 (ttp) REVERT: E 56 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8784 (tp30) REVERT: E 70 GLU cc_start: 0.9191 (pt0) cc_final: 0.8915 (pm20) REVERT: E 81 ASP cc_start: 0.9047 (t0) cc_final: 0.8460 (p0) REVERT: E 99 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8569 (mtp-110) REVERT: F 56 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8475 (tm-30) REVERT: F 81 ASP cc_start: 0.9390 (t0) cc_final: 0.9084 (t0) REVERT: F 95 GLU cc_start: 0.9113 (tp30) cc_final: 0.8566 (tp30) REVERT: F 102 ARG cc_start: 0.9416 (OUTLIER) cc_final: 0.8272 (tpt-90) REVERT: F 206 GLN cc_start: 0.8939 (tt0) cc_final: 0.8516 (tm-30) REVERT: G 81 ASP cc_start: 0.9062 (t0) cc_final: 0.8740 (t0) REVERT: H 81 ASP cc_start: 0.8816 (t0) cc_final: 0.8562 (t70) REVERT: H 149 ASN cc_start: 0.9673 (t0) cc_final: 0.9375 (t0) REVERT: H 190 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9055 (mm-30) REVERT: H 206 GLN cc_start: 0.8664 (pp30) cc_final: 0.8457 (pp30) outliers start: 62 outliers final: 48 residues processed: 191 average time/residue: 0.1327 time to fit residues: 38.9653 Evaluate side-chains 194 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 140 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 132 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 78 optimal weight: 7.9990 chunk 68 optimal weight: 30.0000 chunk 151 optimal weight: 9.9990 chunk 67 optimal weight: 0.0270 chunk 31 optimal weight: 30.0000 chunk 174 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN F 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.121590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.074944 restraints weight = 152371.626| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 8.00 r_work: 0.2804 rms_B_bonded: 6.12 restraints_weight: 2.0000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17260 Z= 0.211 Angle : 0.598 13.905 23435 Z= 0.313 Chirality : 0.040 0.272 2704 Planarity : 0.004 0.050 2877 Dihedral : 4.067 59.520 2417 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.59 % Allowed : 22.41 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.18), residues: 2183 helix: 2.67 (0.14), residues: 1342 sheet: -1.08 (0.45), residues: 133 loop : -0.35 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 102 TYR 0.016 0.001 TYR H 32 PHE 0.013 0.001 PHE D 663 TRP 0.016 0.001 TRP D 667 HIS 0.005 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00485 (17252) covalent geometry : angle 0.59777 (23419) SS BOND : bond 0.00306 ( 8) SS BOND : angle 0.88649 ( 16) hydrogen bonds : bond 0.04279 ( 1114) hydrogen bonds : angle 4.05390 ( 3251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 136 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 MET cc_start: 0.6211 (ppp) cc_final: 0.5586 (ppp) REVERT: A 498 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9061 (tp) REVERT: A 520 GLU cc_start: 0.9025 (mp0) cc_final: 0.8691 (mp0) REVERT: A 637 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8206 (ptmt) REVERT: A 657 ARG cc_start: 0.8933 (mmt180) cc_final: 0.8307 (mtt-85) REVERT: B 666 MET cc_start: 0.7799 (mtp) cc_final: 0.7276 (mtp) REVERT: B 686 MET cc_start: 0.8859 (tmm) cc_final: 0.8387 (ppp) REVERT: C 403 MET cc_start: 0.5210 (OUTLIER) cc_final: 0.4863 (mtm) REVERT: C 459 MET cc_start: 0.5968 (mpp) cc_final: 0.5148 (tpp) REVERT: D 492 MET cc_start: 0.1775 (ptt) cc_final: -0.0587 (ttp) REVERT: E 56 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8792 (tp30) REVERT: E 70 GLU cc_start: 0.9174 (pt0) cc_final: 0.8898 (pm20) REVERT: E 81 ASP cc_start: 0.9001 (t0) cc_final: 0.8414 (p0) REVERT: F 56 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8193 (mp0) REVERT: F 81 ASP cc_start: 0.9349 (t0) cc_final: 0.9045 (t0) REVERT: F 95 GLU cc_start: 0.9100 (tp30) cc_final: 0.8558 (tp30) REVERT: F 102 ARG cc_start: 0.9433 (OUTLIER) cc_final: 0.8354 (tpt-90) REVERT: F 206 GLN cc_start: 0.8924 (tt0) cc_final: 0.8502 (tm-30) REVERT: G 81 ASP cc_start: 0.9066 (t0) cc_final: 0.8755 (t0) REVERT: H 37 ARG cc_start: 0.9213 (ttm-80) cc_final: 0.8993 (mmm160) REVERT: H 78 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8834 (ptpp) REVERT: H 81 ASP cc_start: 0.8794 (t0) cc_final: 0.8509 (t70) REVERT: H 149 ASN cc_start: 0.9671 (t0) cc_final: 0.9354 (t0) REVERT: H 206 GLN cc_start: 0.8602 (pp30) cc_final: 0.8392 (pp30) outliers start: 57 outliers final: 49 residues processed: 182 average time/residue: 0.1331 time to fit residues: 37.3157 Evaluate side-chains 192 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 137 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 128 HIS Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 132 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 2 optimal weight: 20.0000 chunk 216 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 chunk 207 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 82 optimal weight: 30.0000 chunk 147 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 HIS F 160 ASN H 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.124071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.077610 restraints weight = 145758.925| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 7.86 r_work: 0.2864 rms_B_bonded: 5.98 restraints_weight: 2.0000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17260 Z= 0.117 Angle : 0.542 13.949 23435 Z= 0.280 Chirality : 0.039 0.262 2704 Planarity : 0.003 0.049 2877 Dihedral : 3.950 58.724 2417 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.23 % Allowed : 23.07 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.19), residues: 2183 helix: 2.80 (0.14), residues: 1343 sheet: -1.04 (0.45), residues: 133 loop : -0.29 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 74 TYR 0.014 0.001 TYR A 669 PHE 0.014 0.001 PHE D 663 TRP 0.011 0.001 TRP D 667 HIS 0.005 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00261 (17252) covalent geometry : angle 0.54179 (23419) SS BOND : bond 0.00204 ( 8) SS BOND : angle 0.84050 ( 16) hydrogen bonds : bond 0.03784 ( 1114) hydrogen bonds : angle 3.80169 ( 3251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5269.08 seconds wall clock time: 90 minutes 34.99 seconds (5434.99 seconds total)